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
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.
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:
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.