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Simon bon min size fix #781

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Merged
carsen-stringer merged 5 commits into from
Sep 13, 2023
Merged

Simon bon min size fix #781

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d07eef7
added min_size=min_size argument to dynamics.compute_masks in models.py
SimonBon Aug 28, 2023
e6e19c7
added min_size=min_size argument to dynamics.compute_masks in models.py
SimonBon Aug 28, 2023
e89c20e
Merge branch 'min_size_fix' of https://github.com/SimonBon/cellpose i…
carsen-stringer Sep 13, 2023
958e0a6
adding if statement for 3D stitching
carsen-stringer Sep 13, 2023
da6201c
bug with min_size
carsen-stringer Sep 13, 2023
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3 changes: 2 additions & 1 deletion cellpose/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -654,7 +654,8 @@ def _run_cp(self, x, compute_masks=True, normalize=True, invert=False,
resize = [shape[1], shape[2]] if not resample else None
for i in iterator:
outputs = dynamics.compute_masks(dP[:,i], cellprob[i], niter=niter, cellprob_threshold=cellprob_threshold,
flow_threshold=flow_threshold, interp=interp, resize=resize,
flow_threshold=flow_threshold, interp=interp, resize=resize,
min_size=min_size if stitch_threshold==0 or nimg==1 else -1, # turn off for 3D stitching
use_gpu=self.gpu, device=self.device)
masks.append(outputs[0])
p.append(outputs[1])
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