Closed shoyip closed 12 months ago
Note Cellpose expects the labelled masks (0=no mask, 1,2…=masks) in a separate file, that is, in the mask images, different objects have different values 1,2,3…
Yes, I have seen. I used opencv to perform the relabelling. Is this something that would be meaningful to include (at least the correct error message) in Cellpose? I think it would be useful. I can make the request in case.
img = cv2.imread(filename_in, cv2.IMREAD_GRAYSCALE)
labeled = cv2.connectedComponents(img)[1]
@shoyip that would work for datasets that don't have touching cells. For datasets that have touching cells, connected components mask reconstruction would fail.
At this level, you (users in general) will know your data better than we can predict, so it makes the most sense to leave it as is.
More explicit documentation is warranted, however, and we'll remedy that.
did anyone figure this out? I'm having the same issue
Describe the bug I am running a CellPose workflow for the
nuclei
model fine-tuning. I have greyscale images with 0/255 mask tiff.To Reproduce Steps to reproduce the behavior:
python -m cellpose --train --train_size --use_gpu --dir data/train/ --pretrained_model nuclei --verbose --mask_filter _masks --chan 0 --n_epochs 10
This is what I get.
What could be the cause of this? The error doesn't seem to be too explanatory by itself. Thanks in advance