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Data download

The raw imaging data for all studies published in the Image Data Resource (IDR) is available for download using the Aspera protocol.


General instructions

The raw data of all studies published in IDR can be downloaded using the Aspera protocol. The Aspera server is available using the following details:

  • server: fasp.ebi.ac.uk
  • port: 33001

Each published study has an associated passwordless username matching the IDR accession number e.g. idr0001.

Desktop client

Download and install the Aspera desktop client.

You must also download and configure the Aspera public key asperaweb_id_dsa.openssh to connect to the server.

Click on Connections to open the connection manager and add the following:

  • Host: fasp.ebi.ac.uk
  • User: idrNNNN where NNNN is the IDR study identifier, e.g. idr0047
  • Authentication: Public Key
  • Manage KeysImport a key from the filesystem → select asperaweb_id_dsa.openssh (this only needs to be done if you haven’t previously imported this key)
  • Select asperaweb_id_dsa.openssh
  • Test Connection

You should now be able to connect to the Aspera server and see the raw data for your chosen IDR study.

Aspera Desktop connection manager Aspera Desktop SSH keys

Command-line instructions

The Aspera command line client can be downloaded here. The following command will download all the raw data associated with the idr0008 submission:

$ ascp -TQ -l40m -P 33001 -i "path/to/asperaweb_id_dsa.openssh" idr0008@fasp.ebi.ac.uk:. /tmp/data/idr0008/

Refer to the Aspera documentation for more details about the command-line options.

Docker instructions

For convenience, a Docker image is available with the IDR download options. You can use it as follows:

$ docker run -ti --rm -v /tmp/data/idr0008:/data imagedata/download idr0008 . /data

Partial download

The two examples above will download the entire content of a submission. The size of each study varies from a few GB to several tens of TB.

Sometimes it is desirable to download only a subset of the submission e.g. only one plate from a screen.

First you need to find the relative path to be downloaded. The easiest way is to use the TSV files available for all IDR studies in the curated metadata repository. For example,

After removing the leading /uod/idr/filesets/<idrNNN>-<author>-<description>/, you can then download a subfolder using the same commands as above:

$ ascp -TQ -l40m -P 33001 -i "path/to/asperaweb_id_dsa.openssh" idr0040@fasp.ebi.ac.uk:20180215/3105/Pos0 /tmp/data/idr0040_partial

or

$ docker run -ti --rm -v /tmp/data/idr0040_partial:/data imagedata/download idr0040 20180215/3105/Pos0 /data

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© 2016-2019 University of Dundee & Open Microscopy Environment. Creative Commons Attribution 4.0 International License.

OMERO is distributed under the terms of the GNU GPL. For more information, visit openmicroscopy.org


IDR logo version: devel. Last updated: 2019-11-06.