Add Optuna Documentation and Pre-Optimized Configuration Parameters#402
Open
timsmsmsm wants to merge 3 commits intoquantumjot:mainfrom
Open
Add Optuna Documentation and Pre-Optimized Configuration Parameters#402timsmsmsm wants to merge 3 commits intoquantumjot:mainfrom
timsmsmsm wants to merge 3 commits intoquantumjot:mainfrom
Conversation
|
Codecov ReportAll modified and coverable lines are covered by tests ✅
❗ Your organization needs to install the Codecov GitHub app to enable full functionality. Additional details and impacted files@@ Coverage Diff @@
## main #402 +/- ##
==========================================
- Coverage 85.70% 85.58% -0.12%
==========================================
Files 31 31
Lines 2203 2206 +3
Branches 404 405 +1
==========================================
Hits 1888 1888
- Misses 233 235 +2
- Partials 82 83 +1 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
|
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
This draft pull request adds several .rst files to the btrack documentation. These files are currently in progress and, when completed, will provide comprehensive guidance on how to use the optuna package to optimize btrack config parameters for any appropriately annotated cell microscopy dataset.
The new documentation will include a section that guides users on how to use an annotated portion of their data to optimize parameters based on this annotated data, and apply these optimized parameters to their unannotated data. This approach should theoretically yield parameters that are effective for the entire dataset.
In addition to the optuna usage guide, this pull request will also introduce a file containing pre-optimized parameters for various datasets from the Cell Tracking Challenge. This file will include details about each dataset, enabling users with similar data to use these pre-optimized parameters as a starting point.
Please note that the added .rst files are still under development
Checklist