Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Improvements for Cellpose segmentation #90

Merged
merged 4 commits into from
Jul 12, 2024

Conversation

pakiessling
Copy link
Contributor

Made the following changes:

  • Cellpose weights are now correctly used, previously Cyto3 was always applied instead
  • Added an optional parameter clahe_kernel_size for skimage.exposure.equalize_adapthist which can be relevant for very big cells or patches. The default still is 1/8 of patch width and height
  • Blur and CLAHE can be disabled by setting the parameter to 0
  • If segmentation is run on multiple channels (e.g Nucleus marker + cell boundary marker) blur and CLAHE are now run on every channel separately which prevents spillover of intensities

Copy link
Collaborator

@quentinblampey quentinblampey left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks @pakiessling, looking very good overall, I added a few comments!

sopa/segmentation/stainings.py Outdated Show resolved Hide resolved
sopa/segmentation/stainings.py Outdated Show resolved Hide resolved
sopa/cli/segmentation.py Outdated Show resolved Hide resolved
sopa/cli/segmentation.py Outdated Show resolved Hide resolved
@quentinblampey
Copy link
Collaborator

All the tests passed, I'm merging, thanks again @pakiessling 🎉

@quentinblampey quentinblampey merged commit 4de91f4 into gustaveroussy:dev Jul 12, 2024
5 checks passed
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.

2 participants