Difference between revisions of "Documentation/Nightly/Extensions/TCIABrowser"

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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.
 
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 [https://wiki.cancerimagingarchive.net/display/Public/Collections 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
 +
 +
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 included in the accessible public collections is included below.
 +
 +
<gallery widths="300px" perrow="5">
 +
Image:TCIA_public_collections-modalities.png
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Image:TCIA_public_collections-body_parts.png
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Image:TCIA_public_collections-manufacturers.png
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</gallery>
 
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* [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin Quantitative Imaging Network (QIN)]
 
* [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin Quantitative Imaging Network (QIN)]
 
* [http://cancerimagingarchive.net/ TCIA Home Page]
 
* [http://cancerimagingarchive.net/ TCIA Home Page]
 +
* [https://wiki.cancerimagingarchive.net/display/Public/Collections Description of TCIA Collections]
 
* [https://wiki.cancerimagingarchive.net/display/Public/TCIA+Programmatic+Interface+%28REST+API%29+Usage+Guide TCIA Rest API Documentation]
 
* [https://wiki.cancerimagingarchive.net/display/Public/TCIA+Programmatic+Interface+%28REST+API%29+Usage+Guide TCIA Rest API Documentation]
 
* [http://www.na-mic.org/Wiki/index.php/2014_Project_Week:TCIA_Browser_Extension_in_Slicer Project page at NAMIC 2014 Project Week]
 
* [http://www.na-mic.org/Wiki/index.php/2014_Project_Week:TCIA_Browser_Extension_in_Slicer Project page at NAMIC 2014 Project Week]
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Revision as of 23:52, 12 February 2014

Home < Documentation < Nightly < 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 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

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 included in the accessible public collections is included below.

  • TCIA public collections-modalities.png
  • TCIA public collections-body parts.png
  • TCIA public collections-manufacturers.png


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
Module GUI
  • Step 3: Download a Series
Module GUI


Similar Modules

References

Information for Developers

Work in progress
 Section under construction.
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