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.

Sign up for GitHub

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

Jump to bottom

Support unmyelinated axons in morphometrics #796

Merged
merged 13 commits into from
Apr 18, 2024
Merged

Support unmyelinated axons in morphometrics #796

merged 13 commits into from
Apr 18, 2024

Conversation

hermancollin
Copy link
Member

Checklist

  • I've given this PR a concise, self-descriptive, and meaningful title
  • I've linked relevant issues in the PR body
  • I've applied the relevant labels to this PR
  • I've added relevant tests for my contribution
  • I've updated the documentation and/or added correct docstrings
  • I've assigned a reviewer
  • I've consulted ADS's internal developer documentation to ensure my contribution is in line with any relevant design decisions

Description

I'll add test/documentation when the feature is ready.

In its current state, this feature can be used as follows:

  1. the user specifies the -u flag. This will toggle unmyelinated_mode and the morphometrics script will only look for prediction suffixed "_seg-uaxon". Axon and myelin masks will NOT be loaded/processed in this mode.
  2. a CSV file is saved alongside the _index and _uaxon-index images.

Note that currently, in unmyelinated_mode:

  • colorization flag is ignored
  • border info flag is ignored

Linked issues

Resolves #795

@hermancollin hermancollin added enhancement category: the change expands an existing functionality or refactoring priority:MEDIUM morphometrics related to morphometrics script unmyelinated axon labels Mar 26, 2024
@hermancollin hermancollin self-assigned this Mar 26, 2024
@hermancollin
Copy link
Member Author

Ok so the feature is ready to test. To try this, simply run the axondeepseg_morphometrics with the -u flag. I suggest taking an arbitrary image + axon segmentation, the renaming the prediction to have suffix _seg-uaxon instead of _seg-axon.

@hermancollin hermancollin mentioned this pull request Mar 26, 2024
Closed
@coveralls
Copy link

coveralls commented Mar 26, 2024 •
edited

Pull Request Test Coverage Report for Build 8637948778

Details

  • 24 of 27 (88.89%) changed or added relevant lines in 1 file are covered.
  • No unchanged relevant lines lost coverage.
  • Overall coverage decreased (-0.1%) to 88.982%
Changes Missing Coverage Covered Lines Changed/Added Lines %
AxonDeepSeg/morphometrics/launch_morphometrics_computation.py 24 27 88.89%
Totals Coverage Status
Change from base Build 7465877323: -0.1%
Covered Lines: 1163
Relevant Lines: 1307
💛 - Coveralls

@Stoyan-I-A
Copy link
Member

I tested it and it works on my end. I can review it once it is not marked as a draft.

@hermancollin hermancollin marked this pull request as ready for review April 1, 2024 18:07
@hermancollin
Copy link
Member Author

@Stoyan-I-A thank you for testing. The PR is now ready for review. I'll add tests + documentation if the logic is ok with you and @mathieuboudreau.

Stoyan-I-A
Stoyan-I-A reviewed Apr 7, 2024
View reviewed changes
Copy link
Member

@Stoyan-I-A Stoyan-I-A left a comment

Choose a reason for hiding this comment

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

Looks good to me so far

@hermancollin
Copy link
Member Author

Ok everything is finalized here - ready for final review.

Stoyan-I-A
Stoyan-I-A approved these changes Apr 14, 2024
View reviewed changes
Copy link
Member

@Stoyan-I-A Stoyan-I-A left a comment

Choose a reason for hiding this comment

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

Looks food to me. I suggest waiting for Mathieu to have a look at is as well.

docs/source/index.rst
@@ -8,7 +8,7 @@ Welcome to AxonDeepSeg !

Welcome to the AxonDeepSeg framework. In this site you will find the documentation on how to install and how to use AxonDeepSeg to obtain segmentations of your own microscopy data.

AxonDeepSeg is a segmentation software for microscopy data of nerve fibers. It is based on a convolutional neural network.
AxonDeepSeg is a segmentation software for microscopy data of nerve fibers. It is based on convolutional neural networks. The package also includes a tool for automatic morphometrics computation.
Copy link
Member

Choose a reason for hiding this comment

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

Thanks for adding this

mathieuboudreau
mathieuboudreau approved these changes Apr 17, 2024
View reviewed changes
Copy link
Member

@mathieuboudreau mathieuboudreau left a comment

Choose a reason for hiding this comment

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

LGTM! Great work - thanks Armand!

@hermancollin hermancollin merged commit 8f1f2fe into master Apr 18, 2024
5 checks passed
@hermancollin hermancollin deleted the ac/unmyelinated_morphometrics branch April 18, 2024 13:39
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@mathieuboudreau mathieuboudreau mathieuboudreau approved these changes

@Stoyan-I-A Stoyan-I-A Stoyan-I-A approved these changes

Assignees

@hermancollin hermancollin

Labels
enhancement category: the change expands an existing functionality or refactoring morphometrics related to morphometrics script priority:MEDIUM unmyelinated axon
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Support unmyelinated axons in morphometrics
4 participants
@hermancollin @coveralls @Stoyan-I-A @mathieuboudreau