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MouseLand / cellpose-napari

napari plugin for cellpose (see www.cellpose.org) - an anatomical segmentation tool
https://cellpose-napari.readthedocs.org
BSD 3-Clause "New" or "Revised" License
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[FEATURE] Segmentation on 4D stacks #9

Open rdemets opened 3 years ago

rdemets commented 3 years ago

Hi,

I saw on the documentation that it was possible to do the segmentation on 3D/4D stacks. My understanding is that ticking the process as 3D box and putting a threshold value would trigger the algorithm to detect 4D stacks. I don't know if the issue is coming from the shape of the stack, but I drag/drop a tif file with the dimension 34,81,1270,1270 (TZXY). I tried to transpose in every possible order, but the output of the code is always : [INFO] multi-stack tiff read in as having 34 planes 1270 channels

Correcting the Z/T issue is ok, but I can't get it to see the stack as a TZXY

I also tried to use the notebook that I found here but I didn't get any better result.

Can you please help me to see what I am doing wrong ? Thanks a lot. Regards, Richard.

chili-chiu commented 2 years ago

I tried running cellpose plugin on a 4D image (TZYX = 92x5x443x512), with "process stack as 3D" checked. The resulting Label layer returns the size of (92 x 443 x 512), missing one dimension.

Used cellpose 0.6.5.

carsen-stringer commented 6 days ago

cellpose itself doesn't yet have support for TZYX, this is on the to-do list