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Add 3D visualization notebooks (trame-slicer, ipyniivue, Slicer desktop) #104

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3 changes: 3 additions & 0 deletions README.md
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Expand Up @@ -52,6 +52,9 @@ Notebooks in this folder focus on topics that will require understanding of the
* [Direct access to tags/frames from GCS/AWS buckets](https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/advanced_topics/gcs_aws_direct_access.ipynb): learn how to access individual frames or tags of large DICOM files from the bucket without having to download the entire file (this notebook accompanies documentation article here: https://learn.canceridc.dev/data/downloading-data/direct-loading)
* [Using DICOMweb to access IDC data](https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/advanced_topics/idc_dicomweb_access.ipynb): both metadata and pixel data can be access using DICOMweb, which is particularly important while working with digital pathology, as it enables granular access to the individual pyramid tiles (frames)
* [IDC on AWS](https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/advanced_topics/idc_on_aws/idc-on-aws-tutorial.ipynb): learn how to work with IDC data using AWS services, including AWS HealthImaging.
* [Visualizing IDC data in 3D with trame-slicer](https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/advanced_topics/trame_slicer_visualization.ipynb): view IDC images and segmentations interactively in 3D inside a Colab cell using [trame-slicer](https://github.com/KitwareMedical/trame-slicer), which brings the 3D Slicer rendering engine to the browser (multi-planar reformat, volume rendering, segmentation overlay).
* [Interactive visualization of IDC images and segmentations with ipyniivue](https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/advanced_topics/image_visualization_with_ipyniivue.ipynb): render IDC images and DICOM Segmentation overlays interactively inside a Colab cell using [ipyniivue](https://github.com/niivue/ipyniivue), the Jupyter widget for the WebGL-based [NiiVue](https://github.com/niivue/niivue) viewer (multiplanar + 3D views, multi-organ overlays colored using the colors stored in the DICOM SEG, no desktop software needed).
* [Running the full 3D Slicer desktop in Colab with IDC data](https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/advanced_topics/image_visualization_with_slicer_desktop.ipynb): launch the complete [3D Slicer](https://www.slicer.org) desktop application headlessly and stream its live GUI into a Colab cell using the [desktopia](https://github.com/pieper/desktopia) project, loading an IDC DICOM image and DICOM SEG natively (every Slicer module available, no desktop install).

## [`viewers_deployment`](https://github.com/ImagingDataCommons/IDC-Tutorials/tree/master/notebooks/viewers_deployment)

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