Extension: TCIABrowser
Extension Category: Informatics
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).
Contributors: Alireza Mehrtash(SPL), Andrey Fedorov(SPL), Adam Li(GU), Justin Kirby(FNLCR)
Contact: Alireza Mehrtash, [email protected]; Justin Kirby, [email protected]
License: Slicer License
The Cancer Imaging Archive (TCIA) hosts a large collection of Cancer medical imaging data which is available to the 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 available within TCIA.
By opening the TCIABrowser module, it will show the settings. There are two settings currently available: Account and Storage Folder. By default, the username field is filled by "nbia_guest" with an empty password field. To browse and download public data, click "Login" and proceed. To access the NLST(National Lung Screening Trial) dataset, check the "nlst" box and proceed with the default login information. When the "nlst" box is checked, all entered account information will be discarded. Click the folder box and change the path to change where images are downloaded. To reset the storage folder back to its original location, click the "Reset Path" button. When done using the browser, click "logout" to exit or click "Show Browser" to check other available datasets.
- A: Login area
- B: Storage location
After logging into an account, it will connect to the TCIA server and list all available collections. Select a collection from the "Current Collection" combo box. The browser will get the patient data from the TCIA server and populate the Patients table. The use Cache checkbox will cache the query results on your hard drive, making further recurring queries faster. The user can uncheck this box if a direct query from the TCIA server is desired. In the 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.
- A: Collection selector combobox
- B: Cache server response to the local storage
- C: Tables are expandable
- D: Status of the series (Available on local database / Available on TCIA server)
- E: Download and Index to the Slicer DICOM database (local storage)
- F: Download and load into the Slicer scene
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 the 3D Slicer DICOM database. So you can review them, check the meta-data, and load them into the scene later with the Slicer DICOM module. Pressing the "Download and Load" button will download and load the images 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 the '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, 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 the 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.
- A: Progress bar showing the download status of the selected series
- B: Status bar showing the current process and the status of server responses
- C: Cancel downloads button
- Quantitative Image Informatics for Cancer Research (QIICR)
- Quantitative Imaging Network (QIN)
- TCIA Home Page
- TCIA Rest API Documentation
- Project page at NAMIC 2014 Project Week
- Rapid API page for testing TCIA API endpoint
Source Code
Extension Dependencies:
Checking the API from the Python console:
import TCIABrowserLib as tblib
client = tblib.TCIAClient.TCIAClient()
response = client.get_collection_values()
print(response_string)