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April 26, 2022 (Dev Meeting)

David Manthey edited this page Apr 27, 2022 · 12 revisions

Agenda:

# Owner Title Time (min)
1 Sachi, David MONAI Label update 20
2 All Pathology Annotations and Inference Outputs 20
3 Behrooz, Jonny WSI Datasets 20

Attendees

  • MONAI Pathology: Jonny, David, Shan, Lee, Fernando, Kenza, Behrooz, Andres, Gigon, Ziyue, Jeff

Notes

  • David has proposed some changes in MONAI Label to Sachi
  • The current implementation support training and annotation
  • No need to standardize the annotation since it is fairly easy to convert between existing ones.
  • Usually the available tool define what research use. Supporting GeoJson would be a good idea.
  • We can use post-transforms to generate heatmaps in MONAI label, tools needed to put together inference outputs.
  • Augmentation using slide specific information (random, derived, or fixed)

Action items:

PIC Item
Sachi Give a demo in the next meeting
David Share the tools to create a single tiff file from numpy arrays of patches
All Add feedbacks and feature request to https://github.com/Project-MONAI/MONAI/discussions/3608

Follow up:

There is some documentation on using the large-image-source-vips package to create a single tiff from numpy arrays: https://girder.github.io/large_image/example_usage.html#writing-an-image . This is used, for example, here: https://github.com/DigitalSlideArchive/HistomicsTK/blob/master/histomicstk/cli/PositivePixelCount/PositivePixelCount.py

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