add note about possible error and fix for problems opening czi images

[stellaprins]

Why is this PR needed
After following the setup instructions, napari crashed with the following error when I tried to open Plate1-Blue-A-12-Scene-3-P3-F2-03.czi.

13:43:06 : WARNING : MainThread : Attempted file (C:/Users/prins/Downloads/Plate1-Blue-A-12-Scene-3-P3-F2-03.czi) load with reader: <class 'bioio_bioformats.reader.Reader'> failed with error: bioformats  does not support the image: 'C:/Users/prins/Downloads/Plate1-Blue-A-12-Scene-3-P3-F2-03.czi'. Can't find org.jpype.jar support library

Kimberly and I did some trouble shooting, and could fix the issue.

@K-Meech

This dependency is coming from the bioio-bioformats reader (which is automatically installed by napari-bioio-reader). Specifically, it's a dependency of Scyjava that sets up the required java / maven dependencies.
Looks like there are some similar reports there, of it not working on particular windows systems.

We should probably add something about this to the installation instructions. An easier solution might be uninstalling bioio-bioformats as we don't use it.

I'd suggest putting it as an optional note in the check napari opens a czi image section (as it only appears to affect some windows systems and not others). Ideally we can keep bioio-bioformats for most people - as it supports the widest range of file formats!
What do you think? You could add something like, if you see X error..., then run...

What does this PR do
Adds a warning box with description of the potential issue and the fix to Check napari opens a czi image section.

See Potential error section

[github-actions]

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⏱️ Updated at 2025-11-04 13:48:02 +0000

[stellaprins]

I've tried to build the lesson locally to see whether things are displayed properly before opening my PR for review, but was unable to do this using these instructions. @K-Meech anything obvious I am doing wrong? Will troubleshoot more later :)

> remotes::install_github("HealthBioscienceIDEAS/sandpaper", dependencies = TRUE)
Using GitHub PAT from the git credential store.
Error: Failed to install 'unknown package' from GitHub:
  HTTP error 404.
  Not Found

  Did you spell the repo owner (`HealthBioscienceIDEAS`) and repo name (`sandpaper`) correctly?
  - If spelling is correct, check that you have the required permissions to access the repo.

[K-Meech]

Thanks @stellaprins - yes I recently noticed these instructions are out of date! See #91

Could you try it like this instead?:

remotes::install_github("HealthBioscienceIDEAS/varnish", dependencies = TRUE)

(we have a varnish fork, but the sandpaper one doesn't exist anymore - hence the error 😅 )

[stellaprins]

Ah yes, I actually removed that link earlier. Thanks @K-Meech! Will try this later.

[K-Meech]

Thanks @stellaprins ! I put a couple of minor comments below:

[K-Meech]

Thanks @stellaprins - looks good!