Documentation/4.6/Extensions/TCIABrowser

For the latest Slicer documentation, visit the read-the-docs.

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 Research (QIICR) (U24 CA180918) (PIs Kikinis and Fedorov). Authors: Alireza Mehrtash(SPL), Andrey Fedorov (SPL) Contact: Alireza Mehrtash, <email>mehrtash@bwh.harvard.edu</email> 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, patient subjects, studies and series, download the images and visualize them in 3D Slicer.

TCIA metrics dashboard provides extensive details on the types of imaging data by anatomy and other characteristics that are available within TCIA.

Panels and their use

• Browsing Collections, patients and studies

By opening TCIABrowser module it will automatically connect to the the TCIA server and list all of the available collections. First from the "Current Collection" combobox select a collection. The browser will get the patient data from the TCIA server and will populate the patients table. For some of the collections some extra clinical information is available through The Cancer Genome Atlas (TCGA) website. Collections with available information at TCGA are marked with a unique icon

TCGA Data Available

besides their patient ID. The TCGA information can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".

The use Cache checkbox will cache the query results on your hard drive which makes further recurring queries faster. If direct query from TCIA server is desired the user can uncheck this box. In case of caching server responses the latest access time is provided for each table separately. Further selecting a patient will populate the study table for the selected one and selecting a study will update the series table.

• Downloading Series

After selecting at least one series the download icons will become activated. Pressing the "Download and Index" button will download the images from TCIA to your computer and index the DICOM files inside 3D Slicer DICOM database. So you can review them, check the meta-data and load into the scene later with Slicer DICOM module. Pressing the "Download and Load" button will download the images and load them into the Slicer scene. You can select multiple items from all of the tables. By holding the Ctrl key and clicking on different patients, the studies for all the selected ones will be added to the studies table. You can select all the studies by pressing 'Select All' button or make a specific selection by Ctrl+Click and all the available series for download will be added to the series table. At the final step you will select series for download from the series table. The total number of images for the selected series is indicated at the bottom right corner of series table. After pressing the download button you can check the download status of each series at the 'Download Status' collapsible button at the module's widget. While the download is in progress you can still browse and add other series to the download queue or view the downloaded images in the 3D Slicer Scene.

TCIA Browser Screesnshots

Browsing Collections, patients and studies. (A) Collection selector combobox (B) Cache server response to the local storage (C) Icon for Clinical Information from TCGA (D) Tables are expandable (E) Status of the series (Available on local database / Available on TCIA server) (F) Download and Index to the Slicer DICOM database (local storage) (G) Download and load into the Slicer scene.   Downloading Series. Multiple series from multiple patients and studies can be downloaded at the same time. (A) Progress bars showing download status of the selected series (B) Status bar showing the current process and the status of server responses (C) Cancel downloads button.   Extra clinical information from TCGA.   Settings. (A) Show Browser button to pop up browser. (B) Selecting folder on the local file system for storing DICOM images and json responses. (C) Adding custom API keys for accessing non-public data.

Similar Modules

• XNATSlicer
• DICOM

References

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

Information for Developers

• Source Code

Checking the API from the python console:

import TCIABrowserLib as tblib
client = tblib.TCIAClient()
client.get_collection_values()
response = client.get_collection_values()
response_string = response.read()[:]
print(response_string)