TCIA_Notebooks

This is a home for notebooks which demonstrate how to access and work with TCIA datasets.

General Notebooks

• TCIA_Linux_Data_Retriever_App.ipynb - A tutorial on how to install the NBIA Data Retriever command-line Data Retriever utility on Linux and use it to download TCIA datasets
• TCIA_REST_API_Queries_for_Public_Datasets.ipynb - A Python tutorial on how to use TCIA's REST API to query public datasets (no user account required)
• TCIA_REST_API_Downloads_for_Public_Datasets.ipynb - A Python tutorial on how to use TCIA's REST API to download public datasets (no user account required)
• TCIA_Series_UID_Report.ipynb - Ingests a TCIA manifest file and creates reports about what it contains

AI and Visualization Notebooks

• [TCIA_Image_Visualization_with_itkWidgets.ipynb] - Example of downloading TCIA DICOM images and visualizing them in 3D using interactive cinematic volume rendering or as 2D slices.
• [TCIA_RTStruct_SEG_Visualization_with_itkWidgets.ipynb] - Tutorial of downloading DICOM SEG and RTSTRUCT objects that contain expert annotations, converting them to labelmaps for use in training and evaluating AI models, and visualizing them with their source images in 3D or as overlays on 2D slices.
• [TCIA_STL_Visualization_with_itkWidgets.ipynb] - Shows how to download convert, and visualize expert annotations and CAD models stored in STL format on TCIA for use in training and evaluating AI models.

Collection-specific Notebooks

• ACNS0332.ipynb - A tutorial on accessing DICOM images, clinical data, and tumor annotations (3d segmentations & seed points) from the "Annotations for Chemotherapy and Radiation Therapy in Treating Young Patients With Newly Diagnosed, Previously Untreated, High-Risk Medulloblastoma/PNET (ACNS0332)" dataset hosted on TCIA