Error while enabling the Plugin in Napari

[MalteMederacke]

No description provided.

[MalteMederacke]

Hi,

Ive got a problem.

I can successfully download the napery-aicsimageio plugin (v0.2.0) via pip. After starting napari, I try to tick the plugins in the plug in menu (they appear there as installed.) But then an error pops up, I attached the log file.

Best,

Malte
error.log

[evamaxfield]

Hey! Sorry about this. It's because we released aicsimageio==4.0.0 and didn't update the version pin on this. If you install aicsimageio==3.3.4 you should be all set to go. I will try to release a new version of this that pins below v4.

[evamaxfield]

Oh maybe not the same issue....

To be honest I want to entirely rewrite this plugin and haven't actively been developing it or maitaining it in a while. I made a fork for new v1.0 work that will pick up with aicsimageio v4 but that is also under-developed at the moment.

I am not sure when I will actively look into this.

[MalteMederacke]

Thanks for your fast reply!!

Okay, I need to analyse Zeiss leightsheet microscopy data. Any suggestion in how to tackle this under these circumatances?

[evamaxfield]

I would say trying just aicsimageio[czi]>=4.0.0

Here is the readme: https://github.com/AllenCellModeling/aicsimageio

I would recommend reading the file with aicsimageio and then in python passing the numpy or dask array to napari.view_image

from aicsimageio import AICSImage
import napari

with napari.gui_qt():
    img = AICSImage("your-file.czi")
    napari.view_image(img.data)  # in memory
    # napari.view_image(img.dask_data)  # delayed chunk reading

Note that we have had issues with light sheet data so hard to say really.