Installation

Install spatialproteomics with

pip install spatialproteomics

Extras

Some of the functionalities depend on external tools (e. g. stardist, cellpose, spatialdata). Since having lots of external tools also leads to lots of dependencies, installing all of them into one environment is prone to cause dependency conflicts.

Depending on your needs, you can choose which tools you want to install together with the spatialproteomics core like this:

pip install "spatialproteomics[stardist]"
pip install "spatialproteomics[cellpose]"
pip install "spatialproteomics[spatialdata]"
pip install "spatialproteomics[astir]"
pip install "spatialproteomics[spotiflow]"
pip install "spatialproteomics[all]"

The latter one will install all external packages automatically.

You can also combine dependencies like this:

pip install "spatialproteomics[cellpose,spatialdata]"

Deprecated Packages

Mesmer only supported python<=3.10, which has reached its end of life in October 2026. It has hence been removed from spatialproteomics. If you want to run segmentation using mesmer, please downgrade to python==3.10 and spatialproteomics==0.8.6.