Repository navigation
Allow to have stitch_threshold=0 and to shuffle labels - #90
Merged
Merged
Conversation
This was referenced Sep 17, 2026
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
In 3D stack, in 2D+stitch_mode, in cellpose, stitch_threshold cannot be 0. Changed it so that it can be 0 and in that case it will segment the stack as a list of 2D images.
For the display, when there are lot of labels (if stithc_threshold=0 and it's a 3D stack, it's likely), in the label image, labels are sorted (close values are close to each other). The LUT are limited ot 256 values, so close values will have close colors as soon as there are more than 256 labels. So added an option (in imglib2-cellpose) and in the GUI in this plugin to shuffle the labels after cellpose's run, allowing more contrast between neighbor objects.