This page contains links to documentation that can help you get better use out of the AIDA Data Hub.

Working with DICOM

Digital Imaging and Communications in Medicine (DICOM) is the international standard to transmit, store, retrieve, print, process, and display medical imaging information. It is prevalent in radiology and is gaining traction also in pathology.

Some datasets on the AIDA Data Hub are provided in DICOM format. In DICOM, data is provided in nested and interlinking structures, which can be nontrivial for newcomers to the field to navigate.

For an introduction to how one can work with DICOM data, AIDA is providing a Jupyter notebook, which is publicly available through the SciLifeLab/NBIS GitHub organization:

Instructions with an example to download a dataset from AIDA Nextcloud using rclone


It takes two commands to download a dataset from a Nextcloud share link:

  1. Setup a remote
  2. Download from the remote

Setup a remote

rclone config create drsk webdav url= vendor=nextcloud user=<USERNAME> pass=<PASSWORD>

Here, we have chosen the name drsk for the remote. You can of course choose whatever name you want. Probably use something short that doesn’t contain spaces.

Your username is the last part of the share link you got from us, i.e:

Your username could for example be something like Y4gVyiVyyiF6fug.

Your password is the string of random characters you got from us separately. You will probably need to “quote” or ‘quote’ it on the command line, as it very likely contains special characters.

If you’d rather answer questions interactively, do this instead, and do what it says: rclone config

The exact questions may differ depending on what version rclone you have.

Download from the remote

Use the same name here that you chose in the previous step.

rclone copy drsk: .

Or if you want progress written to the terminal:

rclone copy --progress drsk: .