https://github.com/imagingdatacommons/sliceridcbrowser

A 3D Slicer extension to support access to the content of NCI Imaging Data Commons
https://github.com/imagingdatacommons/sliceridcbrowser

3d-slicer-extension

Last synced: 9 months ago
JSON representation

A 3D Slicer extension to support access to the content of NCI Imaging Data Commons

• Host: GitHub
• URL: https://github.com/imagingdatacommons/sliceridcbrowser
• Owner: ImagingDataCommons
• License: bsd-3-clause
• Created: 2023-05-31T03:02:34.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2024-11-18T22:20:47.000Z (about 1 year ago)
• Last Synced: 2025-04-01T06:52:30.251Z (10 months ago)
• Topics: 3d-slicer-extension
• Language: Python
• Homepage:
• Size: 1.08 MB
• Stars: 6
• Watchers: 2
• Forks: 5
• Open Issues: 14
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

          
3D Slicer IDC Browser extension

===========

![logo](https://github.com/ImagingDataCommons/SlicerIDCBrowser/blob/c9519809522aaac59bb65fb558b1197cf05c3e72/IDCBrowser/Resources/Icons/IDCBrowser.png?raw=true)

## About

IDCBrowser is a [3D Slicer](http://slicer.org/) extension for browsing and downloading DICOM files from [NCI Imaging Data Commons](https://imaging.datacommons.cancer.gov/).

## Getting started

You will need to have a latest preview or stable 5.6.2 release of 3D Slicer, which you can donwload for your platform here: [https://download.slicer.org](https://download.slicer.org). You can next install the extension via 3D Slicer [Extensions Manager](https://slicer.readthedocs.io/en/latest/user_guide/extensions_manager.html). 

Once the extension is installed, it provides interface to choose from any of the imaging collections available in Imaging Data Commons, and select and download imaging data at the patient, study or series level. 

[![SlicerIDCBrowser basics](https://img.youtube.com/vi/m_jfSTWIYvc/0.jpg)](https://www.youtube.com/watch?v=m_jfSTWIYvc)

You can also use this extension to download items (referred to by identifiers of the collection, patient, DICOM study or series) as shown in the demo below!

[![SlicerIDCBrowser downloading](https://img.youtube.com/vi/_KQDL9JzMB4/0.jpg)](https://www.youtube.com/watch?v=_KQDL9JzMB4)

## Development

This extension relies on the [`idc-index`](https://pypi.org/project/idc-index/) package for searching IDC and downloading IDC content. 

See current status of the extension builds in the 3D Slicer Preview dashboard [here](https://slicer.cdash.org/index.php?project=SlicerPreview&filtercount=1&showfilters=1&field1=buildname&compare1=63&value1=idcbrowser).

## Acknowledgments

This project has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under Task Order No. HHSN26110071 under Contract No. HHSN261201500003l.

The overview of IDC is available in this open access publication. If you use IDC, please acknowledge us by citing it!

> Fedorov, A., Longabaugh, W. J. R., Pot, D., Clunie, D. A., Pieper, S., Aerts, H. J. W. L., Homeyer, A., Lewis, R., Akbarzadeh, A., Bontempi, D., Clifford, W., Herrmann, M. D., Höfener, H., Octaviano, I., Osborne, C., Paquette, S., Petts, J., Punzo, D., Reyes, M., Schacherer, D. P., Tian, M., White, G., Ziegler, E., Shmulevich, I., Pihl, T., Wagner, U., Farahani, K. & Kikinis, R. NCI Imaging Data Commons. Cancer Res. 81, 4188–4193 (2021). http://dx.doi.org/10.1158/0008-5472.CAN-21-0950