Documentation/Nightly/Extensions/TCIABrowser

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Introduction and Acknowledgements

Extension: TCIABrowser Acknowledgments: This work is funded by the National Institutes of Health, National Cancer Institute through the Grant Quantitative Image Informatics for Cancer Reasearch (QIICR) (U24 CA180918) (PIs Kikinis and Fedorov). Authors: Alireza Mehrtash(SPL), Andrey Fedorov (SPL) Contact: Alireza Mehrtash, mehrtash at bwh dot harvard dot edu License: Slicer License Quantitative Image Informatics for Cancer Research   Surgical Planning Laboratory (SPL)   National Alliance for Medical Image Computing (NA-MIC)

Module Description

The Cancer Imaging Archive (TCIA) hosts a large collection of Cancer medical imaging data which is available to public through a programmatic interface (REST API). TCIA Browser is a Slicer module by which the user can connect to the TCIA archive, browse different collections, patients, studies and series, download the images and visualize them in 3D Slicer.

As of February 2014, the following collections of TCIA are available via public TCIA API interface (see description of TCIA collections for details):

• QIBA CT-1C
• TCGA-GBM *
• RIDER PHANTOM PET-CT
• RIDER PHANTOM MRI
• Phantom FDA
• TCGA-LGG *
• TCGA-KIRC *
• TCGA-BRCA *
• BREAST-DIAGNOSIS
• PROSTATE-DIAGNOSIS
• LIDC-IDRI
• TCGA-LUAD *
• RIDER Lung CT
• RIDER NEURO MRI
• RIDER Lung PET-CT
• CT COLONOGRAPHY
• REMBRANDT
• RIDER Breast MRI

For the collections marked with *, available clinical data is linked from The Cancer Genome Atlas.

TCIABrowser gives you access to 18 collections, which contain a total of over 23,000 image series from a variety of manufacturers and of different modalities and organs. Some of the summary statistics of the data available from the public collections listed is provided below.

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Tutorials

Not available at this time.

Panels and their use

• Step 1: Connect to the server

Press connect button to connect to TCIA archive with 3D Slicer unique API-KEY. TCIA will provide a list of available collections and the browser will pop up automatically. If you have your own unique API and want to use that you can add your own API using the "+" button and then select it using the combo box.

Module GUI

• Step 2: Browse the collections

In the browser window from the combo box select a collection. The browser will get the patient data from the TCIA server and will populate the Patients table. In patient table, the report icon besides the patient ID

Module GUI

means that the clinical data for that specific patient is available in TCGA.

Module GUI

• Step 3: Access Clinical Data from TCGA

Module GUI

Module GUI

• Step 4: Download a Series

Module GUI

Similar Modules

• XNATSlicer

References

• Quantitative Image Informatics for Cancer Research (QIICR)
• Quantitative Imaging Network (QIN)
• TCIA Home Page
• Description of TCIA Collections
• TCIA Rest API Documentation
• Project page at NAMIC 2014 Project Week

Information for Developers

• Source Code