Merge branch 'devel' into pr/140

Author: ehrenfeu

src/imcflibs/imagej/objects3d.py

@@ -80,7 +80,7 @@ def segment_3d_image(
     max_vol=None,
     remove_touching_borders=False,
     remove_touching_borders_z=False,
-):  # cover:jython
+):  # pragma: no cover (jython)
     """Segment a 3D binary image to get a labelled stack.
 
     Parameters

tests/interactive-imagej/test_trackmate.md

@@ -1,27 +1,40 @@
-This is a testing file for the trackmate branch and for the trackmate python class.
+# Testing the `imcflibs.imagej.trackmate` module
 
-The following Fiji script needs a `.jar` of the trackmate branch to be installed into Fiji already.
+Instructions for *interactive* testing (i.e. manually running a script in Fiji's
+*Script Editor*) of the `imcflibs.imagej.trackmate` module.
 
-You can open the a blobs image (`CTRL+SHIFT+B`) and then run the following script: 
+## Testing instructions
 
-```python
+1. An updated `python-imcflibs.jar` containing the changes to be tested has to
+   be installed into Fiji already.
+1. Next, open the blobs image, e.g. using `Ctrl` + `Shift` + `B`.
+1. Then, launch the *Script Editor* using `Ctrl` + `Shift` + `N`, paste the
+   following script and finally run it:
+
+```Python
 from imcflibs.imagej import trackmate
 from ij import IJ
 
 imp = IJ.getImage()
-# Detector
+
+# Select the trackmate LoG detector:
 settings = trackmate.log_detector(imp, 5, 1, 0)
-# settings = trackmate.cellpose_detector(imp, "S:\cellpose_env", "NUCLEI", 23.0, 1, 0) # WORKS, tested
-# settings = trackmate.stardist_detector(imp, 1) # WORKS, tested 
 
-# Manual tracker addition, run_trackmate does this otherwise
+# Alternatively, use the Cellpose or StarDist detector:
+# settings = trackmate.cellpose_detector(imp, "S:\cellpose_env", "NUCLEI", 23.0, 1, 0)
+# settings = trackmate.stardist_detector(imp, 1)
+
+# Manual tracker addition, run_trackmate does this otherwise:
 # settings = trackmate.sparseLAP_tracker(settings)
 
-# Spot and track filtering
+# Spot and track filtering:
 # settings = trackmate.spot_filtering(settings, None, 1.0, None, None)
 # settings = trackmate.track_filtering(settings, 15.0, 15.0, 3, 1, 1)
 
 res_img = trackmate.run_trackmate(imp, settings)
 res_img.show()
+```
+
+## Expected behavior / results
 
-```
+FIXME!!