Issues related to napari-mm3 installation

[GaoCheng22]

After installtion of napari-mm3, i encountered two difficulties.

1. It reported ModuleNotFoundError: No module named 'javabridge' after running TIFFConverter, and during the installation of javabridge, it reported that cl.exe' failed with exit code 2
2. It reported IndexError: list index out of range after running other function.

I am here to ask for your help, thank you very much!!!

[rthiermann]

Hi,

Unfortunately it sounds like these are issues with your javabridge installation, so you may be better served by asking on the javabridge repository or StackOverflow.

What format is your raw data in? Right now we do rely on Bioformats (which needs javabridge) to convert all file formats other than .nd2 or tiff, but if you can convert your data to one of these formats you should not need it.

[GaoCheng22]

Thank you very much!
My raw data format is TIFF, and i still confused about 'IndexError: list index out of range'

[rthiermann]

Can you share the stack trace for the error you got? (i.e. which line specifically caused the IndexError).

Make sure that you have "image_source" set to "Bioformats/other" in the Compile widget. The widget expects the tiff files to have a format ending in t000xy00c0.tiff with the time point t, FOV xy and color channel c.

If you want, you can share a sample of your raw data with me and I can try to reproduce the error.

[GaoCheng22]

Thank you very much！I tried reinstall my python and napari-mm3 can be called successfully.
But it still report an error when I try to run the compile step.
EmitLoopError:
While emitting signal 'magicgui.widgets.PushButton.changed', an error occurred in callback 'napari_mm3._deriving_widgets.Compile._save_settings'.
The args passed to the callback were: (False,)
This is not a bug in psygnal. See 'AttributeError' above for details.

[rthiermann]

Can you share the full stack trace you get? (including initial 'AttributeError')

[rthiermann]

We had a similar bug to what you describe a few months ago but it should be resolved in the most recent version of the code - make sure you are pulling the current version from Github (git clone https://github.com/junlabucsd/napari-mm3.git), not downloading from PyPI or napari-hub.

[GaoCheng22]

Thank you very much！
I tried to install the current version from Github, but it still exist some problem.
I wonder if napari-mm3 supports Windows 64？

[rthiermann]

Sorry that you're still having trouble! Yes, it's been tested on Windows 10 (64 bit). Can you share the errors you get?