spatialdata requires Python version >= 3.9 to run and the installation time requires a few minutes on a standard desktop computer.


Install spatialdata by running::

    pip install spatialdata

Visualization and IO#

The SpatialData ecosystem is designed to work with the following packages:

They can be installed with:

pip install "spatialdata[extra]"

Additional dependencies#

To use the PyTorch dataloader in spatialdata, torch needs to be installed. This can be done with:

pip install "spatialdata[torch]"

Installation on a M1/M2 (Apple Silicon) Mac#

The framework supports the Apple Silicon architecture, but napari-spatialdata cannot be installed with pip, because PyQt5 leads to an installation error.

Thus pip install "spatialdata[extra]" will not work (as it installs napari-spatialdata).

The solution is to pre-install napari via conda (which will install PyQt5 correctly), and pyqt, and then install napari-spatialdata without the option [extra].

This is what is done in the following commands, which perform a correct installation on a M1/M2 Mac.

mamba create -n my_env python==3.10 -y
conda activate my_env

mamba install -c conda-forge napari pyqt -y
pip install spatialdata spatialdata-io spatialdata-plot napari-spatialdata

Development version#

To install spatialdata from GitHub, run:

pip install git+

Alternative you can clone the repository (or a fork of it if you are contributing) and do an editable install with:

pip install -e .

This is the reccommended way to install the package in case in which you want to contribute to the code. In this case, to subsequently update the package you can use git pull.

A note on editable install#

If you perform an editable install of spatialdata and then install spatialdata-plot, spatialdata-io or napari-spatialdata, they may automatically override the installation of spatialdata with the version from PyPI.

To check if this happened you can run

python -c "import spatialdata; print(spatialdata.__path__)"

if you get a path that contains site-packages, then your editable installation has been overridden and you need to reinstall the package by rerunning pip install -e . in the cloned spatialdata repo.