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Fix/150 trackmate issues #151

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Fix/150 trackmate issues #151

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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -118,3 +118,4 @@ docs/api/*
docs/_build/*
cover/*
MANIFEST
AGENTS.md
11 changes: 10 additions & 1 deletion src/imcflibs/imagej/trackmate.py
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Expand Up @@ -69,6 +69,13 @@ def cellpose_detector(
... optional_channel=0
... )
"""

dims = imageplus.getDimensions()
cal = imageplus.getCalibration()

if imageplus.getNSlices() > 1:
imageplus.setDimensions(dims[2], dims[4], dims[3])

settings = Settings(imageplus)

settings.detectorFactory = CellposeDetectorFactory()
Expand All @@ -94,10 +101,12 @@ def cellpose_detector(
return

settings.detectorSettings["CELLPOSE_MODEL"] = selected_model
settings.detectorSettings["CELL_DIAMETER"] = obj_diameter
settings.detectorSettings["CELL_DIAMETER"] = Double(obj_diameter)
settings.detectorSettings["USE_GPU"] = use_gpu
settings.detectorSettings["SIMPLIFY_CONTOURS"] = simplify_contours

imageplus.setDimensions(dims[2], dims[3], dims[4])

return settings


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