Add upper and lower quantile rescaling to calculate_registration_image_based.py for more robust registration #848
Conversation
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
…e_based.py for more robust registration
Collaborator
|
@adrtsc This looks good to me. I've fixed the import order & added a changelog entry. If the CI passes, I'll merge & release :) |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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Outdated suggestions cannot be applied.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.
After running an old pipeline again on Fractal 2.0, Kelvin reported to me that his registration is worse. Back on Fractal 1.0, he used the apx_fractal_task_collection task for image registration, utilizing the chi2_shift algorithm for shift calculation. In Fractal 2.0, this has been integrated as an additional method in fractal-tasks-core. However, the original apx task additionally did a quantile rescaling, which helped when registering images that had very bright artifacts. This pull request adds a quantile rescaling step to the "Calculate Registration (image-based)" task to restore this behaviour.
Checklist before merging
CHANGELOG.md