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[all]
The latter one will install all external packages automatically (apart from deepcell, the package behind mesmer, which strictly requires python==3.10. To reduce potential conflicts with other packages, this package needs to be installed by the user manually).