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Tutorials on working with DICOM annotations in pathology whole-slide images

Key Investigators

Presenter location: In-person

Project Description

This project aims to create tutorials on how to work with DICOM annotations in pathology whole-slide images (WSIs). We will focus on nuclei annotations stored as DICOM Microscopy Bulk Simple Annotations and compute nuclei density (cellularity) on tile-level from them. The computed cellularity values are then stored as DICOM parametric maps.


  1. Objective A: Have a Colaboratory notebook ready that at least reads DICOM Microscopy Bulk Simple Annotation files (currently from a Google Storage bucket, ideally later from the IDC directly) and computes cellularity values.
  2. Objective B: Encode computed cellularity values as DICOM parametric map that can be stored back to the IDC.

Approach and Plan

  1. Testing and documentation of the current capabilities
    • Establish a repository of test samples that will contain standard-compliant examples of bulk annotations (different number of points, 2D vs 3DSCOORD), segmentations (binary and fractional) and parametric maps (floating point and integer).
    • Share code samples that were used to generate the examples above
    • Test different combinations of Slim viewer, DICOMweb backend (Google, dcm4chee, orthanc) and test samples to understand what is supported by various components (i.e., perhaps only 3DSCOORD is supported by Slim, there may be limits on maximum size of SQ in Google Healthcare)
  2. Development of the tutorial
    • Investigate nuclei annotations for plausibility
    • Read nuclei annotations
    • Efficiently compute cellularity values
    • Encode cellularity values as DICOM parametric maps

Progress and Next Steps

  1. We created different DICOM stores in Google (re-used the Google Cloud platform (GCP) project idc-external-031):
  2. We tested and documented current capabilities of reading and visualizing annotations
    • Results are summarized here
  3. We implemented code for cellularity computation and prepared a Colab notebook on which further work will be done following the project week.


Overview DICOM annotations: Segmentation IOD, Microscopy Bulk Simple Annotations IOD. Taken from https://doi.org/10.1038/s41467-023-37224-2.

Background and References