tqdm
psutil
numba
h5py
alphabase
anndata<0.12
spatialdata<0.6,>=0.3.0
pyarrow<22.0.0
py-lmd>=1.3.1
spatialdata-plot
matplotlib
tifffile
zarr
ome-zarr
scipy
scikit-image>=0.22.0
scikit-learn
mahotas
scikit-fmm
cellpose<4,>=3.1.1
torch
pytorch-lightning
torchvision

[all]
pre-commit
pytest
sphinx
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
ashlar>=1.19.0
networkx
seaborn
yattag

[convnext]
transformers>=4.44.2

[dev]
pre-commit

[docs]
sphinx
sphinx-argparse
sphinx-rtd-theme==2.0.0
nbsphinx
nbsphinx-link
sphinx-book-theme
sphinx-design
sphinx-copybutton
sphinx-gallery

[plotting]
napari-spatialdata
pyqt5
matplotlib_scalebar
spatialdata-plot

[stitching]
ashlar>=1.19.0
networkx
seaborn
yattag

[tests]
pytest
