napari-spatialdata: interactive exploration and annotation of spatial omics data

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.

Installation

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.

Using napari-spatialdata as default zarr reader

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.

Development Version

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.

Getting started

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:

• Annotating regions of interest with napari
• Use landmark annotations to align multiple -omics layers

Contributing

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.

License

Distributed under the terms of the BSD-3 license, "napari-spatialdata" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.

Citation

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