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

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Extension: [[Documentation/{{documentation/version}}/Extensions/TCIABrowser|TCIABrowser]]<br>
 
Extension: [[Documentation/{{documentation/version}}/Extensions/TCIABrowser|TCIABrowser]]<br>
 
Acknowledgments:
 
Acknowledgments:
This work is funded by the National Institutes of Health, National Cancer Institute through the Grant [http://qiicr.org Quantitative Image Informatics for Cancer Reasearch (QIICR)] (U24 CA180918) (PIs Kikinis and Fedorov).<br>
+
This work is funded by the National Institutes of Health, National Cancer Institute through the Grant [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] (U24 CA180918) (PIs Kikinis and Fedorov).<br>
 
Authors: Alireza Mehrtash({{collaborator|name|spl}}), Andrey Fedorov ({{collaborator|name|spl}})<br>
 
Authors: Alireza Mehrtash({{collaborator|name|spl}}), Andrey Fedorov ({{collaborator|name|spl}})<br>
Contact: Alireza Mehrtash, mehrtash at bwh dot harvard dot edu<br>
+
Contact: Alireza Mehrtash, <email>mehrtash@bwh.harvard.edu</email><br>
  
 
License: [http://www.slicer.org/pages/LicenseText Slicer License]
 
License: [http://www.slicer.org/pages/LicenseText Slicer License]
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<!-- ---------------------------- -->
 
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{{documentation/{{documentation/version}}/module-section|Module Description}}
 
{{documentation/{{documentation/version}}/module-section|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 [https://wiki.cancerimagingarchive.net/display/Public/Collections description of TCIA collections] for details):
+
[[Image:TCIABrowser_logo.png]]
  
* QIBA CT-1C           
+
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.
* 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.
+
[https://cancerimagingarchive.net/dashboard2/ TCIA metrics dashboard] provides extensive details on the types of imaging data by anatomy and other characteristics that are available within TCIA.
  
<gallery widths="500px" heights="500px" perrow="5">
 
Image:TCIA_public_collections-modalities.png
 
Image:TCIA_public_collections-body_parts.png
 
Image:TCIA_public_collections-manufacturers.png
 
</gallery>
 
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
  
  
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<!--
 
{{documentation/{{documentation/version}}/module-section|Tutorials}}
 
{{documentation/{{documentation/version}}/module-section|Tutorials}}
 
Not available at this time.
 
Not available at this time.
 +
 +
---------------------------- -->
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/module-section|Panels and their use}}
 
{{documentation/{{documentation/version}}/module-section|Panels and their use}}
  
 
{|
 
{|
* '''Step 1: Connect to the server'''
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* '''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. 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 [[Image:Report-icon-tcia.png|thumb|25px|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".
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.
+
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.
   
 
|[[Image:Tcia-browser-1.png|thumb|360px|Module GUI]]
 
|}
 
  
{|
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* '''Downloading Series'''
* '''Step 2: Browse the collections'''
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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.
|[[Image:Tcia-browser-4.png|thumb|820px|Module GUI]]
 
|}
 
  
{|
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{{Gallery
* '''Step 3: Download a Series'''
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|title=TCIA Browser Screenshots
|[[Image:Tcia-browser-5.png|thumb|720px|Module GUI]]
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|width=480
|
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|height=360
 +
|lines=4
 +
|align=center
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|File:TCIA-Browser-1.png|alt1= Browsing Collections|'''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.
 +
|File:TCIA-Browser-2.png|alt2= Downloading Series|'''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.
 +
|File:TCIA-Browser-3.png|alt3= Extra clinical information from TCGA|'''Extra clinical information from TCGA.'''
 +
|File:TCIA-Browser-4.png|alt4= Settings|'''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.
 +
}}
  
 
|}
 
|}
  
  
 
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{|
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{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]]
 +
|}
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<!-- ---------------------------- -->
 
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{{documentation/{{documentation/version}}/module-section|References}}
 
{{documentation/{{documentation/version}}/module-section|References}}
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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]
 +
* [http://www.cbioportal.org/public-portal/web_api.jsp cBioPortal for Cancer Genomics Web Interface]
 
* [https://wiki.cancerimagingarchive.net/display/Public/Collections Description of TCIA Collections]
 
* [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]
 +
* [https://www.mashape.com/tcia/the-cancer-imaging-archive# Mashape page for testing TCIA API endpoint]
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/module-section|Information for Developers}}
 
{{documentation/{{documentation/version}}/module-section|Information for Developers}}
 
* [https://github.com/QIICR/TCIABrowser Source Code]
 
* [https://github.com/QIICR/TCIABrowser Source Code]
{{documentation/{{documentation/version}}/module-developerinfo}}
+
Checking the API from the python console:
 +
<pre>
 +
import TCIABrowserLib as tblib
 +
client = tblib.TCIAClient()
 +
client.get_collection_values()
 +
response = client.get_collection_values()
 +
response_string = response.read()[:]
 +
print(response_string)
 +
</pre>
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->

Latest revision as of 15:36, 18 December 2019

Home < Documentation < Nightly < Extensions < TCIABrowser

For the stable Slicer documentation, visit the 4.10 page.

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.

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 Screenshots
Browsing Collections
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
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
Extra clinical information from TCGA.  
Settings
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


References

Information for Developers

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)