spex-tools
Comprehensive spatial transcriptomics analysis library with advanced segmentation, clustering, and spatial analysis tools
Installation
In a virtualenv (see these instructions if you need to create one):
pip3 install spex-tools
Dependencies
- requests
- bioformats-jar
- jaxtyping
- tifffile
- fastapi
- packaging
- ome-types
- zarr
- scikit-learn
- pegasusio
- numexpr
- mrc
- scanpy
- pydantic
- jaxlib
- decoupler
- keras
- typing-extensions
- nd2
- bfio
- squidpy
- flax
- scipy
- imagecodecs
- fsspec
- opencv-python-headless
- aicsimageio
- treescope
- pyarrow
- pydantic-extra-types
- scvi-tools
- scikit-image
- protobuf
- cellpose
- pydantic-core
- csbdeep
- pandas
- tensorflow
- dask
- leidenalg
- scikit-misc
- imageio-ffmpeg
- phenograph
- pillow
- cython
- jpype1
- anndata
- jax
- opencv-python
- numpy
- pegasuspy
- stardist
- numcodecs
- cmake
- louvain
Releases
| Version | Released | Bullseye Python 3.9 |
Bookworm Python 3.11 |
Trixie Python 3.13 |
Files |
|---|---|---|---|---|---|
| 0.3.1059 | 2025-09-21 | ||||
| 0.3.1058 | 2025-08-23 | ||||
| 0.3.1057 | 2025-08-23 | ||||
| 0.3.1056 | 2025-08-20 | ||||
| 0.3.1055 | 2025-08-20 | ||||
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