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@d33bs d33bs commented Oct 23, 2025

Description

This PR fixes an issue where individual z-slice files referenced to create a composite are not sorted properly by their z-slice filename ordering specification.

Changes are made to the function which reads file-based data and also to the test data to help demonstrate that all z-slices are in order. We now simulate cell-like sphere images and labels within the test data.

Along the journey here I also found that Napari was crashing frequently during tests. I was able to resolve some of these crashes by using the show parameter with "headless" (non-Napari window appearing) mode for views.

Many thanks to @MattsonCam who helped uncover this bug.

What kind of change(s) are included?

  • Documentation (changes docs or other related content)
  • Bug fix (fixes an issue).
  • Enhancement (adds functionality).
  • Breaking change (these changes would cause existing functionality to not work as expected).

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Please ensure that all boxes are checked before indicating that this pull request is ready for review.

  • I have read and followed the CONTRIBUTING.md guidelines.
  • I have searched for existing content to ensure this is not a duplicate.
  • I have performed a self-review of these additions (including spelling, grammar, and related).
  • These changes pass all pre-commit checks.
  • I have added comments to my code to help provide understanding
  • I have added a test which covers the code changes found within this PR
  • I have deleted all non-relevant text in this pull request template.

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@d33bs d33bs marked this pull request as ready for review October 23, 2025 18:09
@d33bs d33bs requested a review from MattsonCam October 23, 2025 18:09
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LGTM @d33bs, good job! I didn't check the z-slice images, but I want to include an example in our GFF discord channel. Can you DM me on discord to lmk how I can apply these changes? I anticipate it will just be updating the version of nViz.

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d33bs commented Oct 26, 2025

Thanks @MattsonCam for the review! I'm going to merge this in after making some changes based on your comments. Afterwards, I'll plan to deploy a new release for nviz so it may be used readily with these fixes via uvx without special handling. Like we talked about, there is likely a way to reference remote packages through uvx, but if not, we should be able to use the PyPI package.

@d33bs d33bs merged commit 2d28443 into WayScience:main Oct 26, 2025
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@d33bs d33bs deleted the fix-slice-ordering branch October 26, 2025 12:43
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d33bs commented Oct 27, 2025

Hi @MattsonCam - this fix is now deployed within v0.0.5 of nviz (and should be available to uvx).

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2 participants