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Improve TCIA Browser extension

Key Investigators

• Justin Kirby (Frederick National Laboratory for Cancer Research, USA)
• Adam Li (Georgetown University, USA)
• Andrey Fedorov (Brigham and Women's Hospital, USA)

Presenter location: Online

Project Description

The Cancer Imaging Archive (TCIA) is an NCI-funded service which de-identifies and publishes cancer imaging datasets. The imaging data are organized as “collections” or “analysis result” datasets defined by a common disease (e.g. lung cancer), image modality or type (MRI, CT, digital histopathology, etc) or research focus. An emphasis is made to provide supporting data related to the images such as patient outcomes, treatment details, genomics and expert analyses where available.

TCIA Browser is an extension that lets users easily download and import TCIA data into 3D Slicer. This project seeks to improve the TCIA Browser extension for 3D Slicer by updating it to leverage TCIA-Utils to access TCIA’s APIs.

Objective

The major improvements we’d like to address with TCIA Browser include:

Approach and Plan

1. Identify locations in the code that use the older API to download or query data and update them to leverage TCIA-Utils functions such as downloadSeries(), getCollections(), getPatients(), getStudies() and getSeries().
2. Implement a new feature to support logging in to TCIA Browser using the getToken() function in TCIA-Utils.
3. Review the existing metadata fields in the Browser GUI. Perform queries of the TCIA database to determine how often these fields are populated.
4. Discuss and agree on other available metadata fields that may be useful to Slicer users. Run queries to find out how often they’re populated. Include external sources from NCI’s Cancer Research Data Commons that may include genomic, proteomic and clinical data on the same subjects that TCIA hosts.
5. Update the GUI with a “Download TCIA Manifest” button and leverage the TCIA-Utils downloadSeries() function with the input_type = “manifest” option to pass the path of a *.TCIA manifest file as the series_data parameter.

Progress and Next Steps

1. Identified the code that used the old API and updated them to use the new API.
2. Added and removed some columns/metadata fields within the browser widget.
3. Set the default cache option to off.
4. Next Step: Implement the login function; Update the new API further to use the tcia_utils modules directly; Implement the manifest file download function.

For anyone interested, click here to view the PR

Illustrations

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Background and References

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