napari spatialdata
Interactive visualization of spatial omics data with napari
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:
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
GitHub activity:
- Stars: 29
- Forks: 9
- Issues + PRs: 36
GitHub activity:
- Stars: 29
- Forks: 9
- Issues + PRs: 36
Requirements:
- anndata
- click
- cycler
- dask
- geopandas
- loguru
- matplotlib
- napari>=0.4.19
- napari-matplotlib
- numba
- numpy
- packaging
- pandas
- pillow
- qtpy
- scanpy
- scipy
- shapely
- scikit-learn
- spatialdata>=0.0.15
- superqt
- typing-extensions>=4.8.0
- vispy
- xarray