diff --git a/.gitignore b/.gitignore index 7125412..6e22d86 100644 --- a/.gitignore +++ b/.gitignore @@ -118,3 +118,4 @@ docs/api/* docs/_build/* cover/* MANIFEST +AGENTS.md \ No newline at end of file diff --git a/src/imcflibs/imagej/trackmate.py b/src/imcflibs/imagej/trackmate.py index 7f16b32..1148ef1 100644 --- a/src/imcflibs/imagej/trackmate.py +++ b/src/imcflibs/imagej/trackmate.py @@ -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() @@ -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