{"data": [{"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 101, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0018-neff-histopathology/experimentA", "Description": "Experiment Description\nHistopathology raw images and annotated tiff files of tissues from mice with 10 different single gene knockouts.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/101/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/101/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 51, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0021-lawo-pericentriolarmaterial/experimentA", "Description": "Publication Title\nSubdiffraction imaging of centrosomes reveals higher-order organizational features of pericentriolar material.\n\nExperiment Description\nImages relating to Figure 1e in Lawo et al 2012. These are the 3D-SIM reconstructed, maximum intensity projected and aligned images of centriole or PCM proteins of cycling HeLa cells in interphase.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/51/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/51/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 52, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0023-szymborska-nuclearpore/experimentA", "Description": "Publication Title\nNuclear pore scaffold structure analyzed by super-resolution microscopy and particle averaging.\n\nExperiment Description\nSystematic immunolabelling of the Nup107-160 complex and (monomeric) enhanced GFP [(m)EGFP] fusions of members of the Nup107-160 complex with an anti-GFP nanobody.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/52/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/52/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 301, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0026-weigelin-immunotherapy/experimentA", "Description": "Publication Title\nFocusing and sustaining the antitumor CTL effector killer response by agonist anti-CD137 mAb.\n\nExperiment Description\nCombination therapy of adoptive CTL transfer and anti-CD137 monoclonal antibody. Mice were injected with B16F10/OVA melanoma cells and after 3 or 7 days were treated with OVA-specific CD8+ T cells (Cytotoxic T lymphocytes CTL) plus 1D8 antibody (anti-CD137).  4D timelapse images were taken at either 3 or 6 days after CTL + antibody treatment.\n\nVersion History\nAugust 2017 - added additional phenotype to CMPO ontology mapping", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/301/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/301/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 151, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0027-dickerson-chromatin/experimentA", "Description": "Publication Title\nHigh resolution imaging reveals heterogeneity in chromatin states between cells that is not inherited through cell division.\n\nExperiment Description\nTo monitor the organisation of chromatin in live cells were engineered with fluorescent fusion proteins which recognize specific operator sequences to tag pairs of syntenic gene loci. The separation of these loci was then tracked in three dimensions over time using fluorescence microscopy. Data generated for this manuscript are made accessible here. This includes the movies generated from yeast strains with different genomic separations. These are available within subfolders titled \"Colocalising\", \"Genomic separation 100kb\", \"Genomic separation 25kb\" etc. Tracking data generated from these movies is also available as idr0027-AnalysisAllData.csv in the Attachments section below. This includes x, y and z co-ordinates of foci in the red and green channels following two stages of correction for channel alignment, the distance between the red and green foci in nanometers,  the offset of the red channel foci with respect to the green channel foci in x, y, and z. The maximum intensity, background intensity and standard deviation of the background intensity for both the red and green channels. The contrast (maximum spot intensity - nuclear background intensity) for each channel. The name originally assigned to the video, the genomic separation of the strain in kb. The string in column AE starts with the letter assigned to the video in supplementary figure 2. Some videos include two cells. In these cases the higher cell (on the y axis) is indicated as \"upper\" and the other as \"lower\". One of the two cells can often be assigned as the mother and the other as daughter. This is indicated as m or d in column AF. The systematic name of the strain is indicated in column AG.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/151/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/151/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 201, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0032-yang-meristem/experimentA", "Description": "Publication Title\nRegulation of Meristem Morphogenesis by Cell Wall Synthases in Arabidopsis.\n\nExperiment Description\nWe performed systematic RNA in situ hybridization assays to examine the expression patterns of the SAM-expressed GTs at single-cell spatial resolution, including those transcripts that show either relative increases, reductions, or no change between SAM and flower samples.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/201/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/201/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 354, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0038-held-kidneylightsheet", "Description": "Publication Title\nEx vivo live cell tracking in kidney organoids using light sheet fluorescence microscopy.\n\nStudy Description\nWe have adapted the mouse kidney rudiment assay to generate renal organoids. We have immunostained endpoint fixed organoids and E13.5 embryonic kidneys and imaged them with a light sheet fluorescent microscope. The data generated for this manuscript is made accessible here and includes immunofluorescence staining after end point fixation revealing that organotypic structures develop within the organoids. Furthermore, we have performed an assay to ascertain tubular functionality. Following, we have imaged organoids containing Wt1-GFP knock-in cells live on the light sheet microscope to evaluate the ability to follow cells long-term and generate previously unavailable quantitative tracking data.\\n\\nidr0038 consists of a set of 3 experiments: experimentA (immunofluorescence staining after end point fixation), experimentB (assays to ascertain tubular functionality) and experimentC (Wt1-GFP knock-in cells followed long term).", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/354/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/354/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 351, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0038-held-kidneylightsheet/experimentA", "Description": "Publication Title\nEx vivo live cell tracking in kidney organoids using light sheet fluorescence microscopy.\n\nExperiment Description\nWe have adapted the mouse kidney rudiment assay to generate renal organoids. To demonstrate that the organoid culture method of re-aggregated kidney rudiments in PDMS discs resulted in 3D kidney organoids with organotypic structures, we stained fixed six day old organoids for various developmental markers and imaged them with a light sheet fluorescent microscope. We have stained for the following markers: Megalin, Laminin, Cytokeratin, Pax2, Six2, Wt1, Synaptopodin and Nephrin and have also used the lectin stain PNA (peanut agglutinin). The spheroids were usually imaged as z stacks from five angles.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/351/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/351/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 352, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0038-held-kidneylightsheet/experimentB", "Description": "Publication Title\nEx vivo live cell tracking in kidney organoids using light sheet fluorescence microscopy.\n\nExperiment Description\nAll assays were performed on live cultures. The intact kidney rudiments were cultured at air liquid interface for 4 days following dissection. The organoids were cultured under medium immersion for six days following dissection. The samples cultured at air liquid interface were gently removed from the membranes before starting the assay. The samples were incubated for one hour at 25oC with PBS containing 1uM 5(6)-Carboxyfluorescein (6-CF) and 20 ug/ml of PNA (Vector Laboratories). For the control samples, 2 mM probenecid was also added to the solution to inhibit the organic anion transport. After incubation, the samples were washed with ice cold PBS for 10 mins followed by an incubation with 8mM probenecid in PBS for 15 mins to arrest any transport. The functional assay was concluded by two PBS washes and samples were then embedded in 1.5% agarose for imaging.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/352/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/352/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 353, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0038-held-kidneylightsheet/experimentC", "Description": "Publication Title\nEx vivo live cell tracking in kidney organoids using light sheet fluorescence microscopy.\n\nExperiment Description\nWe have adapted the mouse kidney rudiment assay to generate renal organoids. 24 hours after pelleting 100,000 mouse kidney cells, organoids had formed in the PDMS dishes. For the PNA vital stain test we used kidney cells from wildtype mice and for the tracking time series we used cells from the Wt1tm1Nhsn strain, expressing GFP together with the transcription factor Wt1. One organoid was embedded in a hydrogel matrix (1.5% Agarose + 3% gelatine). In the microscope chamber, the hydrogel cylinder was extruded from the capillary so that the hydrogel column containing the organoid was located outside the capillary and immersed in medium (phenol red-free MEM + 10% FBS, 1% pen/strep, 3ug/ml PNA-rh) at 37oC and with 5% CO2. We recorded z stacks of the spheroids from multiple angles every 30 mins to record the location of the GFP expressing cells in three dimensions over time. There are three time series. These are available in the subfolders \"Time PNA-rh vital\", \"Wt1-GFP PNA Time Series 1\" and \"Wt1-GFP PNA Time Series 2\".  The time series data was processed in Fiji by opening the green channel only, binning in X and Y by a factor of two and converting it to 8 bit for processing in TrackMate (v.2.8.2) where we used the LoG (Laplacian of Gaussian) Detector and LAP (Linear Assignment Problem) Tracker options. Tracking data generated from the time series using the Track Mate plug in for Fiji is also provided in the time series data sets as \"Nspots vs Time.txt\", \"Track statistics.txt\", \"Links in tracks statistics.txt\" and \"Spots in tracks statistics.txt\". The data was analysed and plotted via the Matlab script provided as \"TrackMateDataAnalysis.txt\" in conjunction with the functions \"NSpotsFunction.txt\", \"SpotsInTracksFunction.txt\", \"TrackStatisticsFunction.txt\", \"Violin.txt\" and \"violinplot.txt\".", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/353/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/353/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 401, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0040-aymoz-singlecell/experimentA", "Description": "Publication Title\nTiming of gene expression in a cell-fate decision\u00a0system.\n\nExperiment Description\nTime-lapse with addition of 1uM alpha-factor at time 0", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/401/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/401/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 404, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0041-cai-mitoticatlas/experimentA", "Description": "Publication Title\nExperimental and computational framework for a dynamic protein atlas of human cell division.\n\nExperiment Description\nImage data used to build the mitotic cell atlas. This consists of three subsets: raw images, segmentation masks for the landmarks and protein concentration maps.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/404/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/404/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 402, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0042-nirschl-wsideeplearning/experimentA", "Description": "Publication Title\nA deep-learning classifier identifies patients with clinical heart failure using whole-slide images of H&E tissue.\n\nExperiment Description\nHistopathology sub-image from patient whole-slide images from patients with end-stage clinical heart failure or cadaveric donor hearts from patients without heart failure.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/402/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/402/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 501, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0043-uhlen-humanproteinatlas/experimentA", "Description": "Publication Title\nProteomics. Tissue-based map of the human proteome.\n\nExperiment Description\nMapping of protein expression across all major tissues and organs in the human body", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/501/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/501/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 502, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0044-mcdole-tardislightsheet/experimentA", "Description": "Publication Title\nIn Toto Imaging and Reconstruction of Post-Implantation Mouse Development at the Single-Cell Level.\n\nExperiment Description\nLight-sheet imaging of post-implantation mouse development from E6.5 to E8.5", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/502/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/502/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 405, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0045-reichmann-zygotespindle/experimentA", "Description": "Publication Title\nDual-spindle formation in zygotes keeps parental genomes apart in early mammalian embryos.\n\nExperiment Description\nCharacterization of mitotic spindle formation in live mouse zygotes by light-sheet microscopy.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/405/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/405/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 503, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0047-neuert-yeastmrna/experimentA", "Description": "Publication Title\nMultiplex RNA single molecule FISH of inducible mRNAs in single yeast cells.\n\nExperiment Description\nWe performed single molecule in-situ hybridization on yeast cells that have been exposed to osmotic stress and measured mRNA expression for two genes. The goal of this study was to generate data sets for single cell transcription modeling.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/503/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/503/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1201, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0048-abdeladim-chroms/experimentA", "Description": "Publication Title\nMulticolor multiscale brain imaging with chromatic multiphoton serial microscopy\n\nExperiment Description\nMulticolor brain-wide anatomical mapping and high-resolution continuous multicolor imaging of a >5mm3 cortical portion.  Astrocytes and layer 2/3 neurons are 'Brainbow-labeled'.  The dataset consists of a sequence of 92 high-resolution multicolor 2D whole-brain sections with high-content anatomical details and gives access to single-cell astrocyte morphologies with subcellular resolution over an unprecedented millimetric spatial scale.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1201/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1201/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 505, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0050-springer-cytoskeletalsystems/experimentA", "Description": "Publication Title\nUnbiased pattern analysis reveals highly diverse responses of cytoskeletal systems to cyclic straining.\n\nExperiment Description\nCharacterization of cytoskeletal systems (actin, microtubules, vimentin networks) to cyclic straining using confocal laser scanning microscopy, including experiments with nocodazole to depolymerize microtubules.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/505/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/505/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 552, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0051-fulton-tailbudlightsheet/experimentA", "Description": "Publication Title\nNeuromesodermal progenitors are a conserved source of spinal cord with divergent growth dynamics.\n\nExperiment Description\nLightsheet imaging of tailbud from 18 somite stage with one frame per 2 minutes", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/552/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/552/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 751, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0052-walther-condensinmap", "Description": "Publication Title\nA quantitative map of human Condensins provides new insights into mitotic chromosome architecture.\n\nStudy Description\nHomozygous genome editing was used to fluorescently tag subunits of Condensin I and II in HeLa cells. Absolute abundance, spacing, and dynamic localization of the tagged proteins during mitosis was recorded by fluorescence correlation spectroscopy (FSC)-calibrated live-cell imaging and superresolution microscopy.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/751/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/751/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 752, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0052-walther-condensinmap/experimentA", "Description": "Publication Title\nA quantitative map of human Condensins provides new insights into mitotic chromosome architecture.\n\nExperiment Description\nGenome-edited cells with homozygously mEGFP-tagged Condensin subunits and chromosomes stained by SiR-DNA were imaged every 90 s for a total of 60 min by 3D confocal microscopy, which was automatically triggered after prophase onset. Images were calibrated by FCS to convert fluorescence intensities into cellular protein concentration maps and cellular protein number maps.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/752/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/752/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 753, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0052-walther-condensinmap/experimentB", "Description": "Publication Title\nA quantitative map of human Condensins provides new insights into mitotic chromosome architecture.\n\nExperiment Description\nFRAP experiments of Condensin-mEGFP subunits on the metaphase plate.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/753/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/753/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 754, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0052-walther-condensinmap/experimentC", "Description": "Publication Title\nA quantitative map of human Condensins provides new insights into mitotic chromosome architecture.\n\nExperiment Description\nSingle Colour - Condensin subunits were immunostained (with an anti-GFP antibody), and mitotic cells with chromatids oriented in parallel to the focal plane were selected for imaging. DNA (Hoechst) and Condensins (mEGFP tag and anti-GFP immunostaining) were imaged by diffraction-limited microscopy, whereas immunostained Condensin was also imaged by STED microscopy.  Double Colour -  NCAPH2-mEGFP and NCAPH-Halo were immunostained respectively with anti-GFP (1:500; ab13970; Abcam) + goat secondary anti-chicken Alexa Fluor 594 (1;500; A-11042; Thermo Fisher Scientific) and anti-Halo (1:500; G9281; Promega) + anti-rabbit Abberior STAR RED then imaged by STED microscopy.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/754/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/754/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 504, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0053-faas-virtualnanoscopy/experimentA", "Description": "Publication Title\nVirtual nanoscopy: generation of ultra-large high resolution electron microscopy maps.\n\nExperiment Description\n\tUltra-large high resolution electron microscopy maps of the mouse glomerulus, mouse embryonic fibroblasts, human dendritic cells and a zebrafish embryo slice were generated using virtual nanoscopy.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/504/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/504/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 701, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0054-segura-tonsilhyperion/experimentA", "Description": "Publication Title\nHuman lymphoid organ cDC2 and macrophages play complementary roles in T follicular helper responses.\n\nExperiment Description\nImaging mass cytometry of tonsil sections", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/701/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/701/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 801, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0062-blin-nuclearsegmentation/experimentA", "Description": "Publication Title\nNesSys: a novel method for accurate nuclear segmentation in 3D\n\nExperiment Description\nWe provide a user-friendly 3D editing tool to rapidly correct segmentation errors.  We test our method alongside other previously-published user-friendly methods, with focus on mid-gestation embryos, 3D cultures of pluripotent stem cells and pluripotent stem cell-derived neural rosettes.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/801/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/801/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1751, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0063-newman-chromosomalloci/experimentA", "Description": "Publication Title\nHomologous locus pairing is a transient, diffusion-mediated process in meiotic prophase\n\nExperiment Description\nLive-cell imaging was used to measure the distance between two fluorescently-tagged chromosomal loci over time in yeast nuclei throughout prophase I of meiosis.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1751/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1751/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 903, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0065-camsund-crispri", "Description": "Publication Title\nTime-resolved imaging-based CRISPRi screening\n\nStudy Description\nOur ability to connect genotypic variation to biologically important phenotypes has been seriously limited by the gap between live-cell microscopy and library-scale genomic engineering. Here, we show how in situ genotyping of a library of strains after time-lapse imaging in a microfluidic device overcomes this problem. We determine how 235 different CRISPR interference knockdowns impact the coordination of the replication and division cycles of Escherichia coli by monitoring the location of replication forks throughout on average >500 cell cycles per knockdown. Subsequent in situ genotyping allows us to map each phenotype distribution to a specific genetic perturbation to determine which genes are important for cell cycle control. The single-cell time-resolved assay allows us to determine the distribution of single-cell growth rates, cell division sizes and replication initiation volumes. The technology presented in this study enables genome-scale screens of most live-cell microscopy assays.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/903/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/903/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 901, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0065-camsund-crispri/experimentA", "Description": "Publication Title\nTime-resolved imaging-based CRISPRi screening\n\nExperiment Description\nTime-lapse imaging of cells using phase contrast and SeqA-YFP foci using wide-field fluorescence on a CRISPRi library of knock-downs loaded into a microfluidic device.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/901/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/901/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 902, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0065-camsund-crispri/experimentB", "Description": "Publication Title\nTime-resolved imaging-based CRISPRi screening\n\nExperiment Description\nAfter phenotyping, barcode RNAs were expressed by T7 RNApol induction and the cells were subsequently fixed and permeabilized. The strains were identified in situ by sequential FISH probing using widefield epi-fluorescence in four colors. Each round of probing identifies the positions of four unique strains.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/902/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/902/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 855, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0066-voigt-mesospim", "Description": "Publication Title\nThe mesoSPIM initiative \u2013 open-source light-sheet microscopes for imaging cleared tissue\n\nStudy Description\nThe mesoscale selective plane illumination microscope (mesoSPIM) designed in this study was tested with various cleared tissue samples.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/855/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/855/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 851, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0066-voigt-mesospim/experimentA", "Description": "Publication Title\nThe mesoSPIM initiative \u2013 open-source light-sheet microscopes for imaging cleared tissue\n\nExperiment Description\nComparison of whole-mouse brain data acquired from a CLARITY-cleared VIP-tdTomato mouse with and without ASLM mode engaged", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/851/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/851/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 852, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0066-voigt-mesospim/experimentB", "Description": "Publication Title\nThe mesoSPIM initiative \u2013 open-source light-sheet microscopes for imaging cleared tissue\n\nExperiment Description\nImaging a whole mouse central nervous system with the mesoSPIM", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/852/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/852/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 853, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0066-voigt-mesospim/experimentC", "Description": "Publication Title\nThe mesoSPIM initiative \u2013 open-source light-sheet microscopes for imaging cleared tissue\n\nExperiment Description\nImaging a whole mouse central nervous system with the mesoSPIM", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/853/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/853/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 854, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0066-voigt-mesospim/experimentD", "Description": "Publication Title\nThe mesoSPIM initiative \u2013 open-source light-sheet microscopes for imaging cleared tissue\n\nExperiment Description\nImaging a chicken embryo with the mesoSPIM", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/854/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/854/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 904, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0067-king-yeastmeiosis/experimentA", "Description": "Publication Title\nMeiotic cellular rejuvenation is coupled to nuclear remodeling in budding yeast\n\nExperiment Description\nTime-lapse and fixed cell fluorescence microscopy or transmission electron microscopy images depicting budding yeast cells progressing through meiosis. The goal of this study was to characterize nuclear remodeling during budding yeast meiosis, with a focus on determining how various nuclear senescence factors are eliminated.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/904/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/904/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2152, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0068-shah-zebrafishlightsheet/experimentA", "Description": "Publication Title\nMulti-scale imaging and analysis identifies pan-embryo cell dynamics of germlayer formation in zebrafish\n\nExperiment Description\nLight-sheet imaging of all three germ layers during early zebrafish development (4 - 18 hpf).", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2152/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2152/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1104, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0070-kerwin-hdbr/experimentA", "Description": "Publication Title\nThe HUDSEN Atlas: a three-dimensional (3D) spatial framework for studying gene expression in the developing human brain.\n\nExperiment Description\nImmunohistochemistry and in situ hybridization analysis in early human development from 3 to 17 weeks post conception.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1104/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1104/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1551, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0071-feldman-crisprko", "Description": "Publication Title\nOptical pooled screens in human cells\n\nStudy Description\nGenetic screens are critical for the systematic identification of genes underlying cellular phenotypes. Pooling gene perturbations greatly improves scalability, but is not compatible with imaging of complex and dynamic cellular phenotypes. Here, we introduce a pooled approach for optical genetic screens in mammalian cells. We use targeted in situ sequencing to demultiplex a library of genetic perturbations following image-based phenotyping. We screened a set of 952 genes across millions of cells for involvement in NF-\u03baB signaling by imaging the translocation of RelA (p65) to the nucleus. Screening at a single time point across 3 cell lines recovered 15 known pathway components, while repeating the screen with live-cell imaging revealed a novel role for Mediator complex subunits in regulating the duration of p65 nuclear retention. These results establish a new approach to perform highly multiplexed, image-based screens of spatially and temporally defined phenotypes with pooled libraries.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1551/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1551/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1503, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0071-feldman-crisprko/experimentA", "Description": "Publication Title\nOptical pooled screens in human cells\n\nExperiment Description\nOptical pooled CRISPR knockout screen in HeLa cells for regulators of p65 translocation upon stimulation by IL-1b or TNF-a, detected by imaging a p65-mNeonGreen fluorescent reporter. CRISPR sgRNAs are detected by sequencing proxy barcodes in cells transduced with the lentiGuide-BC vector. Included cycles of sequencing-by-synthesis (SBS): 1, 2, 3, 4, 5, 6, 7, 8, 9.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1503/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1503/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1505, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0071-feldman-crisprko/experimentB", "Description": "Publication Title\nOptical pooled screens in human cells\n\nExperiment Description\nOptical pooled CRISPR knockout screen in HeLa cells for regulators of p65 translocation upon stimulation by IL-1b or TNF-a, detected by indirect immunofluorescence of endogenous p65. CRISPR sgRNAs are detected by sequencing from the 5' end of the sgRNA sequence in cells transduced with the CROPseq-Puro vector. Included cycles of sequencing by synthesis (SBS): 1, 2, 3, 5, 6, 7, 8, 9, 10", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1505/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1505/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1504, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0071-feldman-crisprko/experimentC", "Description": "Publication Title\nOptical pooled screens in human cells\n\nExperiment Description\nOptical pooled CRISPR knockout screen in A549 cells for regulators of p65 translocation upon stimulation by IL-1b or TNF-a, detected by indirect immunofluorescence of endogenous p65. CRISPR sgRNAs are detected by sequencing from the 5' end of the sgRNA sequence in cells transduced with the CROPseq-Puro vector. Included cycles of sequencing-by-synthesis (SBS): 1, 2, 3, 4, 5, 7, 8, 9, 10.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1504/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1504/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1506, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0071-feldman-crisprko/experimentD", "Description": "Publication Title\nOptical pooled screens in human cells\n\nExperiment Description\nOptical pooled CRISPR knockout screen in HCT-116 cells for regulators of p65 translocation upon stimulation by IL-1b or TNF-a, detected by indirect immunofluorescence of endogenous p65. CRISPR sgRNAs are detected by sequencing from the 5' end of the sgRNA sequence in cells transduced with the CROPseq-Puro vector. Included cycles of sequencing-by-synthesis (SBS): 1, 2, 3, 4, 5, 6, 7, 8, 9.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1506/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1506/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1502, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0071-feldman-crisprko/experimentE", "Description": "Publication Title\nOptical pooled screens in human cells\n\nExperiment Description\nTwelve cycles of in situ sequencing in HeLa cells expressing barcodes from the lentiGuide-BC lentiviral vector. Included cycles of sequencing-by-synthesis (SBS): 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1502/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1502/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1507, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0071-feldman-crisprko/experimentF", "Description": "Publication Title\nOptical pooled screens in human cells\n\nExperiment Description\nCombinatorial detection of multiple CRISPR sgRNAs per cell in HeLa cells serially transduced with the CROPseq-Puro and CROPseq-Zeo vectors. Included cycles of sequencing-by-synthesis (SBS): 1, 2, 3, 4, 5, 6.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1507/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1507/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1002, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0073-schaadt-immuneinfiltrates/experimentA", "Description": "Publication Title\nGraph-based description of tertiary lymphoid organs at single-cell level\n\nExperiment Description\nBased on cell coordinates detected in the full image, a Delaunay triangulation and distance criteria were used to build neighborhood graphs. The composition of nodes and edges are used for classification, e.g. using a support vector machine.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1002/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1002/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 951, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0075-cabirol-honeybee/experimentA", "Description": "Publication Title\nAutomated quantification of synaptic boutons reveals their 3D distribution in the honey bee mushroom body\n\nExperiment Description\nTo study the spatial distribution of synaptic complexes called microglomeruli in the mushroom body neuropils of the honeybee brain, those structures where imaged by two-photon microscopy. A data analysis method was developed to automatically obtain the loci of those structures from large volume samples allowing to analyse their 3D density distribution.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/951/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/951/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1302, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0076-ali-metabric/experimentA", "Description": "Publication Title\nImaging mass cytometry and multiplatform genomics define the phenogenomic landscape of breast cancer\n\nExperiment Description\nMultiplexed imaging of breast cancer tissues for 37 proteins", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1302/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1302/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1101, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0077-valuchova-flowerlightsheet/experimentA", "Description": "Publication Title\nImaging plant germline differentiation within Arabidopsis flowers by light sheet microscopy\n\nExperiment Description\nUsing the light sheet microscope we acquired 16 different datasets of Arabidopsis flower development.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1101/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1101/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1105, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0079-hartmann-lateralline", "Description": "Publication Title\nAn Image-Based Data-Driven Analysis of Cellular Architecture in a Developing Tissue\n\nStudy Description\nA data-driven analysis of cell morphology and intracellular organization in the developing zebrafish posterior lateral line primordium, a model tissue for the study of self-organized morphogenesis. 3D image stacks were acquired using AiryScan FAST-mode confocal fluorescence microscopy. Automated single-cell segmentation and point cloud-based morphometry were developed to extract numerical features representing cell morphology and intracellular protein distributions. Machine learning was used with the extracted numerical features to perform data integration across experiments and context-guided data visualization. The resulting data was analyzed to discover biologically meaningful patterns at the cell and tissue scale.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1105/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1105/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1102, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0079-hartmann-lateralline/experimentA", "Description": "Publication Title\nAn Image-Based Data-Driven Analysis of Cellular Architecture in a Developing Tissue\n\nExperiment Description\n3D confocal live imaging of the zebrafish posterior lateral line primordium labeled with the membrane marker cldnB:lyn-EGFP for segmentation and optionally with one of several additional labels.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1102/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1102/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1103, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0079-hartmann-lateralline/experimentB", "Description": "Publication Title\nAn Image-Based Data-Driven Analysis of Cellular Architecture in a Developing Tissue\n\nExperiment Description\n3D confocal imaging of fixed samples of the zebrafish posterior lateral line primordium labeled with the membrane marker cldnB:lyn-EGFP and stained for pea3 mRNA using single molecule Fluorescence In-Situ Hybridization (smFISH).", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1103/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1103/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1251, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0082-pennycuick-lesions/experimentA", "Description": "Publication Title\nImmune surveillance in clinical regression of pre-invasive squamous cell lung cancer\n\nExperiment Description\nH&E Imaging of 112 lung carcinoma in-situ lesions, with CIS and stromal regions annotated, and quantification of infiltrating lymphocytes.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1251/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1251/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1051, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0083-lamers-sarscov2/experimentA", "Description": "Publication Title\nSARS-CoV-2 productively Infects Human Gut Enterocytes\n\nExperiment Description\nTEM analysis of SARS-CoV-2 infected intestine organoids", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1051/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1051/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1151, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0084-oudelaar-alphaglobin/experimentA", "Description": "Publication Title\nDynamics of the 4D genome during in vivo mouse erythroid lineage specification and differentiation\n\nExperiment Description\nWe performed RNA-FISH assays to determine the proportion of cells at three different stages of early erythroid differentiation that display nascent transcription of alpha-globin genes.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1151/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1151/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1202, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0085-walsh-mfhrem/experimentA", "Description": "Publication Title\nMulti-fluorescence high-resolution episcopic microscopy (MF-HREM) for three dimensional imaging of adult murine organs\n\nExperiment Description\nApplication of MF-HREM to imaging and analysis of adult mouse: kidney glomeruli, xenograft tumour vasculature and cell migration, brain microsvasculature and white matter orientation, brain white matter orientation and cell nuclei distribution", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1202/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1202/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1152, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0086-miron-micrographs", "Description": "Publication Title\nChromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin\n\nStudy Description\nThree-dimensional (3D) chromatin organization plays a key role in regulating mammalian genome function, however many of its physical features at the single-cell level remain underexplored. Here we use 3D super-resolution and scanning electron microscopy to analyze structural and functional nuclear organization in somatic cells. We identify linked chromatin domains (CDs) composed of irregular ~200-300-nm-wide aggregates of nucleosomes that can overlap with individual topologically associating domains and are distinct from a surrounding RNA-populated interchromatin region. High-content mapping uncovers confinement of cohesin and active histone modifications to surfaces and enrichment of repressive modifications towards the core of CDs in both hetero- and euchromatic regions. This nanoscale functional topography is temporarily relaxed in postreplicative chromatin, but remarkably persists after ablation of cohesin. Our findings establish CDs as physical and functional modules of mesoscale genome organization.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1152/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1152/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1158, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0086-miron-micrographs/experimentA", "Description": "Publication Title\nChromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin\n\nExperiment Description\nMicrographs of G1 interphase chromatin of C127 cells with super resolved immunofluorescence (IF) signals of over 16 epigenetic markers (Nascent RNA, Elongating RNAPolII, CTCF, Cohesin subunits, SAF-A and histone modifications such as H3K4me3, H3K27me3, H3K9me3, etc), all from commercially available antibodies.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1158/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1158/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1159, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0086-miron-micrographs/experimentB", "Description": "Publication Title\nChromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin\n\nExperiment Description\nMicrographs of a subset of the markers in experiment A with chromatin of different phenotype due to different stages of cell cycle: early, mid and late S phase as identified by EdU incorporation in nascent replicating regions.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1159/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1159/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1160, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0086-miron-micrographs/experimentC", "Description": "Publication Title\nChromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin\n\nExperiment Description\nMicrographs of G1 interphase chromatin of HCT116 cells with and without auxin inducible degradation (AID) of a cohesin subunit with IF on a subset of the previous markers to compare the way the epigenetic regulatory landscape changes when cells are not able to use the cohesin complex to sculpt the 3D chromatin landscape.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1160/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1160/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1161, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0086-miron-micrographs/experimentD", "Description": "Publication Title\nChromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin\n\nExperiment Description\nElectron Micrographs of the nucleus", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1161/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1161/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1157, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0087-paci-nuclearimport/experimentA", "Description": "Publication Title\nMolecular determinants of large cargo transport into the nucleus\n\nExperiment Description\nConfocal time-lapse images of nuclear import into permeabilised  cells. All experiments are labelled according to the different cargo used: capsid MS2_S37P, I53-47 and MS2, and number of NLSs on the capsid surface. For each experiment, 12 areas containing approximately 10 cells were imaged at the same time. Where independent biological replicates of the same sample are available, these are labelled as R1, R2 etc.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1157/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1157/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1305, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0089-fischl-coldtemp", "Description": "Publication Title\nCold-induced chromatin compaction and nuclear retention of clock mRNAs resets the circadian rhythm\n\nStudy Description\nCooling patients to sub-physiological temperatures is an integral part of modern medicine. We show that cold exposure induces temperature-specific changes to the higher-order chromatin and gene expression profiles of human cells. These changes are particularly dramatic at 18\u00b0C, a temperature synonymous with that experienced by patients undergoing controlled deep-hypothermia during surgery. Cells exposed to 18\u00b0C exhibit largely nuclear-restricted transcriptome changes. These include the nuclear accumulation of core circadian clock suppressor gene transcripts, most notably REV-ERB\u03b1. This response is accompanied by compaction of higher-order chromatin and hindrance of mRNPs from engaging nuclear pores. Rewarming reverses chromatin compaction and releases the transcripts into the cytoplasm, triggering a pulse of suppressor gene proteins that resets the circadian clock. We show that cold-induced upregulation of REV-ERB\u03b1 alone is sufficient to trigger this resetting. Our findings uncover principles of the cellular cold-response that must be considered for current and future applications involving therapeutic deep-hypothermia.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1305/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1305/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1303, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0089-fischl-coldtemp/experimentA", "Description": "Publication Title\nCold-induced chromatin compaction and nuclear retention of clock mRNAs resets the circadian rhythm\n\nExperiment Description\n3D-SIM of human cardiomyocyte cells (AC16s) exposed to different cold temperatures stained with markers for nuclear features (chromatin modifications: H3K4me3, H3K27me3, H3K9me3; Ser2-phosphorylated C-terminal domain of RNA polymerase II; hnRNPC; Nuclear pore complex) and DAPI. Cells were grown in 6 different temperature conditions prior to fixation: 37 degrees centigrade; 28 degrees centigrade for 24 h; 18 degrees centigrade for 5 h; 18 degrees centigrade for 24 h; 18 degrees centigrade for 24 h then returned to 37 degrees centigrade for 2 h; 8 degrees centigrade for 24 h.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1303/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1303/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1304, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0089-fischl-coldtemp/experimentB", "Description": "Publication Title\nCold-induced chromatin compaction and nuclear retention of clock mRNAs resets the circadian rhythm\n\nExperiment Description\nRNA-FISH of human cardiomyocyte cells (AC16s), U2OS cells or U2OS cells with Nr1d1 knocked-out exposed to different cold temperatures stained with RNA-FISH probes for Cry2, Tp53 or Nr1d1 and DAPI. Cells were grown in 5 different temperature conditions prior to fixation: 37 degrees centigrade; 18 degrees centigrade for 5 h; 18 degrees centigrade for 5 h then returned to 37 degrees centigrade for 2h; 18 degrees centigrade for 24 h; 18 degrees centigrade for 24 h then returned to 37 degrees centigrade for 2 h.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1304/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1304/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1351, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0091-julou-lacinduction/experimentA", "Description": "Publication Title\nSubpopulations of sensorless bacteria drive fitness in fluctuating environments\n\nExperiment Description\nBacteria are inoculated in Mother Machine microfluidic channels and exposed sequentially to two different media (e.g. 4h glucose, 4h lactose, 12h glucose, 4h lactose).", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1351/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1351/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1401, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0095-ali-asymmetry", "Description": "Publication Title\nInherent regulatory asymmetry emanating from network architecture in a prevalent autoregulatory motif\n\nStudy Description\nPredicting gene expression from DNA sequence remains a major goal in the field of gene regulation. A challenge to this goal is the connectivity of the network, whose role in altering gene expression remains unclear. Here, we study a common autoregulatory network motif, the negative single-input module, to explore the regulatory properties inherited from the motif. Using stochastic simulations and a synthetic biology approach in E. coli, we find that the TF gene and its target genes have inherent asymmetry in regulation, even when their promoters are identical; the TF gene being more repressed than its targets. The magnitude of asymmetry depends on network features such as network size and TF binding affinities. Intriguingly, asymmetry disappears when the growth rate is too fast or too slow and is most significant for typical growth conditions. These results highlight the importance of accounting for network architecture in quantitative models of gene expression.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1401/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1401/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1402, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0095-ali-asymmetry/experimentA", "Description": "Publication Title\nInherent regulatory asymmetry emanating from network architecture in a prevalent autoregulatory motif\n\nExperiment Description\nStudying the asymmetry when the strength of regulation for Transcription factor is kept fixed (O1 operator) and the strength of regulation for target is altered (stronger than TF, same as TF or weaker than TF).", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1402/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1402/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1403, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0095-ali-asymmetry/experimentB", "Description": "Publication Title\nInherent regulatory asymmetry emanating from network architecture in a prevalent autoregulatory motif\n\nExperiment Description\nStudying the asymmetry when the turnover rate of transcription factor is altered by introducing degradation tags.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1403/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1403/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1404, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0095-ali-asymmetry/experimentC", "Description": "Publication Title\nInherent regulatory asymmetry emanating from network architecture in a prevalent autoregulatory motif\n\nExperiment Description\n: Studying the asymmetry between TF and target gene when the protein dilution rate is altered by growing cells in different media.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1404/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1404/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2104, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0096-tratwal-marrowquant", "Description": "Publication Title\nMarrowQuant in Aging and Aplasia: A Digital Pathology Workflow For Quantification of Bone Marrow Compartments in Histological Sections\n\nStudy Description\nWe report the development of a semi-automated image analysis plug-in, MarrowQuant, which employs the open-source software QuPath, to systematically quantify multiple bone components in H&E sections in an unbiased manner. MarrowQuant discerns and quantifies the areas occupied by bone, adipocyte ghosts, hematopoietic cells and the interstitial/microvascular compartment. A separate feature, AdipoQuant, fragments adipocyte ghosts in H&E-stained sections of extramedullary adipose tissue sections to render adipocyte area and size distribution. Quantification of BM hematopoietic cellularity with MarrowQuant lies within the range of scoring by four independent pathologists, while quantification of the total adipocyte area in whole bone sections compares with volumetric measurements.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2104/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2104/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2102, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0096-tratwal-marrowquant/experimentA", "Description": "Publication Title\nMarrowQuant in Aging and Aplasia: A Digital Pathology Workflow For Quantification of Bone Marrow Compartments in Histological Sections\n\nExperiment Description\nMarrowQuant, a digital and quantitative pathology tool was used to quantify the different compartments within the bone marrow at different conditions, mainly aplasia and aging conditions. By using our tool, we can compare the skeletal map induced by lethal irradiation(aplasia), with longitudinal quantification of the \u201cred-to-yellow-to-red\u201d transition over 2 months (aging) in C57BL/6 mouse femurs and tibiae.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2102/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2102/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2103, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0096-tratwal-marrowquant/experimentB", "Description": "Publication Title\nMarrowQuant in Aging and Aplasia: A Digital Pathology Workflow For Quantification of Bone Marrow Compartments in Histological Sections\n\nExperiment Description\nAway from the Mouse H&E quantification, the current version of MarrowQuant was tested on a small set of H&E bone marrow biopsies from anonymised patients. The tool performs in a comparable way as compared to the gold standard (Pathologists\u2019 scorings), but it needs many optimisations before validating at the level of the human bone marrow biopsies quantifications and in clinical context.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2103/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2103/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1601, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0097-reicher-proteintag", "Description": "Publication Title\nPooled protein tagging, cellular imaging, and in situ sequencing for monitoring drug action in real time\n\nStudy Description\nThe levels and subcellular localizations of proteins regulate critical aspects of many cellular processes and can become targets of therapeutic intervention. However, high-throughput methods for unbiased discovery of proteins that change localization either by shuttling between compartments, by binding larger complexes or by localizing to distinct membraneless organelles are not available. Here we describe a scalable strategy to characterize effects on protein localizations and levels in response to different perturbations. We use CRISPR-Cas9 based intron tagging to generate cell pools expressing hundreds of GFP-fusion proteins from their endogenous promoters and monitor localization changes by time-lapse microscopy followed by clone identification using in situ sequencing. We show that this strategy can characterize cellular responses to drug treatment and thus identify non-classical effects such as modulation of protein-protein interactions, condensate formation and chemical degradation.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1601/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1601/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1602, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0097-reicher-proteintag/experimentB", "Description": "Publication Title\nPooled protein tagging, cellular imaging, and in situ sequencing for monitoring drug action in real time\n\nExperiment Description\nWe use CRISPR-Cas9 based intron tagging to generate cell pools expressing more than 900 GFP-fusion proteins (one GFP-tagged protein per cell). For this experiment, we seeded the cell pool in a single well of 384-well plate and imaged the entire well twice (0h and 3h timepoint, 289 fields of view per timepoint, raw tiff files were merged to 9 tiles per well). Cells in the same well were then fixed and we performed in situ sequencing to identify the expressed sgRNA in each cell indicating which protein is GFP tagged (7 cycles of in situ sequencing by synthesis, 289 fields of view per cycle,  raw tiff files were merged to 9 tiles per well).", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1602/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1602/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1603, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0097-reicher-proteintag/experimentC", "Description": "Publication Title\nPooled protein tagging, cellular imaging, and in situ sequencing for monitoring drug action in real time\n\nExperiment Description\nWe use CRISPR-Cas9 based intron tagging to generate cell pools expressing more than 900 GFP-fusion proteins (one GFP-tagged protein per cell). For this experiment, we seeded the cell pool in a single well of 384-well plate and treated the cells with dBET6, a BRD4-targeting PROTAC. We imaged the entire well at three timepoints (before treatment, after 1h and 3h after treatment, 289 fields of view per timepoint). Cells in the same well were then fixed and we performed in situ sequencing to identify the expressed sgRNA in each cell indicating which protein is GFP tagged (8 cycles of in situ sequencing by synthesis, 289 fields of view per cycle).", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1603/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1603/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1604, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0098-huang-octmos", "Description": "Publication Title\nOCT-MoS, a dataset of mouse skin squamous cell carcinoma stages by full-field optical coherence tomography\n\nStudy Description\nThe incidence of cutaneous squamous cell carcinoma (SCC) has increased in recent years, while it remains as an understudied subject. Current methods for the diagnose of skin cancer are either invasive, present a low resolution, or images that are difficult to interpret. Full-field optical coherence tomography (FF-OCT) has proven its potential as a non-invasive imaging technique of epithelial tissue. The sub-micrometer resolution offered by FF-OCT is able to show fine features such as cell nuclei, blood vessels, and fibrous structures in the dermis. However, not many physicians are familiar with the images derived from this technique. Using a well-known mouse model of SCC, we acquired volumetric data from skin samples at different stages of the disease using our home-made FF-OCT system. We present OCT-Mouse Skin (OCT-MoS) dataset, a curated dataset of 3400 annotated tomograms distributed into four classes, representing different stages in the development of SCC: normal, dysplasia, papilloma, and SCC. This dataset has a high potential for reuse in areas such as cancer research, medical training, image processing, and deep learning.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1604/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1604/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1605, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0098-huang-octmos/experimentA", "Description": "Publication Title\nOCT-MoS, a dataset of mouse skin squamous cell carcinoma stages by full-field optical coherence tomography\n\nExperiment Description\nAbdominal skin from FVB/N mice was untreated to serve as control samples for the normal class. Back skin from FVB/N mice was treated with immunosupresant and tumor promoter solutions to study different stages of cutaneous squamous cell carcinoma. All samples were excised and imaged by full-field optical coherence tomography.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1605/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1605/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1606, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0098-huang-octmos/experimentB", "Description": "Publication Title\nOCT-MoS, a dataset of mouse skin squamous cell carcinoma stages by full-field optical coherence tomography\n\nExperiment Description\nMicroscopy images of 9 H&E stain samples from mouse skin. Each slide contains different tissue samples corresponding to four different classes: normal, dysplasia, papilloma, and scc.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1606/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1606/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1651, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0099-jain-beetlelightsheet/experimentA", "Description": "Publication Title\nRegionalized tissue fluidization is required for epithelial gap closure during insect gastrulation\n\nExperiment Description\nThis dataset contains multiview fused images of Tribolium castaneum embryos labelled with a uniform nuclear localized eGFP signal, a uniform Histone-eGFP signal, a uniform LifeAct-eGFP signal, a uniform Tc-Squash-eGFP signal and a Gap43-eYFP signal. Selective Plane Illumination Microscopy (SPIM), was carried out on a Zeiss Lightsheet Z.1 microscope equipped with a 20x/1.0 NA Plan Apochromat water-immersion detection objective and two 10x/0.2 NA dry illumination objectives. Individual views were registered using bead-based registration and then fused to form combined 3D Tiff stacks using the Multiview reconstruction plugin in Fiji.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1651/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1651/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1451, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0100-capar-myelin/experimentA", "Description": "Publication Title\nA Multi-Spectral Myelin Annotation Tool for Machine Learning Based Myelin Quantification\n\nExperiment Description\nImmunolabeling of mouse embryonic stem cell derived neurons (TUJ1) and oligodendrocytes (MBP) and their nuclei (DAPI). Cells were grown in microfluidic chambers. Myelin is annotated on images.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1451/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1451/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2054, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0101-payne-insitugenomeseq", "Description": "Publication Title\nIn situ genome sequencing resolves DNA sequence and structure in intact biological samples\n\nStudy Description\nUnderstanding genome organization requires integration of DNA sequence and 3D spatial context, however, existing genome-wide methods lack either base-pair sequence resolution or direct spatial localization. Here, we describe in situ genome sequencing (IGS), a method for simultaneously sequencing and imaging genomes within intact biological samples. We applied IGS to human fibroblasts and early mouse embryos, spatially localizing thousands of genomic loci in individual nuclei. Using these data, we characterized parent-specific changes in genome structure across embryonic stages, revealed single-cell chromatin domains in zygotes, and uncovered epigenetic memory of global chromosome positioning within individual embryos. These results demonstrate how in situ genome sequencing can directly connect sequence and structure across length scales from single base pairs to whole organisms.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2054/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2054/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2051, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0101-payne-insitugenomeseq/experimentA", "Description": "Publication Title\nIn situ genome sequencing resolves DNA sequence and structure in intact biological samples\n\nExperiment Description\nIn situ genome sequencing of human PGP1 fibroblasts.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2051/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2051/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2052, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0101-payne-insitugenomeseq/experimentB", "Description": "Publication Title\nIn situ genome sequencing resolves DNA sequence and structure in intact biological samples\n\nExperiment Description\nIn situ genome sequencing of early mouse embryos", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2052/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2052/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1501, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0103-coomer-hiv1fusion/experimentA", "Description": "Publication Title\nSingle-cell glycolytic activity regulates membrane tension and HIV-1 fusion\n\nExperiment Description\nTZM-bl cells stably expressing CD4 and CCR5 receptors and charged with CCF2, were exposed to HIV-1 pseudoparticles where the Vpr is cloned with BlaM (Vpr-Blam) at MOI = 1. When treating the cells with 100 mM 2-Deoxyglucose (2DG), HIV-1 fusion is blocked. Successive treatment of these cells with 100, 200 and 400 ug/mL of Cholesterol rescues HIV-1 fusion. This experiment shows that cholesterol is key for HIV-1 fusion and that 2DG might downregulate the concentration of cholesterol in the plasma membrane of the host, impeding HIV-1 to effectively fuse in the host.  There are 3 different repeats and in each repeat 6 different experiments (images acquired in different conditions).", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1501/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1501/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1701, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0106-kubota-lunglightsheet/experimentA", "Description": "Publication Title\nWhole-organ analysis of TGF-beta-mediated remodelling of the tumour microenvironment by tissue clearing\n\nExperiment Description\nWhole lung image of metastatic model mouse.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1701/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1701/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1854, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0107-morgan-hei10/experimentA", "Description": "Publication Title\nDiffusion-mediated HEI10 coarsening explains meiotic crossover positioning in Arabidopsis\n\nExperiment Description\nImages used for HEI10 focus patterning and intensity measurements in Morgan et al., 2021. These are multichannel 3D-SIM reconstructed images of Arabidopsis pachytene cells labelled for ZYP1 and HEI10 and stained with DAPI. 3D skeleton traces of each of the 5 bivalent paths for each cell are also included to facilitate downstream image analysis.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1854/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1854/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1951, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0108-sabinina-nuclearporecomplex/experimentA", "Description": "Publication Title\n3D super-resolution fluorescence microscopy maps the variable molecular architecture of the Nuclear Pore Complex\n\nExperiment Description\nDual color super-resolution imaging of ELYS and NUP107, NUP133, RANBP2, SEH1, TPR.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1951/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1951/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1801, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0109-zaritsky-melanoma/experimentA", "Description": "Publication Title\nInterpretable deep learning uncovers cellular properties in label-free live cell images that are predictive of highly metastatic melanoma\n\nExperiment Description\nLive melanoma single cell phase contrast imaging with multiple labels: cell category (PDX, cell line, melanocyte, clonal expansion), PDX metastatic efficiency (high, low, unknown), cell type (e.g. A375, MV3, m405).", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1801/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1801/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1902, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0110-rodermund-xistrna/experimentA", "Description": "Publication Title\nTime-resolved structured illumination microscopy reveals key principles of Xist RNA spreading\n\nExperiment Description\nIn this project, XX mESCs with inducible endogenous Xist RNA, as well as XY mESCs with inducible autosomal transgenic Xist RNA, were used to study the localisation, dynamics and spreading behaviour of Xist RNA during the early phases of XCI. The Bgl-stem-loop labelling system was used in this project to label endogenous Xist RNA. A transgene encoding the BglG-Halo fusion protein was engineered to be doxycycline inducible. Later, different mutant cell lines were created using CRISPR/Cas9 genome editing. Considering the technical difficulties associated with live imaging of Xist foci, a different approach to studying Xist RNA dynamics was developed: RNA-SPLIT (Sequential Pulse Localisation Imaging over Time). In order to add temporal information one can make use of the fact that HaloTag technology enables addition of cell permeable ligands with different properties to cells, with excess ligand being washed out prior to fixation. Specifically, instead of a single HaloTag ligand, two different wavelength emitting HaloTag ligands were added sequentially after induction with doxycycline. Cells were induced for 1.5 h and 24 h before the start of the experiment to assess Xist localisation and dynamics in expansion and steady state respectively. Subsequent addition of the HaloTag ligands allowed for splitting the RNA into two differently labelled pools, pre-synthesised RNA labelled with Halo ligand 1 and newly synthesised RNA labelled with Halo ligand 2. This novel technique is especially powerful because variations of the set up can be used to study different aspects of RNA dynamics and localisation, and it can potentially be applied to any RNA and any stem-loop labelling system. Firstly, localisation of Xist to the X chromosome territory at the different stages of XCI and in different cellular backgrounds can be assessed by measuring the molecule density and volume of spread. Moreover, one can determine RNA turnover by scoring the number of pre-synthesised RNA molecules over time, while gradually increasing the staining time of newly synthesised RNA molecules for up to 4 h. Full turnover of the RNA can be assumed when no pre-synthesised RNA signal can be detected anymore. Turnover rates can be complemented by analysis of RNA transcription dynamics, quantified by scoring the number of newly synthesised RNA molecules while gradually increasing the staining time of newly synthesised RNA in 10 min intervals. Finally, RNA-SPLIT can be used to assess the localisation of newly synthesised RNA with respect to pre-synthesised RNA by measuring the distance of each newly synthesised molecule to the nearest pre-synthesised molecule. Image processing and analysis is critical for successful RNA-SPLIT experiments. After image acquisition with 3D-SIM, the data is reconstructed and undergoes quality checks through the SIMcheck plugin. Artefacts are reduced by generating modulation contrast maps and applying suitable and consistent filters to discard low modulation contrast signal. Then, background stemming from free diffusing BglG-Halo is discarded by manual thresholding. Channels are aligned using the open-source software package Chromagnon and EdU calibration data acquired on the date of image acquisition. In the final step of image processing, Xist territories are manually cropped. The volume of the cropped Xist territory gives first insights into the spreading volume of the RNA. To analyse the fully processed images, the signal is masked and the centroids of each molecule are determined by a Watershed algorithm. This allows for the counting of pre-synthesised and newly synthesised molecules at different time points and under various experimental conditions. RNA turnover and transcription dynamics can be deduced from this information. The localisation of each molecule in 3D determined by the Watershed algorithm can then be used to conduct NNA, where the distance of each newly synthesised molecule to its nearest neighbouring pre-synthesised molecule is measured. Variations of NNA, where distances between all RNA molecules or between the approximate transcription site and newly synthesised RNA are determined, can be used to examine RNA density and spreading behaviour. The development of this new tool for studying RNA localisation and dynamics allows for the addition of temporal resolution to super-resolved localisation microscopy data without the need for live cell imaging.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1902/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1902/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1851, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0111-lee-cellmigration", "Description": "Publication Title\nDistinct Roles of Tumor Associated Mutations in Collective Cell Migration\n\nStudy Description\nRecent evidence suggests that groups of cells are more likely to form clinically dangerous metastatic tumors, emphasizing the importance of understanding mechanisms underlying collective behavior. The emergent collective behavior of migrating cell sheets in vitro has been shown to be disrupted in tumorigenic cells but the connection between this behavior and in vivo tumorigenicity remains unclear. We use particle image velocimetry to measure a multidimensional migration phenotype for genetically defined human breast epithelial cell lines that range in their in vivo behavior from non-tumorigenic to aggressively metastatic. By using cells with controlled mutations, we show that PTEN deletion enhances collective migration, while Ras activation suppresses it, even when combined with PTEN deletion. These opposing effects on collective migration of two mutations that are frequently found in patient tumors could be exploited in the development of novel treatments for metastatic disease. Our methods are based on label-free phase contrast imaging, and thus could easily be applied to patient tumor cells. The short time scales of our approach do not require potentially selective growth, and thus in combination with label-free imaging would allow multidimensional collective migration phenotypes to be utilized in clinical assessments of metastatic potential.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1851/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1851/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1852, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0111-lee-cellmigration/experimentA", "Description": "Publication Title\nDistinct Roles of Tumor Associated Mutations in Collective Cell Migration\n\nExperiment Description\nMCF10A, PTEN-/-, KRas, and KRas/PTEN-/- cell lines or the MCF10A and MDA-MB-231 cell lines were plated in a collective migration assay that uses circular cell sheets.  Tiled images of each full cell sheet were taken before and after a set of time lapse images was taken of two ROIs in each cell sheet.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1852/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1852/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1853, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0111-lee-cellmigration/experimentB", "Description": "Publication Title\nDistinct Roles of Tumor Associated Mutations in Collective Cell Migration\n\nExperiment Description\nMCF10A, PTEN-/-, KRas, and KRas/PTEN-/- cell lines were plated in a collective migration assay that uses circular cell sheets.  Duplicates plates were used to create fixed samples at t=0 (plate 1) and t=15 h (plate 2).  The fixed samples were stained with DAPI.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1853/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1853/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 1903, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0113-bottes-opcclones/experimentA", "Description": "Publication Title\nLive imaging of remyelination in the adult mouse corpus callosum\n\nExperiment Description\nWe genetically targeted OPCs using mice expressing a tamoxifen (Tam)-inducible Cre recombinase under the control of the endogenous Achaete-scute homolog 1 (Ascl1) promoter crossed with a tdTomato reporter mouse line (Ascl1-tdTomato mice). To induce focal demyelination in the CC, mice were injected with LPC in the posterior CC. Mice were implanted with a transcortical window allowing for optical access using 2-photon microscopy. Tamoxifen (TAM) was injected 2 and 3 days after LPC injection to induce sparse labeling of Ascl1-targeted OPCs. Labeled OPC clones were imaged every day up to two months.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/1903/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/1903/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2151, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0114-lindsay-hdbr/experimentA", "Description": "Publication Title\nEnabling research with human embryonic and fetal tissue resources\n\nExperiment Description\nImmunohistochemistry, immunofluorescence and RNAscope analysis in early human development from 3 to 19 weeks post conception.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2151/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2151/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2301, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0115-otsuka-nucleoporins/experimentA", "Description": "Publication Title\nA quantitative map of nuclear pore assembly reveals two distinct mechanisms\n\nExperiment Description\n3D time-lapse imaging of nucleoporins and DNA during mitosis exit.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2301/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2301/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2053, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0116-deboer-npod/experimentA", "Description": "Publication Title\nLarge-scale electron microscopy database for human type 1 diabetes\n\nExperiment Description\nScanning transmission electron microscopy of Islets of Langerhans.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2053/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2053/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2001, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0117-croce-marimba/experimentA", "Description": "Publication Title\nske-T, a T-box gene expressed in the skeletogenic mesenchyme lineage of the sea urchin embryo\n\nExperiment Description\nSpatial distribution of ske-T transcripts during development.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2001/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2001/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2101, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0118-keenan-flylightsheet/experimentA", "Description": "Publication Title\nDynamics of Drosophila endoderm specification\n\nExperiment Description\nTime-lapse microscopy was performed on Drosophila embryos containing an endogenous transcriptional reporter for the genes tailless (tll), huckebein (hkb), brachyenteron (byn), forkhead (fkh), and wingless (wg) using a light-sheet microscope.  Images were taken once every minute from the start of nuclear cycle 11 to the start of gastrulation (approximately 90 minutes total) in order to track transcription of genes in individual nuclei in the posterior third of the embryo.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2101/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2101/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2251, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0123-mota-mifish/experimentA", "Description": "Publication Title\nSimultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH\n\nExperiment Description\nDatasets 1 and 2 are replicates of the same experimental design which consists of 16 probes targeting 16 consecutive loci on chromosome 2 using iFISH4U. The 16 probes targeting different loci are spaced with 3 or 20 Mb in order to study relatively small genomic distances and compare them with larger distances. Furthermore, 10 loci are made by a combination of two colours alternating within the locus and 6 loci have only one colour. Dataset 3 is a single colour experiment where one probe with alternated colours (AF488-AF594) was tested together with other two probes in different colours located in distinct genomic sites. There is 1 probe with AF488 dye, 1 probe with AT542, 1 probe with AF594 and 1 probe with AT647N. Dataset 4 is a single colour experiment where one probe with alternated colours (AT542-AT647N) was tested together with two other probes in different colours located in distinct genomic sites. There is 1 probe with AF488 dye, 1 probe with AT542, 1 probe with AF594 and 1 probe with AT647N. Dataset 5 consists of 23 probes targeting 23 consecutive loci on chromosome 1 using iFISH4U. The 23 loci are spaced with 10 Mb. There are 3 probes with AF488 dye, 4 probes with AT542, 4 probes with AF594, 4 probes with AT647N, 4 probes with AF700 and 4 probes with AF790. Datasets 6 and 7 are replicates of the same experimental design which consists of 21 probes targeting 21 consecutive loci on chromosome 2 using iFISH4U. The 23 loci are spaced with 10 Mb. There are 3 probes with AF488 dye, 3 probes with AT542, 3 probes with AF594, 3 probes with AT647N, 6 probes with AF700 and 3 probes with AF790. Datasets 8 and 9 are replicates of the same experimental design which consists of 13 probes targeting 13 consecutive loci on chromosome 10 using iFISH4U. The 23 loci are spaced with 10 Mb. There are 2 probes with AF488 dye, 2 probes with AT542, 3 probes with AF594, 2 probes with AT647N, 2 probes with AF700 and 2 probes with AF790.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2251/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2251/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2201, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0124-esteban-heartmorphogenesis/experimentA", "Description": "Publication Title\nPseudo-dynamic analysis of heart tube formation in the mouse reveals strong regional variability and early left-right asymmetry\n\nExperiment Description\nImaging of a temporally dense collection of mouse embryonic heart morphologies between E7.75 and E8.5.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2201/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2201/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2252, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0127-baer-phenotypicheterogeneity", "Description": "Publication Title\nQuantification of within patient Staphylococcus aureus phenotypic heterogeneity as a proxy for presence of persisters across clinical presentations\n\nStudy Description\nStaphylococcus aureus was isolated from patients suffering cardiovascular, prosthetic joint or other infections and plated on Columbia sheep blood agar. Macroscopic time-lapse imaging was performed to quantify colony appearance-time and growth-rate. As a baseline reference, the same time-lapse imaging protocol was used after subculturing clinical isolates in tryptic soy broth until bacteria reached exponential growth phase.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2252/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2252/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2253, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0127-baer-phenotypicheterogeneity/experimentA", "Description": "Publication Title\nQuantification of within patient Staphylococcus aureus phenotypic heterogeneity as a proxy for presence of persisters across clinical presentations\n\nExperiment Description\nBacteria were directly isolated from patient material and then spread-plated on Columbia Sheep Blood agar plates. Samples were time-lapse imaged.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2253/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2253/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2254, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0127-baer-phenotypicheterogeneity/experimentB", "Description": "Publication Title\nQuantification of within patient Staphylococcus aureus phenotypic heterogeneity as a proxy for presence of persisters across clinical presentations\n\nExperiment Description\nBacteria were directly isolated from patient material and then spread-plated on Columbia Sheep Blood agar plates. Samples were endpoint (single isolated timepoint, usually 24h and 48h) imaged.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2254/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2254/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2255, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0127-baer-phenotypicheterogeneity/experimentC", "Description": "Publication Title\nQuantification of within patient Staphylococcus aureus phenotypic heterogeneity as a proxy for presence of persisters across clinical presentations\n\nExperiment Description\nAfter Experiment A or B, bacteria were stored at -80C. Bacteria were restreaked on columbia sheep blood agar and single colonies inoculated in tryptic soy broth for overnight growth. These cultures were dilute 1:10 and incubated for 2h. From these exponential cultures, time-lapse imaging was started.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2255/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2255/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2401, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0134-peters-bryophytes/experimentA", "Description": "Publication Title\nReference bioimaging to assess the phenotypic trait diversity of bryophytes within the family Scapaniaceae\n\nExperiment Description\nRepresentative voucher specimens were received from herbaria and fresh samples of Diplophyllum taxifolium, Scapania cuspiduligera, Scapania gymnostomophila and Scapania subalpina were additionally collected, put into envelopes on-site, identified and photographed afterwards. Information regarding the date, site (including geographical coordinates), habitat, substrate and other further information are available in the meta-data. For microscopy, a Zeiss Axio Scope.A1 HAL 100/HBO, 6x HD/DIC, M27, 10x/23 microscope with an achromatic-aplanatic 0.9 H D Ph DIC condenser was used with the objectives EC Plan Neofluar 2.5x/0.075 M27 (a=8.8mm), Plan-Apochromat 5x/0.16 M27 (a=12.1mm), Plan-Apochromat 10x/0.45 M27 (a=2.1mm), Plan-Apochromat 20x/0.8 M27 (a=0.55mm), and Plan-Apochromat 40x/0.95 Korr M27 (a=0.25mm) using the EC PN and the Fluar 40x/1.30 III and PA 40x/0.95 III filters for DIC. The conversion filter CB3 and the interference filter wideband green were used to improve digital reproduction of colors. For macroscopy and for preparing microscopy slides, a binocular microscope Zeiss Stemi 2000c was used (apochromatic Greenough system with a stereo angle of 11\u00b0 and 100/100 switchover of camera and ocular viewing). For stand-alone macroscopic images, the objectives Canon MP-E 65mm 2.8 1-5x macro and Laowa 25mm 2.5-5.0x ultra-macro for Canon EF and the Canon EF-RF adapter. To acquire digital images, a full-frame, high-resolution camera (Canon EOS RP, 26 megapixel) was used and adapted to the microscopes using binocular phototubes with sliding prism 30\u00b0/23 (Axio Scope.A1) and 100:0/0:100 reversed image (Stemi 2000c) using 60-T2 camera adapter for Canon EOS and Canon EF-RF adapter. The objectives Canon MP-E and Laowa 25mm were adapted directly through the Canon EF-RF adapter. To construct images with extended depth of field using computational methods, multiple images were recorded at different focal planes. This \u201cfocus stacking\u201d approach was automatized for macroscopy by attaching the camera to a Cognisys StackShot macro rail fixed on a Novoflex macro stand, and for microscopy by adapting a Cognisys StackShot motor to the fine adjustment of the microscope using two cogged wheels, one small wheel (1 cm diameter) adapted on the motor and one large wheel (8.5 cm diameter) on the fine adjustment of the microscope. The two cogged wheels were coupled with a toothed belt to obtain very fine step increments of the stepping motor for high magnifications. A Cognisys StackShot controller was used to control the amount and distance of the stepping motor with the following controller settings: Dist/Rev: 3200 stp, Backlash: 0 steps, # pics: 1, Tsettle: 100.0 ms, Toff: 450.0 ms, Auto Return: yes, Speed: 3000 st/sec, Tlapse: off, Tpulse: 800.0 ms, Tramp: 100 ms, Units: steps, Torque: 6, Hi Precision: Off, LCD Backlight: 10, Mode: Auto-Step using between 25 steps (magnification 1x) and 50 steps (magnification 25x) and 100 steps (magnification 400x) (number of steps depending on aperture settings and effective magnification). Raw images were recorded in CR3-format and pre-processed with Adobe Camera RAW. Non-destructive image enhancements such as corrections of the field curvature, removal of chromatic aberration, increase of contrast and brightness were performed in Adobe Camera RAW. Images were then exported into TIF-format and any image enhancement steps were recorded in individual XMP-files. Files containing multiple images of one object captured at different steps of the z-axis (for alter multi-focus image fusion) have been saved into one OME-TIFF file. Multi-focus image fusion was performed on the individual images in the z-stacks using the software Helicon Focus and by choosing the algorithms depth map and pyramid with different settings of radius (4, 8, 16, 24) and smoothing (2, 4). The best composite image was chosen manually and retained. When composite images contained specimen that were larger than the frame, several images were stitched together using the software Affinity Photo and the panorama stitching function. Images were manually segmented and interfering background removed using the flood select, brush selection and freehand selection tools in the software Affinity Photo. In order to determine the scale, a stage micrometre was photographed separately with any of the objectives and microscope combinations. The scale was calculated per pixel for each combination and scale bars were put post-hoc onto the segmented images using a simple Python script. Meta-data including species name, taxonomic rank information, voucher specimen id, image acquisition date, an object description including the name of the captured phenotypic properties, used objective-microscope combination and magnification were associated with any raw image based on unique species names and unique respective file names. Individual file names (variable file list), name within an image focus stack (variable stack name) and name within an image stitching stack (variable stitch name) were recorded additionally to facilitate subsequent automized image processing in workflows. A Python script was created to put individual images as part of image stacks into directories. The Python script parses the Label tag in the XMP-files. Any meta-data regarding image enhancement and non-destructive image processing were extracted from XMP-files using a simple Python script. The meta-data was saved in individual TSV-files and merged using a helper Python script. In order to improve data reuse and to enable linking bioimaging data to ecological data repositories such as GBIF, individual segmented images were associated with standardised geolocation information. Swiss Topo CH1903/LV03 coordinates were converted to WGS84 using Swisstopo-WGS84-LV0352. The segmented images and meta-data contained in a TSV file were uploaded to the Image Data Resource repository (IDR).", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2401/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2401/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2351, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0135-hodis-melanocytes/experimentA", "Description": "Publication Title\nStepwise-edited, human melanoma models reveal mutations' effect on tumor and microenvironment\n\nExperiment Description\nAfter euthanizing the mice, solid tumors were collected and fixed with 10% formalin (Patterson Veterinary) for 24 hours. Samples were subsequently transferred into 70% ethanol and submitted to the Histology Core at the Koch Institute for paraffin embedding, in 3 batches, the paraffin blocks were subjected to tissue sectioning, Hematoxylin & Eosin (H&E) staining and digital whole slide scanning.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2351/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2351/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2551, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0137-peters-bryophytes/experimentA", "Description": "Publication Title\nData integration in biodiversity - A principal investigation on three liverwort species of Riccia integrating metabolomics, sequencing and phenotypic data for use in integrative taxonomy\n\nExperiment Description\nSamples of R. glauca, R. sorocarpa, R. warnstorfii were collected by Uwe Schwarz from an arable stubble field near Aichtal Gr\u00f6tzingen in Baden-W\u00fcrttemberg, Germany on 09/13/2021 (geographic coordinates: 48.638275 N, 9.2534083 E, elevation: 376 m, precision: 10 m). To evaluate phylogenetic distances, Lunularia cruciata (L.) Dumort. ex Lindb. was additionally sampled near the lab site on 12/08/2021 at 51.494848 N, 11.942323 E. The specimens were brought to the lab at IPB in sterile petri dishes, where plant material was isolated, washed under a light microscope to remove dirt and other residues, filled into Eppendorf tubes and shock-frozen. Voucher specimens were stored in the herbarium Haussknecht Jena (voucher id\u2019s: Riccia glauca: JE04010991, Riccia sorocarpa: JE04010990, Riccia warnstorfii: JE04010989, Lunularia cruciata: JE04010993). For image acquisition, a Zeiss Axio Scope.A1 HAL 100/HBO, 6x HD/DIC, M27, 10x/23 microscope with an achromatic-aplanatic 0.9 H D Ph DIC condenser was used for microscopy utilizing the objectives EC Plan Neofluar 2.5x/0.075 M27 (a=8.8mm), Plan-Apochromat 5x/0.16 M27 (a=12.1mm), Plan-Apochromat 10x/0.45 M27 (a=2.1mm), Plan-Apochromat 20x/0.8 M27 (a=0.55mm), and Plan-Apochromat 40x/0.95 Korr M27 (a=0.25mm) using the EC PN and the Fluar 40x/1.30 III and PA 40x/0.95 III filters for DIC. The conversion filter CB3 and the interference filter wideband green were used to improve digital reproduction of colors. The color balance was adjusted in the camera and in software accordingly. For macroscopy and for preparing microscopy slides, a binocular microscope Zeiss Stemi 2000c was used. For macroscopic images, the Venus Optics Laowa 25mm 2.5-5.0x ultra-macro for Canon EF and the Canon EF-RF adapter were used. To acquire digital images, a full-frame, high-resolution camera (Canon EOS RP, 26 megapixel) was used and adapted to the photographic objectives or to the microscopes using binocular phototubes with sliding prism 30\u00b0/23 (Axio Scope.A1) and 100:0/0:100 reversed image (Stemi 2000c) using 60-T2 camera adapter for Canon EOS and a Canon EF-RF adapter. To construct images with extended depth-of-field, images were recorded at different focal planes. This \u201cfocus stacking\u201d approach was automatized for macroscopy by attaching the camera to a Cognisys StackShot macro rail fixed on a Novoflex macro stand, and for microscopy by adapting a Cognisys StackShot motor to the fine adjustment of the microscope using two cogged wheels, one small wheel (1 cm diameter) adapted on the motor and one large wheel (8.5 cm diameter) on the fine adjustment of the microscope. The two cogged wheels were coupled with a toothed belt to obtain fine step increments of the stepping motor for high magnifications. A Cognisys StackShot controller was used to control the amount and distance of the stepping motor with the following controller settings: Dist/Rev: 3200 stp, Backlash: 0 steps, # pics: 1, Tsettle: 100.0 ms, Toff: 450.0 ms, Auto Return: yes, Speed: 3000 st/sec, Tlapse: off, Tpulse: 800.0 ms, Tramp: 100 ms, Units: steps, Torque: 6, Hi Precision: Off, LCD Backlight: 10, Mode: Auto-Step using between 25 steps (magnification 1x) and 50 steps (magnification 25x) and 100 steps (magnification 400x) (number of steps depending on aperture settings and effective magnification). Raw images were recorded in CR3-format and pre-processed with Adobe Camera RAW. Non-destructive image processing such as corrections of the field curvature, removal of chromatic aberration, color balance, increase of contrast and brightness were performed in Adobe Camera RAW. Images were then exported to TIFF-format and any image processing steps were recorded in individual Adobe XMP-files. Multi-focus image fusion was performed on the individual images in the z-stacks using the software Helicon Focus 8.1.1 and by choosing the algorithms depth map and pyramid with different settings of radius (4, 8, 16, 24) and smoothing (2, 4). The best composite image was chosen manually and retained. When composite images contained specimen that were larger than the frame, several images were stitched together using the panorama stitching function in the software Affinity Photo 1.10.5. Images were manually segmented and interfering background removed using the flood select, brush selection and freehand selection tools in the software Affinity Photo. In order to determine the scale, a stage micrometer was photographed separately with any of the objectives and microscope combinations. The scale was calculated per pixel for each combination and scale bars were put post-hoc onto the segmented images. Meta-data including species name, taxonomic rank information (NCBI-Taxon and GBIF taxonomy identifiers), voucher specimen id, image acquisition date, an object description including the name of the captured phenotypic character(s), the used objective, microscope, and magnification were associated with any raw image based on unique respective file names. Individual file names, name within an image focus stack and name within an image stitching stack were recorded additionally to facilitate subsequent automized image processing in workflows. Python scripts were created to automatize image fusion and image stitching tasks. Image features were estimated using the R package EBImage (Pau et al., 2010) by extracting the histograms of the red, green, and blue channels of the bioimages representing the visible spectra of the thalli of the different species. To investigate relationships of the image properties and the molecular traits, distance-based ReDundancy Analyses (dbRDA) were performed using the dbrda function of the package vegan (Peters et al., 2018a). Spectral values other than pure black (all RGB channels zero) and pure white (all RGB channels one) were extracted from the histogram models and used as traits in a dbRDA model. A Euclidean distance measure was used for the ordination. The dbRDA-model with the largest explained variance was chosen using forward variable selection and the ordistep function. The goodness of fit statistic (squared correlation coefficient) was determined for the remaining variables by applying the envfit function on the dbRDA ordination model. Raw camera and pre-processed imaging data in CR3 and TIFF format, respectively, were deposited to the BioImage Archive (BioStudies) using the command line IBM Aspera software tool ascp version 3.8.1.161274 to ensure that data has been transmitted without errors. The raw bioimaging data is available under the BioStudies identifier S-BIAD443 (https://www.ebi.ac.uk/biostudies/studies/S-BIAD443). Processed images were converted to the Bio-Formats OME-TIFF format by creating intermediate ZARR-pyramid tiles using the bioformats2raw converter version 0.4.0 and then using the raw2ometiff version 0.3.0 software tool to create the final pyramid images. Processed images and the metadata were first aggregated in a TSV table and then deposited to the Image Data Resource (https://idr.openmicroscopy.org/search/?query=Name:137) under accession number idr0137 using the software Globus Connect Personal 3.1.6.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2551/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2551/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2951, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0138-lohoff-seqfish/experimentA", "Description": "Publication Title\nIntegration of spatial and single-cell transcriptomic data elucidates mouse organogenesis\n\nExperiment Description\nseqFISH study of sagittal sections of mouse embryos at 8-10 somite stage. An additional round of hybridisation to capture cell membrane is performed to accurately segment cell boundaries.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2951/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2951/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2451, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0141-sokol-skinmucosa/experimentA", "Description": "Publication Title\nLarge-Scale Electron Microscopy Maps of Patient Skin and Mucosa Provide Insight into Pathogenesis of Blistering Diseases\n\nExperiment Description\nLarge-scale scanning electron microscopy maps of blistering disease patient skin and mucosa.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2451/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2451/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2501, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0144-baskay-jawbone/experimentA", "Description": "Publication Title\nReconstructing 3D histological structures using machine learning (AI) algorithms\n\nExperiment Description\nBright-field scans of histological sections of trabecular bone from homo sapiens jaw.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2501/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2501/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2601, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0146-dominguez-heartlightsheet/experimentA", "Description": "Publication Title\nGraded mesoderm assembly governs cell fate and morphogenesis of the early mammalian heart\n\nExperiment Description\nLight-sheet imaging of post-implantation mouse development from E6.5 to E8.5.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2601/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2601/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2701, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0147-kuo-kidney3d/experimentA", "Description": "Publication Title\nTerabyte-scale supervised 3D training and benchmarking dataset of the mouse kidney\n\nExperiment Description\nC57BL/6J mice were purchased from Janvier Labs (Le Genest-Saint-Isle, France) and kept in individually ventilated cages with ad libitum access to water and standard diet (Kliba Nafag 3436, Kaiseraugst, Switzerland) in 12 h light/dark cycles. Dataset 1 derives from the left kidney of a male mouse, 15 weeks of age with a body weight of 28.0 g. Dataset 2 is the right kidney of the same mouse. Dataset 3 derives from the right kidney of a female mouse, 15 weeks of age with a body weight of 22.5 g. All animal experiments were approved by the cantonal veterinary office of Zurich, Switzerland, in accordance with the Swiss federal animal welfare regulations (license numbers ZH177/13 and ZH233/15). Mice were anaesthetized with ketamine/xylazine. A blunted 21G butterfly needle was inserted retrogradely into the abdominal aorta and fixed with a ligation. The abdominal aorta and superior mesenteric artery above the renal arteries were ligated, the vena cava opened as an outlet and the kidneys were flushed with 10 ml, 37 \u00b0C phosphate-buffered saline (PBS) to remove the blood, then fixed with 50 ml 37 \u00b0C 4 % paraformaldehyde in PBS (PFA) solution at 150 mmHg hydrostatic pressure.\t2.4 g of 1,3-diiodobenzene (Sigma-Aldrich, Schnelldorf, Germany) were dissolved in 7.5 g of 2-butanone (Sigma-Aldrich) and mixed with 7.5 g PU4ii resin (vasQtec, Zurich, Switzerland) and 1.3 g PU4ii hardener. The mixture was filtered through a paper filter and degassed extensively in a vacuum chamber to minimize bubble formation during polymerization, and perfused at a constant pressure of no more than 200 mmHg until the resin mixture solidified. Kidneys were excised and stored in 15 ml 4 % PFA. For scanning, they were embedded in 2 % agar in PBS in 0.5 ml polypropylene centrifugation tubes. Kidneys were quality-checked with a nanotom\u00ae m (phoenix|x-ray, GE Sensing & Inspection Technologies GmbH, Wunstorf, Germany). Samples showing insufficient perfusion or bleeding of resin into the renal capsule or sinuses were excluded. Kidneys were scanned at the ID19 tomography beamline of the European Synchrotron Radiation Facility (ESRF, Grenoble, France) using pink beam with a mean photon energy of 19 keV. Radiographs were recorded at a sample-detector distance of 28 cm with a 100 \u00b5m Ce:LuAG scintillator, 4\u00d7 magnification lens and a pco.edge 5.5 camera with a 2560 \u00d7 2160 pixel array and 6.5 \u00b5m pixel size, resulting in an effective pixel size of 1.625 \u00b5m. Radiographs were acquired with a half-acquisition scheme in order to extend the field of view to 8 mm. Six height steps were recorded for each kidney, with half of the vertical field of view overlapping between each height step, resulting in fully redundant acquisition of the inner height steps. 5125 radiographs were recorded for each height step with 0.1 s exposure time, resulting in a scan time of 1 h for a whole kidney. 100 flat-field images were taken before and after each height step for flat-field correction. Images were reconstructed using the beamline\u2019s in-house PyHST2 software, using a Paganin-filter with a low \u03b4/\u03b2 ratio of 50 to limit loss in resolution and appearance of gradients close to large vessels. Registration for stitching two half-acquisition radiographs to the full field of view was performed manually with 1 pixel accuracy. Data size for the reconstructed datasets was 1158 GB per kidney. Outliers in intensity in the recorded flat fields were segmented by noise reduction with 2D continuous curvelets, followed by thresholding to calculate radius and coordinates of the ring artefacts. The redundant acquisition of the central four height steps allowed us to replace corrupted data with a weighted average during stitching. The signals of the individual slices were zeroed in the presence of the rings, summed up and normalized by counting the number of uncorrupted signals. In the outer slices, where no redundant data was available, and in locations where rings coincided in both height steps, we employed a discrete cosine transform-based inpainting technique with a simple iterative approach, where we picked smoothing kernels progressively smaller in size and reconstructed the signal in the target areas by smoothing the signal everywhere at each iteration. The smoothed signal in the target areas was then combined with the original signal elsewhere to form a new image. In the next iteration, in turn, the new image was then smoothed to rewrite the signal at the target regions. The final inpainted signal exhibits multiple scales since different kernel widths are considered at different iterations. The alignment for stitching the six stacks was determined by carrying out manual 3D registration and double checking against pairwise stack-stack phase-correlation analysis. The stitching process reduced the dataset dimensions per kidney to 4608 \u00d7 4608 \u00d7 7168 pixels, totaling 567 GB.\tWe performed image enhancement based on 3D discretized continuous curvelets, in a similar fashion as Starck et al., but with second generation curvelets (i.e., no Radon transform) in 3D. The enhancement was carried out globally by leveraging the Fast Fourier Transform with MPI-FFTW, considering about 100 curvelets. The \u201cwedges\u201d (curvelets in the spectrum) have a conical shape and cover the unit sphere in an approximately uniform fashion. For a given curvelet, a per-pixel coefficient is obtained by computing an inverse Fourier transform of its wedge and the image spectrum. We then truncated these coefficients in the image domain against a hard threshold, and forward-transformed the curvelet again into the Fourier space, modulated the curvelets with the truncated coefficients and superposed them. As a result, the pixel intensities were compressed to a substantially smaller range of values, thus helping to avoid over- and under-segmentation of large and small vessels, respectively. A threshold-based segmentation followed the image enhancement. The enhancement parameters and threshold were manually chosen by examining six randomly chosen regions of interest. Spurious islands were removed by 26-connected component analysis, and cavities were removed by 6-connected component analysis. The bulk of the processing workload, required to transform data into an actionable training set, was carried out at the Zeus cluster of the Pawsey supercomputing centre. Zeus consisted of hundreds of computing nodes featuring Intel Xeon Phi (Knights Landing) many-core CPUs, together with 96 GB of ``special\u2019\u2019 high-bandwidth memory (HBM/MCDRAM), as well as 128 GB of conventional DDR4 RAM. The final training and assessments were carried out at the Euler VI cluster of ETH Zurich, with two-socket nodes featuring AMD EPYC 7742 (Rome) CPUs and 512 GB of DDR4 RAM. A machine learning-based approach relying on invariant scattering convolution networks was employed to segment the glomeruli and remove perirenal fat from the blood vessel segment. For the glomerular training data, three selected regions of interest of 512 \u00d7 256 \u00d7 256 voxels in size were selected from the cortical region of one kidney (dataset 2) and segmented by a single annotator by fully manual contouring in all slices. For the fat, manual work was reduced by providing an initial semiautomatic segmentation, which the manual annotation then corrected. The training data were supplemented by additional regions of interest that contained no glomeruli or fat at all, and thus did not require manual annotation. The manual annotations were then used to train a hybrid algorithm that relied on a 3D scattering transform convolutional network topped with a dense neural network. The scattering transform relied upon ad-hoc designed 3D kernels (Morlet\u2019s wavelet with different sizes and orientations) that uniformly covered all directions at different scales. In the scattering convolutional network, filter nonlinearities were obtained by taking the magnitude of the filter responses and convolving them again with the kernels in a cascading fashion. These nonlinearities are designed to be robust against small Lipschitz-continuous deformations of the image. In contrast to our curvelet-based image enhancement approach, we decomposed the image into cubic tiles, then applied a windowed (thus local) Fourier transform on the tiles by considering regions about twice their size around them. While it would have been possible to use a convolutional network based upon a global scattering transform, this would have produced a very large number of features that would have had to be consumed at once, leading to an intermediate footprint in the petabyte-scale, exceeding the available memory of the cluster. The scattering transform convolutional network produced a stack of a few hundred scalar feature maps per pixel. If considered as a \u201cfiber bundle\u201d, the feature map stack is equivariant under the symmetry group of rotations (i.e., the stack is a regular representation of the 3D rotation group SO(3)). This property can be exploited by further processing the feature maps with a dense neural network with increased parameter sharing across the hidden layers, making the output layer-invariant to rotations.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2701/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2701/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2651, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0148-schumacher-kidneytem/experimentA", "Description": "Publication Title\nStructural development of the human fetal kidney: new stages and cellular dynamics in nephrogenesis\n\nExperiment Description\nDevelopment of human fetal kidneys of first trimester were assessed using large transmission electron microscopy tilescans.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2651/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2651/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2757, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0149-batty-sisterchromatids", "Description": "Publication Title\nCohesin-mediated DNA loop extrusion resolves sister chromatids in G2 phase\n\nStudy Description\nGenetic information is stored in linear DNA molecules, which fold extensively inside cells. DNA replication along the folded template path yields two sister chromatids that initially occupy the same nuclear region in a highly intertwined arrangement. Dividing cells must disentangle and condense the sister chromatids into separate bodies such that a microtubule-based spindle can move them to opposite poles. While the spindle-mediated transport of sister chromatids has been studied in detail, the chromosome-intrinsic mechanics pre-segregating sister chromatids have remained elusive. Here, we show that human sister chromatids resolve extensively already during interphase, in a process dependent on the loop-extruding activity of cohesin, but not that of condensins. Increasing cohesin\u2019s looping capability increases sister DNA resolution in interphase nuclei to an extent normally seen only during mitosis, despite the presence of abundant arm cohesion. That cohesin can resolve sister chromatids so extensively in the absence of mitosis-specific activities indicates that DNA loop extrusion is a generic mechanism for segregating replicated genomes, shared across different Structural Maintenance of Chromosomes (SMC) protein complexes in all kingdoms of life.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2757/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2757/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2751, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0149-batty-sisterchromatids/experimentA", "Description": "Publication Title\nCohesin-mediated DNA loop extrusion resolves sister chromatids in G2 phase\n\nExperiment Description\nVisualisation of wild type, SMC4 depleted, and NIPBL depleted HeLa Kyoto cells synchronised to prometaphase or G2 phase, where sister chromatids were labelled on either one or two sister chromatids by F-ara-EdU (as specified), with DNA counterstained using Hoechst 33342, as in Fig. 1, Fig. EV2F, Fig. EV3, Fig. EV4 of Batty et al, 2023.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2751/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2751/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2752, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0149-batty-sisterchromatids/experimentB", "Description": "Publication Title\nCohesin-mediated DNA loop extrusion resolves sister chromatids in G2 phase\n\nExperiment Description\nWild type late prophase HeLa Kyoto cells labelled on one sister chromatid. Control, WAPL depleted, Sororin depleted, WAPL + Sororin depleted, or WAPL +SMC4 depleted G2 HeLa Kyoto cells labelled on one sister chromatid with F-ara-EdU, and synchronised to G2 by RO-3306, as in Fig. 2, 3, EV5 of Batty et al, 2023.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2752/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2752/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2753, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0149-batty-sisterchromatids/experimentC", "Description": "Publication Title\nCohesin-mediated DNA loop extrusion resolves sister chromatids in G2 phase\n\nExperiment Description\nWAPL depleted, WAPL/SMC4 depleted, and WAPL/SMC4/Sororin HeLa Kyoto cells labelled on one sister chromatid with F-ara-EdU, and synchronised to prometaphase by STLC, as in Fig. 4A, B of Batty et al, 2023. Control prometaphase chromosomes acutely depleted of condensins for either 120 or 240 min, as in Fig. 4C-E of Batty et al, 2023.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2753/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2753/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2754, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0149-batty-sisterchromatids/experimentD", "Description": "Publication Title\nCohesin-mediated DNA loop extrusion resolves sister chromatids in G2 phase\n\nExperiment Description\nMeasurement of mean intensity in central slice of 3D stack. Validation of cell cycle stage for wild type and WAPL depleted cells as in Fig. EV2, EV5 of Batty et al, 2023. Measurement of mean SMC4 intensity in Fig. 4D of Batty et al, 2023.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2754/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2754/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2755, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0149-batty-sisterchromatids/experimentE", "Description": "Publication Title\nCohesin-mediated DNA loop extrusion resolves sister chromatids in G2 phase\n\nExperiment Description\nValidation of protein depletion across different cell lines by measurement of mean nuclear intensities of proteins of interest, as in Fig. EV3, EV4, Appendix Fig. S1, S2, S4 of Batty et al, 2023.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2755/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2755/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2756, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0149-batty-sisterchromatids/experimentF", "Description": "Publication Title\nCohesin-mediated DNA loop extrusion resolves sister chromatids in G2 phase\n\nExperiment Description\nImmunofluorescence of nuclear Sororin fluorescence and SCC1 axis formation in WAPL depleted G2 cells, as in Appendix Fig. S2D of Batty et al, 2023.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2756/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2756/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2801, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0150-friedman-cafs/experimentA", "Description": "Publication Title\nCancer-associated fibroblast compositions change with breast cancer progression linking the ratio of S100A4+and PDPN+CAFs to clinical outcome\n\nExperiment Description\nImmunofluorescent staining performed on FFPE sections from a cohort of triple-negative breast cancer patients and a cohort of breast cancer patients.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2801/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2801/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 3201, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0151-clark-patterning/experimentA", "Description": "Publication Title\nA timer gene network is spatially regulated by the terminal system in the Drosophila embryo\n\nExperiment Description\nFluorescent hybridisation chain reaction (HCR) RNA in situ and immunohistochemistry analysis of gene expression during embryonic patterning in wildtype and mutant Drosophila embryos.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/3201/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/3201/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2851, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0154-queen-hdbr/experimentA", "Description": "Publication Title\nSpatial transcriptomics reveals novel genes during the remodelling of the embryonic human arterial valves\n\nExperiment Description\nRNAscope and immunofluorescence data for novel genes identified by spatial transcriptomic analysis of human embryonic arterial valves at CS16 and CS19. H&E sections from mouse wild-type and RBP1 knockout.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2851/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2851/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2852, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0155-fu-alphasynuclein/experimentA", "Description": "Publication Title\nRASP: Optimal single puncta detection in complex cellular backgrounds\n\nExperiment Description\nWe took 5400 field of views from three Parkinson's disease (PD) cases in the anterior cingulate gyrus for microglia and neuron markers respectively, covering dimensions of 4mm x 4mm x 13m per patient. Cells were stained in 488nm channel while alpha-synuclein protein was labelled in 561nm channel. The colocalization study was performed based on the locations of detected cells and alpha-synucleins.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2852/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2852/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 3157, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0156-szabo-tadcnd", "Description": "Publication Title\nRegulation of single-cell genome organization into TADs and chromatin nanodomains\n\nStudy Description\nThe genome folds into a hierarchy of three-dimensional structures within the nucleus. At the sub-megabase scale, chromosomes form topologically associating domains (TADs). However, how TADs fold in single cells is elusive. Here, we reveal TAD features inaccessible to cell population analysis by using super-resolution microscopy. TAD structures and physical insulation associated with their borders are variable between individual cells,  yet chromatin intermingling is enriched within TADs compared to adjacent TADs in most cells. The spatial segregation of TADs is further exacerbated during cell differentiation.  Favored interactions within TADs are regulated by cohesin and CTCF through distinct mechanisms:  cohesin generates chromatin contacts and intermingling while CTCF prevents inter-TAD contacts.  Furthermore, TADs are subdivided into discrete nanodomains, which persist in cells depleted of CTCF or cohesin,  whereas disruption of nucleosome contacts alters their structural organization. Altogether, these results provide a physical basis for the fold\u0002ing of individual chromosomes at the nanoscale.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/3157/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/3157/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 3151, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0156-szabo-tadcnd/experimentA", "Description": "Publication Title\nRegulation of single-cell genome organization into TADs and chromatin nanodomains\n\nExperiment Description\nMouse embryonic stem cells (ESCs) were cultured in the conditions described below (see Protocol Description) and they were fixed on coverslips prior to the Fluorescent in situ Hybridization (DNA FISH) procedure. A large set of Oligopaint probes covering Topologically Associating Domains (TADs) of various size and various epigenetic signatures were used for the DNA FISH. Coverslips with hybridized cells were then observed with Structured Illumination Microscopy (3D-SIM). This approach allows for the description of TAD organization in mouse ESCs (Overlap Fractions (OFs) and 3D distances with consecutive Oligopaint probes within TADs or between TADs, see the article) and the identification of TAD sub-structures, dubbed Chromatin NanoDomains (CNDs), by applying watershed-segmentation on the Oligopaint probe fluorescent signal. Assays TSA and TSA-CTL (control) were performed in parallel with and without trichostatin-A (TSA), respectively. TSA is a potent inhibitor of histone deacetylases that induces histone hyperacetylation.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/3151/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/3151/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 3152, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0156-szabo-tadcnd/experimentB", "Description": "Publication Title\nRegulation of single-cell genome organization into TADs and chromatin nanodomains\n\nExperiment Description\nMouse neural progenitor cells (NPCs) were obtained in the conditions described below (see Protocol Description) and they were fixed on coverslips prior to the Fluorescent in situ Hybridization (DNA FISH) procedure. A large set of Oligopaint probes covering Topologically Associating Domains (TADs) of various size and various epigenetic signatures were used for the DNA FISH. Coverslips with hybridized cells were then observed with Structured Illumination Microscopy (3D-SIM). This approach allows for the description of TAD organization in mouse NPCs (Overlap Fractions (OFs) and 3D distances with consecutive Oligopaint probes within TADs or between TADs, see the article) and the identification of TAD sub-structures, dubbed Chromatin NanoDomains (CNDs), by applying watershed-segmentation on the Oligopaint probe fluorescent signal. These data were compared to the ESC conditions from Experiment Mouse_ESC_TADs. NPC from cryo-section of mouse brain neocortex of  E14.5 C57BL/6J embryos (ncxNPC) were subjected to the DNA FISH procedure as in Experiment Mouse_ESC_TADs. Two pairs of TAD probes were observed and were monitored by pair to compare their degree of intermingling (Overlap Fractions (OFs) and 3D distances with consecutive Oligopaint probes between adjacent TADs, see the article) with ESCs from Experiment Mouse_ESC_TADs and this experiment. Slides with hybridized cells were observed with 3D-SIM.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/3152/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/3152/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 3153, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0156-szabo-tadcnd/experimentC", "Description": "Publication Title\nRegulation of single-cell genome organization into TADs and chromatin nanodomains\n\nExperiment Description\nSame experience as in Mouse_ESC_TADs, but with mouse CTCF-AID ES cells allowing for the rapid degradation of the CTCF factor. Assays CTCF-AID_AUX and CTCF-AID_AUX-CTL (control) were performed in parallel with and without Auxin, respectively. Auxin treatment induces the rapid degradation of CTCF.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/3153/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/3153/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 3154, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0156-szabo-tadcnd/experimentD", "Description": "Publication Title\nRegulation of single-cell genome organization into TADs and chromatin nanodomains\n\nExperiment Description\nSame experience as in  Mouse_ESC_TADs, but with mouse RAD21-AID ES cells allowing for the rapid degradation of RAD21, a cohesin complex subunit. Assays RAD21-AID_AUX and RAD21-AID_AUX-CTL (control) were performed in parallel with and without Auxin, respectively. Auxin treatment induces the rapid degradation of RAD21.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/3154/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/3154/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 3155, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0156-szabo-tadcnd/experimentE", "Description": "Publication Title\nRegulation of single-cell genome organization into TADs and chromatin nanodomains\n\nExperiment Description\nUsing the same cells as in Mouse_ESC_TADs, immobilized cells on a coverslip were fixed and nuclei were counterstained with DAPI for CND segmentation without the FISH procedure. DAPI stained nuclei were then observed with Structured Illumination Microscopy (3D-SIM).", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/3155/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/3155/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 3156, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0156-szabo-tadcnd/experimentF", "Description": "Publication Title\nRegulation of single-cell genome organization into TADs and chromatin nanodomains\n\nExperiment Description\nUsing staged 15-16 Drosophila embryos (Drosophila melanogaster), derived cells were immobilized on a coverslip, fixed and  nuclei were counterstained with DAPI for CND segmentation without the FISH procedure. DAPI stained nuclei were then observed with Structured Illumination Microscopy (3D-SIM).", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/3156/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/3156/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 3158, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0156-szabo-tadcnd/experimentG", "Description": "Publication Title\nRegulation of single-cell genome organization into TADs and chromatin nanodomains\n\nExperiment Description\nUsing staged 15-16 Drosophila embryos (Drosophila melanogaster), derived cells were immobilized on a coverslip, fixed and submitted to the DNA FISH procedure using an Oligopaint probe targetting a drosophila TAD of 110 kb located on the X Chromosome. Coverslips with hybridized cells were then observed with Structured Illumination Microscopy (3D-SIM). This approach allows for the description of TAD organization in Drosphila cells. In this species, TADs ressemble CNDs in term of genomic size, diameter and volume.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/3158/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/3158/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 2902, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0157-peters-bryophytes/experimentA", "Description": "Publication Title\nEstimating essential phenotypic and molecular traits from integrative biodiversity data\n\nExperiment Description\nSamples of were collected in Southern Sweden in September 2022 and Germany in October 2022. The specimens were brought to the lab at IPB in sterile petri dishes and stored for five days in a sample incubator to let plants acclimatize. Plant material was isolated, washed under a light microscope to remove dirt and other residues, filled into Eppendorf tubes and shock-frozen. Voucher specimens were stored in the herbarium Haussknecht Jena (voucher barcodes: JE04010739, JE04010740, JE04010741, JE04010742, JE04010743, JE04010744, JE04010745, JE04010746, JE04010747, JE04010748, JE04010749, JE04010750, JE04010751, JE04010752, JE04010753, JE04010754). For image acquisition, a Zeiss Axio Scope.A1 HAL 50, 6x HD/DIC, M27, 10x/23 microscope with an achromatic-aplanatic 0.9 H D Ph DIC condenser was used for microscopy utilizing the objectives EC Plan Neofluar 2.5x/0.075 M27 (a=8.8mm), Plan-Apochromat 5x/0.16 M27 (a=12.1mm), Plan-Apochromat 10x/0.45 M27 (a=2.1mm), Plan-Apochromat 20x/0.8 M27 (a=0.55mm), and Plan-Apochromat 40x/0.95 Korr M27 (a=0.25mm) using the EC PN and the Fluar 40x/1.30 III and PA 40x/0.95 III filters for DIC. The conversion filter CB3 and the interference filter wideband green were used to improve digital reproduction of colors. The color balance was adjusted in the camera and in software accordingly. For macroscopy and for preparing microscopy slides, a binocular stereo microscope Zeiss Stemi 2000c was used. For macroscopic images, the Venus Optics Laowa 25mm 2.5-5.0x ultra-macro for Canon EF and the Canon EF-RF adapter were used. To acquire digital images, a full-frame, high-resolution camera (Canon EOS RP, 26 megapixel) was used and adapted to the photographic objectives or to the microscopes using binocular phototubes with sliding prism 30\u00b0/23 (Axio Scope.A1) and 100:0/0:100 reversed image (Stemi 2000c) using 60-T2 camera adapter for Canon EOS and a Canon EF-RF adapter. To construct images with extended depth-of-field, images were recorded at different focal planes and by attaching the camera to a Cognisys StackShot macro rail fixed on a Novoflex macro stand, and for microscopy by adapting a Cognisys StackShot motor to the fine adjustment of the microscope using two cogged wheels, one small wheel (1 cm diameter) adapted on the motor and one large wheel (8.5 cm diameter) on the fine adjustment of the microscope. The two cogged wheels were coupled with a toothed belt to obtain fine step increments of the stepping motor for high magnifications. A Cognisys StackShot controller was used to control the amount and distance of the stepping motor with the following controller settings: Dist/Rev: 3200 stp, Backlash: 0 steps, # pics: 1, Tsettle: 100.0 ms, Toff: 450.0 ms, Auto Return: yes, Speed: 3000 st/sec, Tlapse: off, Tpulse: 800.0 ms, Tramp: 100 ms, Units: steps, Torque: 6, Hi Precision: Off, LCD Backlight: 10, Mode: Auto-Step using between 25 steps (magnification 1x) and 50 steps (magnification 25x) and 100 steps (magnification 400x) (number of steps depending on aperture settings and effective magnification). Raw images were recorded in CR3-format and pre-processed with Adobe Lightroom Classic (2022 version) where non-destructive image processing such as corrections of the field curvature, removal of chromatic aberration, color balance, increase of contrast and brightness were performed (NELSON 2012). Images were then exported to TIFF-format and any image processing steps were recorded in individual Adobe XMP-files. Multi-focus image fusion was performed on the individual images in the z-stacks using the software Helicon Focus 8.2.9 and by choosing the algorithms depth map and pyramid with different settings of radius (4, 8, 16, 24) and smoothing (2, 4). The best composite image was chosen manually and retained. When composite images contained specimen that were larger than the frame, several images were stitched together using the Photomerge-Reposition function in the software Adobe Photoshop 2023. Images were manually segmented and interfering background removed using the object selection tools. In order to determine the scale, a stage micrometer was photographed separately with any of the objectives and microscope combinations. The scale was calculated per pixel for each combination and scale bars were put post-hoc onto the segmented images. Measurements of morphometric characters were performed manually with ImageJ / Fiji (SCHINDELIN 2012). After setting up the scales for the individual images in the Image-Properties menu, the following morphometric characters were measured: thallus width [\u00b5m], thallus length [\u00b5m], thallus with violet pigments [0/1], ventral scales [0/1], ventral scales with slime cells [0/1], ventral scales with violet pigments [0/1], ventral scales with hairs [0/1], air pores [0/1], width of ring cells of air pores in adaxial view [\u00b5m], height of ring cells p fair pores in cross section [\u00b5m], number of ring cells of air pores in cross section [#], width of ring cells of air pores in cross section [\u00b5m], height of ring cells of air pores in cross section [\u00b5m], width of epidermis cells in cross section [\u00b5m], height of epidermis cells in cross section [\u00b5m], width of subepidermal cells in cross section [\u00b5m], height of subepidermal cells in cross section [\u00b5m], width of thallus in cross section [\u00b5m], height of thallus in cross section [\u00b5m], height of thallus wing in cross section [\u00b5m], angle of thallus wing in cross section [\u00b0], width of thallus wing in cross section [\u00b5m], area of thallus in cross section [\u00b5m2]. Lengths and widths were measured using the Measure function from the Analyze menu and saved in CSV files. To automate the measurement of areas, a pixel classification model was first trained using the plugin LabKit (Arzt et al. 2022) by selecting representative background and foreground areas, training and saving the classifier, which was then imported in the plugin StarDist (WEIGERT et al. 2020), which was used to automatically segment the images. Segmented areas were then measured using the Measure function from the Analyze menu and results were saved. CSV files with all individual morphometric measurements of all specimens were joined into one single table and used for subsequent data analyses. Metadata including species name, taxonomic rank information (NCBI-Taxon and GBIF taxonomy identifiers), voucher specimen id, image acquisition date, an object description including the name of the captured phenotypic character(s), the used objective, microscope, and magnification were associated with any raw image based on unique respective file names. Individual file names, name within an image focus stack and name within an image stitching stack were recorded additionally to facilitate subsequent automized image processing in workflows. Python scripts were created to automatize image fusion and image stitching tasks. Raw camera and pre-processed imaging data in CR3 and TIFF format, respectively, were deposited to the BioImage Archive (BioStudies) using the command line IBM Aspera software tool ascp version 3.8.1.161274 to ensure that data has been transmitted without errors. The raw bioimaging data is available under the BioStudies identifier S-BIAD824 (https://www.ebi.ac.uk/biostudies/studies/S-BIAD824). Processed images were converted to the Bio-Formats OME-TIFF format by creating intermediate ZARR-pyramid tiles using the bioformats2raw converter version 0.7.0 and then using the raw2ometiff version 0.5.0 software tool to create the final pyramid images. Processed images and the metadata were first aggregated in a TSV table and then deposited to the Image Data Resource using the software Globus Connect Personal 3.1.6.\n\nVersion History\nIn March 2025, sequencing results revealed one species to have a different identification in this study.  The metadata for \"Riccia gougetiana\" has been updated to \"Riccia ciliifera\".", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/2902/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/2902/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 3001, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0158-radtke-lymphoma/experimentA", "Description": "Publication Title\nMulti-omic profiling of follicular lymphoma reveals changes in tissue architecture and enhanced stromal remodeling in high-risk patients\n\nExperiment Description\n40-plex iterative bleaching extends multiplexity (IBEX) imaging was performed on fixed frozen tissues from normal human lymph nodes and follicular lymphoma lymph nodes. Multiplexed immunofluorescence (MxIF) imaging was performed on serial FFPE tissue sections from follicular lymphoma lymph nodes. Four distinct antibody panels were applied to each tissue section referred to as MxIF Panel 1 (MxIF_P1), MxIF Panel 2 (MxIF_P2),  MxIF Panel 3 (MxIF_P3), and MxIF Panel 4 (MxIF_P4). Multiplexed imaging was performed on serial FFPE tissue sections from normal and follicular lymphoma lymph nodes using the Cell DIVE imager and IBEX dye inactivation protocol (Cell DIVE-IBEX). Two panels of antibodies, immune (CellDIVE_IBEX_Immune) or stromal (CellDIVE_IBEX_Stromal), were applied to serial sections. IBEX and MxIF imaging were performed on a discovery cohort of 10 samples. Key spatial findings were extended to a larger validation cohort of 29 samples using the Cell DIVE-IBEX method.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/3001/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/3001/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 3101, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0159-strobl-insectlightsheet/experimentA", "Description": "Publication Title\nNon-invasive long-term fluorescence live imaging of Tribolium castaneum embryos\n\nExperiment Description\nFluorescence live imaging of a Tribolium castaneum embryo.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/3101/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/3101/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 3051, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0161-yayon-thymus/experimentA", "Description": "Publication Title\nA spatial human thymus cell atlas mapped to a continuous tissue axis\n\nExperiment Description\n44-plex iterative bleaching extends multiplexity (IBEX) imaging was performed on fixed frozen tissues from normal human thymus samples.  Plus, 13 to 15-plex one-shot multiplex imaging of human thymus using the RareCyte technology and OCT embedded frozen tissues prepared from human thymus.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/3051/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/3051/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 3052, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0163-greenwald-tnbc/experimentA", "Description": "Publication Title\nTemporal and spatial composition of the tumor microenvironment predicts response to immune checkpoint inhibition\n\nExperiment Description\nGenerated 678 FOVs across 111 patients, 294 tissues, and four timepoints (baseline, primary, pre_nivo, and on_nivo), imaged using multiplexed ion beam imaging. Images are either 1024x1024 or 2048x2048 in size.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/3052/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/3052/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 3159, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0164-alzubi-hdbr/experimentA", "Description": "Publication Title\nTyramide signal amplification coupled with multiple immunolabeling and RNAScope in situ hybridization in formaldehyde-fixed paraffin-embedded human fetal brain\n\nExperiment Description\nImmunohistochemistry, immunofluorescence, RNAscope and in situ hybridization analysis in early human development from Carnegie Stage 12 to 22 weeks post conception.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/3159/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/3159/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 3102, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0165-duinkerken-hyperspectraledx/experimentA", "Description": "Publication Title\nAutomated analysis of ultrastructure through large-scale hyperspectral electron microscopy\n\nExperiment Description\n\tLarge-scale scanning-transmission EM complemented with EDX imaging (STEM-EDX) on conventionally processed human pancreas and skin EM samples. The hyperspectral EDX output was subsequently used as input for automated ultrasctructure feature recognition.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/3102/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/3102/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 3351, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0167-li-cellcyclenet", "Description": "Publication Title\nPredicting cell cycle stage from 3D single-cell nuclear-stained images\n\nStudy Description\nThe cell cycle governs proliferation of all eukaryotic cells. Profiling cell cycle dynamics is therefore central to basic and biomedical research. However, current approaches to cell cycle profiling involve complex interventions that may confound experimental interpretation. We developed CellCycleNet, a machine learning (ML) workflow, to simplify cell cycle staging from fluorescent microscopy data with minimal experimenter intervention and cost. CellCycleNet accurately predicts cell cycle phase using only a fluorescent nuclear stain (DAPI) in fixed interphase cells. Using the Fucci2a cell cycle reporter system as ground truth, we collected two benchmarking image datasets and trained 2D and 3D ML modelsof support vector machine (SVM) and deep neural network architectureto classify nuclei in the G1 or S/G2 phases. Our results show that 3D CellCycleNet outperforms SVM models on each dataset. When trained on two image datasets simultaneously, CellCycleNet achieves the highest classification accuracy (AUROC of 0.94-0.95). Overall, we found that using 3D features, rather than 2D features alone, significantly improves classification performance for all model architectures. We released our image data, models, and software as a community resource.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/3351/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/3351/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 3352, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0167-li-cellcyclenet/experimentA", "Description": "Publication Title\nPredicting cell cycle stage from 3D single-cell nuclear-stained images\n\nExperiment Description\nCellCycleNet 60x Confocal Dataset.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/3352/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/3352/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 3353, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0167-li-cellcyclenet/experimentB", "Description": "Publication Title\nPredicting cell cycle stage from 3D single-cell nuclear-stained images\n\nExperiment Description\nCellCycleNet 40x Epifluorescent  Dataset.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/3353/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/3353/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 3301, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0168-zhang-mllocalization/experimentA", "Description": "Publication Title\nPrediction of protein subcellular localization in single cells\n\nExperiment Description\nThis dataset provides the immunofluorescence images acquired during this study for the experimentally validation of PUPS. Cells of 5 cell lines were stained with antibody targeting a-tubulin, ER, and one kind of proteins out of 9 proteins that PUPS predicted, then imaged with 60x confocal with Z-stacks.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/3301/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/3301/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 3251, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0170-rose-mibitof/experimentA", "Description": "Publication Title\nImaging Mass Cytometry Dataset of Small-Cell Lung Cancer tumors and tumor microenvironments\n\nExperiment Description\nImaging Mass Cytometry multi-channel images.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/3251/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/3251/"}, {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project", "@id": 3303, "omero:details": {"@type": "TBD#Details", "owner": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter", "@id": 2, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rw----", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": false, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "FirstName": "Public", "MiddleName": "", "LastName": "data", "Email": "idr-project@lists.openmicroscopy.org.uk", "Institution": "IDR Project", "UserName": "demo"}, "group": {"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "@id": 3, "omero:details": {"@type": "TBD#Details", "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "Public"}, "permissions": {"@type": "TBD#Permissions", "perm": "rwr---", "canAnnotate": false, "canDelete": false, "canEdit": false, "canLink": false, "isWorldWrite": false, "isWorldRead": false, "isGroupWrite": false, "isGroupRead": true, "isGroupAnnotate": false, "isUserWrite": true, "isUserRead": true}}, "Name": "idr0173-breiter-alphasynuclein/experimentA", "Description": "Publication Title\n\u03b1-synuclein-driven cell susceptibility in Parkinson\u2019s Disease\n\nExperiment Description\nFormalin-fixed paraffin-embedded (FFPE) tissue sections were obtained from the cingulate cortex (see tables S2 and S3) and cut to 8 \u03bcm thickness. FFPE sections were baked at 37 \u2103 for 24 hours followed by 60 \u2103 overnight. Sections were deparaffinized in xylene, and rehydrated using graded alcohols. Non-specific binding was blocked with 10% bovine serum albumin (BSA) solution in PBS for 30 minutes. The tissue was then pressure cooked in citrate buffer at pH 6 for 10 minutes. Tissue sections were incubated with primary antibodies; anti-phosphorylated alpha-synuclein (ab59264, AB_2270761, Abcam, 1:200); and either ionized calcium-binding adapter molecule 1 (GT10312, Thermo Fisher, AB_2735228, 1:500) or Microtubule-Associated Protein 2 (ab254143, Abcam, AB_2936822, 1:500) for 1h at room temperature. The sections were then washed three times for five minutes in PBS followed by the corresponding AlexaFluor secondary antibodies (anti-rabbit 568, A11011, AB_143157, Thermo Fisher, anti-mouse 488, A11001, AB_2534069, Thermo Fisher, all at 1:200) for an additional hour at room temperature in the dark. Sections were then washed three times for five minutes again in PBS and incubated in Sudan Black (0.1% for 10 minutes, 199664-25G, Sigma Aldrich). Removal of Sudan Black occurred with three washes in 30% ethanol (E7148-500ML, Sigma Aldrich) before mounting with Vectashield+ (Vector Labs, H-1900) and coverslipping (VWR, 50 mm \u2715 24 mm #1 thickness, Catalogue Number 48404-453) for imaging. Sections were stored at 4 \u2103 until imaging was completed.", "url:datasets": "https://idr.openmicroscopy.org/api/v0/m/projects/3303/datasets/", "url:project": "https://idr.openmicroscopy.org/api/v0/m/projects/3303/"}], "meta": {"offset": 0, "limit": 200, "maxLimit": 1000, "totalCount": 147}}