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…nnel_index elsewhere
* 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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pyproject.tomlto reflect the change as designated by semantic versioning.ruff checkandruff format.