This repository contains a napari plugin for interactively exploring and annotating SpatialData objects. napari-spatialdata is part of the SpatialData ecosystem. To learn more about SpatialData, please see the documentation.
You can install napari-spatialdata via pip:
pip install napari-spatialdata[extra]
The extra command will install the qt bindings PyQt5.
Note: if you have an M1/M2 Mac then you may get an error when installing PyQt5 via pip. A solution is to first install napari via conda (which will correctly install PyQt5), using
mamba install -c conda-forge napari pyqt
and then install napari-spatialdata via pip, but without the extra option:
pip install napari-spatialdata
You can find more details on this in the installation instructions.
If you would like to use the plugin as the default zarr reader, in napari please go to File -> Preferences
-> Plugins and follow the instructions under File extension readers.
You can install napari-spatialdata from Github with:
pip install git+https://github.com/scverse/napari-spatialdata
Or, you can also install in editable mode after cloning the repo by:
git clone https://github.com/scverse/napari-spatialdata
cd napari-spatialdata
pip install -e .
Note: when performing an editable install of napari-spatialdata, spatialdata will be reinstalled from pip. So, if you previously also made an editable install of spatialdata, you need to re-run pip install -e . on the spatialdata repository. Please find more details on this in the installation instructions.
To learn how to use the napari-spatialdata plugin, please see the documentation. To learn how to integrate napari-spatialdata into your analysis workflows, please see the SpatialData tutorials. In particular:
Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.
Distributed under the terms of the BSD-3 license, "napari-spatialdata" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.
Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and universal data framework for spatial omics. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02212-x