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* added plotting notebook * updated readmed * git merge issues * git merge fixes v2 - docs/landing.md * type * Remove cells that don't have any pixel clusters expressed prior to Pixie (#1051) * Drop cells without any SOM cluster expressions * Add testing for dropping non-expressed cells * Include `img_sub_folder` as parameter in Mantis calls (#1050) * Ensure mantis can read the image sub folder specified * Test on example dataset * Default img_sub_folder to None in create_mantis_dir (standard used elsewhere) * Doc fix and updated example dataset * Update segmentation labels again * Clarify img_sub_folder (mostly for refreshing tests) * Force .github/get_example_dataset.py to use updated revision * Update the file names to look for * fixed clipped plots in the notebooks. * Update HuggingFace version (#1053) * v0.1.10 (#1057) * Added continuous variable segmentation plots * Pin to scikit-image to v0.19.3 (#1060) * pin to 0.19.3 * requirement less than 0.19.3 * Make sure overwrite functionality for pixel clustering propagates into helper functions (#1058) * Propagate overwrite functionality for pixel clustering * Ensure re-normalization prevented on overwrite for pixel SOM re-assignment * normalize_data should be the opposite of overwrite * Single mantis directory (#1061) * single mantis dir, no recopying * post clustering mask suffix * generic clustering adjustments * mask prefix * remove mask prefix * strange merge issue * removed branch filters on CI, so if you branch off of a branch and run GHA, the CI workflow should work * changed ci.yml, filter push on main branch only * python 3.9 doesn't support | for Union type overloading * added fovs parameter for continuous variable plots * updated notebook to include plots * updated cell clustering notebooks to add erosion (default to True), cleaned up some notebook outputs * fixed style imports * re-added test_generate_summary_stats. Was accidently deleted in a refactoring step. * newline at eof fiber_segmentation_test.py * seaborn-paper -> seaborn-v0_8-paper * added cell to view all plotting styles i mask gen nb * pycodestyle --------- Co-authored-by: alex-l-kong <31424707+alex-l-kong@users.noreply.github.com> Co-authored-by: camisowers <38049893+camisowers@users.noreply.github.com>
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.virtual_documents | ||
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- .[lab_ext, colors] |
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