Merge pull request imcf#151 from lguerard/fix/150-trackmate-issues

Fix/150 trackmate issues

Author: ehrenfeu

.gitignore

@@ -118,3 +118,4 @@ docs/api/*
 docs/_build/*
 cover/*
 MANIFEST
+AGENTS.md

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