tqdm
psutil
numba
numpy
pandas
h5py
alphabase
anndata
spatialdata>=0.7.3
dask
xarray
pyarrow
py-lmd>=1.3.1
requests
filelock
PyYAML
deprecation
spatialdata-plot>=0.2.14
matplotlib
Pillow
tifffile
zarr
ome-zarr
scipy
scikit-image>=0.22.0
scikit-learn
cellpose<4,>=3.1.1
torch
pytorch-lightning
torchmetrics
torchvision

[all]
pre-commit
pytest
sphinx
ipython
setuptools<81
sphinx-argparse
sphinx-rtd-theme==2.0.0
nbsphinx
nbsphinx-link
sphinx-book-theme
sphinx-design
sphinx-copybutton
sphinx-gallery
napari-spatialdata
pyqt5
matplotlib_scalebar
spatialdata-plot
scikit-fmm
ashlar>=1.19.0
networkx
seaborn
yattag
mahotas

[convnext]
transformers>=4.44.2

[dev]
pre-commit

[docs]
sphinx
ipython
setuptools<81
sphinx-argparse
sphinx-rtd-theme==2.0.0
nbsphinx
nbsphinx-link
sphinx-book-theme
sphinx-design
sphinx-copybutton
sphinx-gallery
scikit-fmm
mahotas

[plotting]
napari-spatialdata
pyqt5
matplotlib_scalebar
spatialdata-plot

[segmentation]
scikit-fmm

[stitching]
ashlar>=1.19.0
networkx
seaborn
yattag

[tests]
pytest
scikit-fmm
mahotas

[zstack]
mahotas
