trackmate-sc / trackmate-cellpose Goto Github PK

Hi @tinevez ,

here are some observations from trying out the omnipose detector using "TrackMate-Cellpose-0.1.3-SNAPSHOT.jar" on macos.

In a fresh python=3.10 conda environment:

1. pip install omnipose==0.3.6 (the documentation says the plugin is compatible with 0.3.6 but not with 0.4.4)

Results in "could not find results file".

When executing the command shown in a terminal (with omnipose activated) I get:

File "/Users/malbert/miniconda3/envs/omnipose/lib/python3.10/site-packages/omnipose/main.py", line 1, in
from cellpose.main import main
ModuleNotFoundError: No module named 'cellpose.main'

Indeed it seems that code in the wheel shipped over pypi tries to import cellpose instead of cellpose_omni.

2. pip install omnipose, which installed omnipose==0.4.4

It works 🎉

When segmenting images both with a pretrained model and a custom model, it shows sensible results:

I also tried for multichannel images and the field "channel to segment" seems to work properly (tried in combination with optional second channel: 0 none)

Hello!

I am having an issue with the Trackmate cellpose integration. I've tried running it on WIndows and Ubuntu with GPU, as well as Macintosh without GPU. I get the same error every time. Cellpose itself works fine through conda, just not the trackmate plugin.

I tried the LoG detector and that one seems to be fine, so I think it is specific to cellpose?

Thanks for any advice! Can't wait to see if this tool will work for this project!

Using built-in defaults.
Exception in thread "Wizard exec thread" java.lang.NoClassDefFoundError: fiji/plugin/trackmate/detection/LabeImageDetectorFactory
	at fiji.plugin.trackmate.cellpose.CellposeDetector.process(CellposeDetector.java:295)
	at fiji.plugin.trackmate.TrackMate.processGlobal(TrackMate.java:402)
	at fiji.plugin.trackmate.TrackMate.execDetection(TrackMate.java:371)
	at fiji.plugin.trackmate.gui.wizard.descriptors.ExecuteDetectionDescriptor.lambda$getForwardRunnable$0(ExecuteDetectionDescriptor.java:55)
	at fiji.plugin.trackmate.gui.wizard.WizardController$1.run(WizardController.java:191)
Caused by: java.lang.ClassNotFoundException: fiji.plugin.trackmate.detection.LabeImageDetectorFactory
	at java.net.URLClassLoader.findClass(URLClassLoader.java:387)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:419)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:352)
	... 5 more

See e.g.

• https://forum.image.sc/t/trackmate-cellpose-not-working/63950
• https://forum.image.sc/t/no-spots-found-using-trackmate-cellpose/68743

Minh-Son Phan found a fix.

It seems to always give me ‘Found 0 spots’ and Java error:
java.lang.IllegalArgumentException: Stack argument out of range: 1
at ij.ImageStack.getProcessor(ImageStack.java:310)
at net.imglib2.img.imageplus.ShortImagePlus.(ShortImagePlus.java:98)
at net.imglib2.img.ImagePlusAdapter.wrapShort(ImagePlusAdapter.java:172)
at net.imglib2.img.ImagePlusAdapter.wrapLocal(ImagePlusAdapter.java:102)
at net.imglib2.img.ImagePlusAdapter.wrap(ImagePlusAdapter.java:74)
at net.imglib2.img.ImagePlusAdapter.wrapImgPlus(ImagePlusAdapter.java:91)
at fiji.plugin.trackmate.util.TMUtils.rawWraps(TMUtils.java:142)
at fiji.plugin.trackmate.TrackMate.execDetection(TrackMate.java:356)
at fiji.plugin.trackmate.detection.DetectionUtils$1.run(DetectionUtils.java:134)

I am using 16-bit image stack, red channel. Cells ranging from 50-100px.

Thank you!