Secondary object #171
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Secondary object #171
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@akcd1 the tests are failing on something that suggests that you haven't properly rebased main. I would remerge asap. |
added 13 commits
December 8, 2025 13:02
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* streamline cellpose model * update docstrings * push toml --------- Co-authored-by: mdiberna <mdiberna@fry.wi.mit.edu>
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…rieflow into secondary_object
* conditional cytoplasm mask * initial commit, refactoring second obj segmentation * added thresholding options * added visualization of thresholded output * ruff check and format * adds helper visualization function * snakemake integration * updated parameters and added scaffold for ML-based segmentation * ruff check and format * code consolidation * improved documentation * code consolidation and reformatting * remove foci channel from second_obj pheno extraction, rename foci_channel_index elsewhere * fixed bug foci_channel param passing * fixed import of second obj features * conditional cytoplasm mask * Integrated secondary object segmentation with ml models * ruff format * disabled secondary object detection for test data * consistent naming with config and notebook * fixed ML parameter passing in script identify_second_objs.py * fixed general config parameters --------- Co-authored-by: edeny <edeny@fry.wi.mit.edu> Co-authored-by: acepedadiaz <acepedadiaz@fry.wi.mit.edu>
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Description
Thank you for your contribution to Brieflow!
Please succinctly summarize your proposed change.
What motivated you to make this change?
Added the option to segment ang phenotype additional objects contained within cells.
Please also link to any relevant issues that your code is associated with.
What is the nature of your change?
Checklist
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pyproject.tomlto reflect the change as designated by semantic versioning.ruff checkandruff format.