napari spatialdata


Interactive visualization of spatial omics data with napari

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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

Development Version

You can install napari-spatialdata from Github with:

pip install git+

Or, you can also install in editable mode after cloning the repo by:

git clone
cd napari-spatialdata
pip install -e .

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:


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.


  • 0.2.6

Last updated:

  • 13 July 2023

First released:

  • 06 July 2022


  • BSD-3-Clause

Supported data:

  • Information not submitted

Plugin type:

Open extension:

GitHub activity:

  • Stars: 21
  • Forks: 7
  • Issues + PRs: 28

Python versions supported:

Operating system:


  • numpy
  • magicgui
  • qtpy
  • numba
  • anndata
  • scikit-image
  • napari
  • loguru
  • typing-extensions (<=4.5)
  • napari-matplotlib
  • scikit-learn
  • spatialdata

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