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

From Slicer Wiki
Jump to: navigation, search
Line 29: Line 29:
 
[[Image:TCIABrowser_logo.png]]
 
[[Image:TCIABrowser_logo.png]]
  
−
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, patient subjects, 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):
 
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):
Line 72: Line 72:
  
 
{|
 
{|
−
* '''Step 1: Connect to the server'''
+
* '''Browsing Collections, patients and studies'''
−
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.
+
By opening TCIABrowser module it will automatically connect to the the TCIA server and list all of the available collections.
−
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.
 
 
   
 
   
 
|[[Image:TCIA-New01.png|thumb|360px|Module GUI]]
 
|[[Image:TCIA-New01.png|thumb|360px|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 clinical data icon besides the patient ID [[Image:Report-icon-tcia.png|thumb|50px|Clinical Data Icon]] means that the clinical data for that specific patient is available in TCGA. The use Cache check box will cache the query results on your hard drive which makes the next selections much faster. If you want to do the query (connect to TCIA Server) you can uncheck this box. Above the Patients table you can see the last access time. The process is the same for studies and series tables, selecting a patient will populate the study table for the selected one and selecting a study will update the series table.
 
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 clinical data icon besides the patient ID [[Image:Report-icon-tcia.png|thumb|50px|Clinical Data Icon]] means that the clinical data for that specific patient is available in TCGA. The use Cache check box will cache the query results on your hard drive which makes the next selections much faster. If you want to do the query (connect to TCIA Server) you can uncheck this box. Above the Patients table you can see the last access time. The process is the same for studies and series tables, selecting a patient will populate the study table for the selected one and selecting a study will update the series table.
  
Line 87: Line 83:
  
 
{|
 
{|
−
* '''Step 3: Access Clinical Data from TCGA'''
+
* '''Downloading Series'''
−
You can open the context menu with right click on the specific patient ID for patients which have the TCGA clinical data available. Clicking on "Get Clinical Data" will send a request to cBioPortal server and get the available clinical data for the specific patient. Again here like TCIA queries the results will be saved on your local hard drive. You can update the cache by pressing "Update Cache" button.
+
In the final step when you select a 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.
−
|[[Image:TCIA-New03.png|thumb|600px|Module GUI]]
+
[[Image:DownloadAndIndex.png|thumb|100px|Download and Index Button]][[Image:DownloadAndLoad.png|thumb|100px|Download and Load Button]]
−
|[[Image:TCIA-New04.png|thumb|600px|Module GUI]]
 
−
|}
 
−
 
 
−
 
 
−
{|
 
−
* '''Step 4: A-Download a Series'''
 
−
In the final step when you select a 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.[[Image:DownloadAndIndex.png|thumb|100px|Download and Index Button]][[Image:DownloadAndLoad.png|thumb|100px|Download and Load Button]]
 
 
|[[Image:TCIA-New05.png|thumb|800px|Module GUI]]
 
|[[Image:TCIA-New05.png|thumb|800px|Module GUI]]
 
|
 
|
 +
 +
|[[Image:Tcia-multi.png|thumb|800px|Multiple Selections]]
 +
|[[Image:Tcia-download-status.png|thumb|400px|Download Status]]
  
 
|}
 
|}
−
{|
 
−
* '''Step 4: B- Download multiple patients, studies and series'''
 
−
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.
 
  
−
|[[Image:Tcia-multi.png|thumb|800px|Multiple Selections]]
 
−
|[[Image:Tcia-download-status.png|thumb|400px|Download Status]]
 
  
 +
{|
 +
* '''Access Clinical Data from TCGA'''
 +
For some of the collections clinical data is available through The Cancer Genome Atlas (TCGA) website. The patients with this information are marked with a unique icon besides their patient ID. The clinical data can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".
 +
|[[Image:TCIA-New03.png|thumb|600px|Module GUI]]
 +
|[[Image:TCIA-New04.png|thumb|600px|Module GUI]]
 
|}
 
|}
  
 +
{|
 +
 +
* '''Settings '''
 +
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.
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/module-section|Similar Modules}}
 
{{documentation/{{documentation/version}}/module-section|Similar Modules}}
 
* [[Documentation/4.3/Extensions/XNATSlicer|XNATSlicer]]
 
* [[Documentation/4.3/Extensions/XNATSlicer|XNATSlicer]]
 
*[[Documentation/Nightly/Modules/DICOM| DICOM]]
 
*[[Documentation/Nightly/Modules/DICOM| DICOM]]
 +
|}
 +
 +
 +
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/module-section|References}}
 
{{documentation/{{documentation/version}}/module-section|References}}

Revision as of 13:06, 18 May 2015

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 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

TCIABrowser logo.png

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.

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.

  • TCIA public collections-collections.png
  • 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

  • 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.
Module GUI
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 clinical data icon besides the patient ID
Clinical Data Icon
means that the clinical data for that specific patient is available in TCGA. The use Cache check box will cache the query results on your hard drive which makes the next selections much faster. If you want to do the query (connect to TCIA Server) you can uncheck this box. Above the Patients table you can see the last access time. The process is the same for studies and series tables, selecting a patient will populate the study table for the selected one and selecting a study will update the series table.
Module GUI
  • Downloading Series
In the final step when you select a 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.
Download and Index Button
Download and Load Button
Module GUI
Multiple Selections
Download Status


  • Access Clinical Data from TCGA
For some of the collections clinical data is available through The Cancer Genome Atlas (TCGA) website. The patients with this information are marked with a unique icon besides their patient ID. The clinical data can be accessed by right clicking on the Patient ID area to open the context menu and clicking "Get clinical data".
Module GUI
Module GUI
  • Settings
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.

Similar Modules


References

Information for Developers

Tip: The REST API can be checked by REST Console Google Chrome extension.

Work in progress
 Section under construction.
Retrieved from "https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/TCIABrowser&oldid=41555"