Feat
- Add geometri mean filter
Fix
- gen_frame.clip(0) revealed fit_gaussian unstable with large sd
- iteratively_refine_background
- Improve BgParams with optional clip and erosion
- slow env create
- **docs**: Warning for main docstr with \*
Docs
- Compare methods for bg estimation
- Fix an import in usage
Style
- NDArray
Test
- Test PDF output without reference files
Build
- **deps**: update zarr requirement from <=2.17.2 to <=2.18.0 (572)
- **deps**: update nbsphinx requirement from <=0.9.3 to <=0.9.4 (571)
- **pre-commit**: update hooks (570)
- **deps**: update dask[distributed] requirement (569)
- **deps**: update ruff requirement from <=0.4.2 to <=0.4.3 (568)
- **deps**: update coverage[toml] requirement from <=7.5.0 to <=7.5.1 (567)
- **deps**: update tifffile requirement from <=2024.4.24 to <=2024.5.3 (566)
- **deps**: update pygments requirement from <=2.17.2 to <=2.18.0 (565)
- **deps**: bump hatch from 1.9.7 to 1.10.0 in /.github/workflows (564)
- **deps**: bump codecov/codecov-action from 4.3.0 to 4.3.1 (563)
- **deps**: update commitizen requirement from <=3.24.0 to <=3.25.0 (562)
- **pre-commit**: update hooks (561)
- **deps**: update pytest requirement from <=8.1.1 to <=8.2.0 (559)
- **deps**: update ruff requirement from <=0.4.1 to <=0.4.2 (558)
- **deps**: update tifffile requirement from <=2024.4.18 to <=2024.4.24 (557)
- **deps**: update mypy requirement from <=1.9.0 to <=1.10.0 (556)
- **deps**: bump hatch from 1.9.4 to 1.9.7 in /.github/workflows (555)
- **deps**: bump jupyterlab-server from 2.27.0 to 2.27.1 (554)
- **deps**: update coverage[toml] requirement from <=7.4.4 to <=7.5.0 (552)
- **deps**: bump questionary from 2.0.0 to 2.0.1 (550)
- Pin few indirect deps to speed up pip
- **deps**: update jupyterlab-server requirement (548)
- **deps**: update urllib3 requirement from <=1.26.18 to <=2.2.1 (547)
- **deps**: update ipython requirement from <=8.18.0 to <=8.23.0 (546)
- **deps**: update scikit-image requirement from <=0.23.1 to <=0.23.2 (544)
- **deps**: update pyarrow requirement from <=15.0.2 to <=16.0.0 (543)
- **deps**: update ruff requirement from <=0.4.0 to <=0.4.1 (542)
- **deps**: update sphinx requirement from <=7.3.6 to <=7.3.7 (541)
- **deps**: update dask[distributed] requirement (540)
- Move aicsimageio into deps
- Drop types-setuptools
- Drop typeguard test
- Update to py3.12
- Correct mypy configuration
- **deps**: update ruff requirement from <=0.3.7 to <=0.4.0 (539)
- **deps**: update tifffile requirement from <=2024.2.12 to <=2024.4.18 (538)
- **deps**: update commitizen requirement from <=3.22.0 to <=3.24.0 (537)
- **deps**: update sphinx requirement from <=7.3.4 to <=7.3.6 (536)
- **deps**: update sphinx-autodoc-typehints requirement (535)
- **deps**: update sphinx requirement from <=7.2.6 to <=7.3.4 (533)
- **deps**: bump codecov/codecov-action from 4.2.0 to 4.3.0 (524)
- **deps**: update types-setuptools requirement (532)
- **deps**: update ruff requirement from <=0.3.6 to <=0.3.7 (530)
- **deps**: update commitizen requirement from <=3.21.3 to <=3.22.0 (529)
- **deps**: update ruff requirement from <=0.3.5 to <=0.3.6 (528)
- **deps-dev**: update pandas requirement from <=2.2.1 to <=2.2.2 (527)
- **deps-dev**: update sphinx-autodoc-typehints requirement (526)
- **deps-dev**: update scikit-image requirement (525)
- **deps-dev**: update zarr requirement from <=2.17.1 to <=2.17.2 (522)
- **deps-dev**: update dask[distributed] requirement (521)
- **deps**: bump codecov/codecov-action from 4.1.1 to 4.2.0 (520)
- **deps-dev**: update matplotlib requirement from <=3.8.3 to <=3.8.4 (519)
- **deps-dev**: update scipy requirement from <=1.12.0 to <=1.13.0 (518)
- **deps-dev**: update ruff requirement from <=0.3.4 to <=0.3.5 (517)
- **deps-dev**: update dask[distributed] requirement (516)
- **deps-dev**: update commitizen requirement from <=3.20.0 to <=3.21.3 (514)
- **deps**: bump actions/configure-pages from 4 to 5 (513)
Refactor
- Add BgResult grouping dataclass
- Drop myhist()
- bg introducing BgParams
- generat for pylint
- To include pylint rule extract watershed function
- skimage import in nima; d_mask_label
- main cli
- read_tiff
- boolean traps
- exceptions
- Drop data-science-types
- **test**: Use consistently TESTS_PATH
- Add segmentation module
- **build**: From black to ruff format
chore
- Modify pre-commit update message
- update pre-commit hooks (545)