Data download

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

General instructions

The raw data of all studies published in IDR can be downloaded using Globus or anonymous File Transfer Protocol (FTP).

You can download both whole studies as well as parts/single images.

We recommend using the Globus.


Download and install Globus connect personal.

You might have to create an account, or you can use other login providers like ORCiD.

Go to “Web: Transfer files” to get to the Web UI.

Globus Web UI

Then in the File Manager / Collections search for “EMBL-EBI Public Data”.

Globus Collection search

In there you should be able to navigate through the same directory structure like on the FTP server /pub/databases/IDR/ to get to the IDR submission you want to download.

Globus IDR collection


The ftp host is available using the following details:

  • host:

CLI client step by step

Connect to the FTP server:

$ ftp

The FTP server being anonymous only, use ftp or anonymous (with no password) to log in. Make sure that passive mode is on:

ftp> passive

Change the directory:

ftp> cd /pub/databases/IDR/

You may list all the studies in the IDR:

ftp> ls

Or a single one, e.g.:

ftp> ls idr0044-*

Use the get command to download a specific file, and bye to close the connection.

Desktop client step-by-step

Download and install the FileZilla client.

Start the FileZilla application. In the “Host” dialog (top-left corner) paste and click the Quickconnect button.

Click OK in the next window.

FileZilla Warning dialog

The left-hand pane is showing your local machine folders. Select the folder into which you want to download the data.

FileZilla Desktop

In the right-hand pane, browse the IDR studies to be downloaded. Check the sizes of the folders using the README files. Click onto a folder and expand it. Right-click on the desired folder or file and click Download in the context menu.

FileZilla Desktop

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IDR logo version: devel. Last updated: 2024-06-05.