April 26, 2022 (Dev Meeting) - Project-MONAI/MONAI GitHub Wiki

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