Installation

Installation#

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

PyPI#

Install spatialdata by running:

    pip install spatialdata

Visualization and readers#

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]"

Development version#

To install spatialdata from GitHub, run:

pip install git+https://github.com/scverse/spatialdata

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.

Conda#

You can install the spatialdata, spatialdata-io, spatialdata-plot and napari-spatialdata packages from the conda-forge channel using

mamba install -c conda-forge spatialdata spatialdata-io spatialdata-plot napari-spatialdata

Update: currently (Feb 2025), due to particular versions being unavailable on conda-forge for some (dependencies of our) dependencies, the latest versions of the packages of the SpatialData ecosystem are not available on conda-forge. We are waiting for the availability to be unlocked. The latest versions are always available via PyPI.

Docker#

Docker#

A Dockerfile is available in the repository; the image that can be built from it contains spatialdata (with torch), spatialdata-io and spatialdata-plot (not napari-spatialdata)’; the libaries are installed from PyPI.

To build the image, run:

# this is for Apple Silicon machines, if you are not using such machine you can omit the --build-arg
docker build --build-arg TARGETPLATFORM=linux/arm64 --tag spatialdata .
docker run -it spatialdata

We also publish images automatically via GitHub Actions; you can see the list of available images here.

Once you have the image name, you can pull and run it with:

docker pull ghcr.io/scverse/spatialdata:spatialdata0.3.0_spatialdata-io0.1.7_spatialdata-plot0.2.9
docker run -it ghcr.io/scverse/spatialdata:spatialdata0.3.0_spatialdata-io0.1.7_spatialdata-plot0.2.9
Contents