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.
You can install
napari-spatialdata via pip:
pip install napari-spatialdata[extra]
extra command will install the qt bindings
Note: if you have an M1/M2 Mac then you may get an error when installing
pip. A solution is to first install
napari via conda (which will correctly install
mamba install -c conda-forge napari pyqt
and then install
pip, but without the
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
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
pip install -e .
Note: when performing an editable install of
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.