Feature branch transcriptomics #221
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* SC_29 io * SC_29 io * SC_29 io merscope * SC_29 io * SC_29_io
add distance calc notebook
* SC_32 update api * SC_32 cell index adata * SC_32 index name * SC_32 warning message * SC_32 xenium * xenium io pixel size * SC_32 filter gene names * fix import issue * SC_32 filter gene names merscope
Co-authored-by: lotte-vandevreken <[email protected]>
* SC_33 plot shapes on translated shapes layer performance fix * SC_33 vectorize
* SC_34 use size instead of count in transcript density * SC_34 support for plot circles + speed up unit test
* SC_38 rename * SC_38 rename * update notebooks * SC_38 release * SC_38 release * SC_38 release * SC_38 prepare release * SC_38 prepare release
* SC_39 fix docs * SC release
* SC_40 issue with coordinate system cluster intensity * SC_40 update notebook * SC_40 update flowsom clustering notebook * SC_40 example with multiple coordinate systems for flowsom clustering
* SC_40 issue with coordinate system cluster intensity * SC_40 update notebook * SC_40 update flowsom clustering notebook * SC_40 example with multiple coordinate systems for flowsom clustering * SC_40 optimizations in hp.im.flowsom * SC_40 update notebook
* SC_41_z_score * SC_41 plot clusters * SC_41 flowsom * SC_41 flowsom clusering visualization * SC_41 test flowsom * SC_41 docs * SC_41 update docstring * SC_41 docs
* SC_41_z_score * SC_41 plot clusters * SC_41 flowsom * SC_41 flowsom clusering visualization * SC_41 test flowsom * SC_41 docs * SC_41 update docstring * SC_41 docs * SC_41 docs
* SC_44 preprocess cap * SC_44 add histogram plot and cap_max * SC_44 update notebook
* SC_45 instanseg * SC_45 instanseg * SC_45 instanseg intermediate * SC_45 instanseg * SC_45 fix iou false bug if multiple output masks + remove docs * SC_45 docs * SC_45 map labels intermedate zarr store to reduce ram * SC_45 instanseg
* add contents of setup.cfg to pyproject.toml * add lockfiles * remove setup.cfg and MANIFEST * remove relative import * revert hatchling backend
… of table.var_names (table was undefined)
for more information, see https://pre-commit.ci
* fix aggregate + installation * cellpose 4 support * update notebooks * refresh notebook * fix cellpose version * typo
* change init to lazy loader * do not use internal modules * use processes to avoid test crash * remove dask config * filter future and deprecation warnings * lint * remove comments * lint * fix loglevel check * add isort off * dependencies --------- Co-authored-by: ArneDefauw <[email protected]>
for more information, see https://pre-commit.ci
Added channel_names to snr_ratio to fix wrong SNR scatter plot annotion - correction
Update installation
* SC_64 fix unit tests * fix unit test preprocess
* SC67 remove datasets dependency * SC_67 remove datasets depedency * SC_67 bump spatialdata * lock file * uv lock in cache * run tests * update registry * uv lock * sync locked before running tests * update matrix ci cd
* SC_69 pooch env variable * readme
* update docs * update docs
* [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.14 → v0.13.0](astral-sh/ruff-pre-commit@v0.1.14...v0.13.0) - [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v6.0.0](pre-commit/pre-commit-hooks@v4.5.0...v6.0.0) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
updates: - [github.com/astral-sh/ruff-pre-commit: v0.13.0 → v0.13.1](astral-sh/ruff-pre-commit@v0.13.0...v0.13.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* cuda cluster * remove cuda variable * dask dataframe backend through env variable * update notebooks for compatibility with cellpose4 and cuda cluster * remove cellpose pin from installation instructions
updates: - [github.com/astral-sh/ruff-pre-commit: v0.13.1 → v0.13.2](astral-sh/ruff-pre-commit@v0.13.1...v0.13.2) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* supress user warning * test supress user warning * parameterize unit test
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