Skip to content

Update aicsimageio to bioio#392

Merged
mogres merged 2 commits intomainfrom
fix/remove-aicsimageio
Sep 30, 2025
Merged

Update aicsimageio to bioio#392
mogres merged 2 commits intomainfrom
fix/remove-aicsimageio

Conversation

@mogres
Copy link
Copy Markdown
Collaborator

@mogres mogres commented Sep 27, 2025

Problem

aicsimageio package is in maintenance mode, so updating it to bioio for compatibility.

Solution

Changed aicsimageio to use bioio instead in ImageWriter.py

Type of change

  • Bug fix

Change summary:

  • Remove aicsimageio from pyproject.toml
  • Add bioio and bioio-ome-tiff to pyproject.toml
  • Also updated the recipe validation log to debug

Steps to Verify:

Run

pack -r cellpack/tests/recipes/v2/test_image_export.json -c cellpack/tests/packing-configs/test_image_config_base.json

and check output image.

Screenshots:

Max intensity projection of the exported file:
image

- Also update the logging of recipe validation to `debug`
@mogres mogres requested review from meganrm and rugeli September 27, 2025 00:16
@github-actions
Copy link
Copy Markdown
Contributor

github-actions bot commented Sep 27, 2025

Packing analysis report

Analysis for packing results located at cellpack/tests/outputs/test_spheres/spheresSST

Ingredient name Encapsulating radius Average number packed
ext_A 25 236.0

Packing image

Packing image

Distance analysis

Expected minimum distance: 50.00
Actual minimum distance: 50.01

Ingredient key Pairwise distance distribution
ext_A Distance distribution ext_A

@mogres mogres merged commit c9b65d6 into main Sep 30, 2025
7 checks passed
@mogres mogres deleted the fix/remove-aicsimageio branch September 30, 2025 19:55
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

3 participants