Getting an error.

[TroySeman]

I tried running with the default parameters and got an error. I'm not sure if its my segmentation, my data, the parameters or a bug in the software. This was a first run to see what happened with the defaults.

This is what I'm seeing in the console...

[INFO][2023/05/10 01:07:48 AM] Loaded btrack: C:\Users\Tinker\Anaconda3\envs\cellpose\lib\site-packages\btrack\libs\libtracker.DLL
01:07:48 INFO Loaded btrack: C:\Users\Tinker\Anaconda3\envs\cellpose\lib\site-packages\btrack\libs\libtracker.DLL
[INFO][2023/05/10 01:07:48 AM] Starting BayesianTracker session
01:07:48 INFO Starting BayesianTracker session
[INFO][2023/05/10 01:07:48 AM] Localizing objects from segmentation...
01:07:48 INFO Localizing objects from segmentation...
[INFO][2023/05/10 01:07:48 AM] Ending BayesianTracker session
01:07:48 INFO Ending BayesianTracker session
An error occurred while trying to format an error and show it in console.
You can try to uninstall IPython to disable rich traceback formatting
And/or report a bug to napari

[quantumjot]

Is this while trying to run the napari plugin? Also, can you provide a little more context about what you're trying to do? It'll help to debug

[TroySeman]

yes, the napari plug in. I have used a cellpose model in the cellpose plugin to segment the image. All the cells are touching in a zebra fish embryo with the nuclei labeled on the H1 histone.

[TroySeman]

[TroySeman]

[quantumjot]

Thanks for the update. However, I'm not sure what's causing these errors based on what you've provided.

If you run this example script, does it work?
https://gist.github.com/quantumjot/9d56dcd9a3487d7cb760f8421e18553c

[paddyroddy]

It looks like something to do with this https://forum.image.sc/t/napari-has-weird-output-when-starting-from-terminal/78047