Downloading data

If you have questions or feedback about the download tools provided by IDC, please reach out via our forum - we are very interested in hearing your feedback and suggestions!

Depending on whether you would like to download data interactively or programmatically, we provide two recommended tools to help you.

Interactive download: 3D Slicer SlicerIDCBrowser extension

3D Slicer is a free open source, cross-platform, extensible desktop application developed to support a variety of medical imaging research use cases.

IDC maintains SlicerIDCBrowser, an extension of 3D Slicer, developed to support direct access to IDC data from your desktop. You will need to install a recent 3D Slicer 5.7.0 preview application (installers are available for Windows, Mac and Linux), and next use 3D Slicer ExtensionManager to install SlicerIDCBrowser extension. Take a look at the quick demo video in this post if you have never used 3D Slicer ExtensionManager before.

Once installed, you can use SlicerIDCBrowser in one of the two modes:

1. As an interface to explore IDC data: you can select individual collections, cases and DICOM studies and download items of interest directly into 3D Slicer for subsequent visualization and analysis.

2. As download tool: download IDC content based on the manifest you created using IDC Portal, or identifiers of the individual cases, DICOM studies or series.

Copy identifiers for the studies/series of interest from the IDC Portal

Insert the identifiers in the appropriate fields, or download content defined by the s5cmd manifest

Programmatic download: idc-index python package

idc-index package is under development, and its API may change in the future releases!

idc-index is a python package designed to simplify access to IDC data.

Once you installed the package with pip install idc-index, you can use it to explore, search, select and download corresponding files as shown in the examples below.

You can also take a look at a short tutorial on using idc-index here.

pip install idc-index --upgrade

from idc_index import index

client = index.IDCClient()

# get identifiers of all collections available in IDC
all_collection_ids = client.get_collections()

# download files for the specific collection, patient, study or series
client.download_from_selection(collection_id="rider_pilot", \
                               downloadDir="/some/dir")
                               
client.download_from_selection(patientId="rider_pilot", \
                               downloadDir="/some/dir")

client.download_from_selection(studyInstanceUID= \
     "1.3.6.1.4.1.14519.5.2.1.6279.6001.175012972118199124641098335511", \
     downloadDir="/some/dir")
                               
client.download_from_selection(seriesInstanceUID=\
     "1.3.6.1.4.1.14519.5.2.1.6279.6001.141365756818074696859567662357", \
     downloadDir="/some/dir")
                               

idc-index includes a variety of other helper functions, such as download from the manifest created using IDC portal, automatic generation of the viewer URLs, information about disk space needed for a given collection, and more. We are very interested in your feedback to define the additional functionality to add to this package! Please reach out via IDC Forum if you have any suggestions.