napari-spatialdata

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

This repository contains a napari plugin for interactively exploring and annotating SpatialData objects. Here you can find the napari-spatialdata documentation. napari-spatialdata is part of the SpatialData ecosystem. To learn more about SpatialData, please see the spatialdata documentation.

Installation

You can install napari-spatialdata via pip:

pip install napari-spatialdata[all]

The all command will install the qt bindings PyQt5.

Napari now also includes multiple triangulation backends. These improve the speed by which a napari 'Shapes' layer gets loaded (this does not improve the speed of editing large numbers of shapes yet!). See also the napari documentation and already slightly older blog post. For installation via pip:

pip install napari-spatialdata[all, bermuda]

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

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