Open mattersoflight opened 1 year ago
- @ziw-liu I recall you used the fluorescence channel itself as a weight mask. Can you point to that call?
It is the RandWeightedCropd
transform from MONAI:
https://github.com/mehta-lab/viscy/blob/6daf3223372504fc35e6f44e5909061c426cb2c7/viscy/light/data.py#L493-L497
At a recent meeting, we discussed strategies to achieve class balance across the cell cycle. @ziw-liu proposed a selection of FOVs based on the rough measure of the shape of the cells, which I think is a good way to digitally sort the FOVs while constructing a batch.
Let's continue to think about this. We need: a) rough measures of the cell cycle stage:
b) strategies to assign a probability of sampling to a FOV or a patch: