napari-spacetx-explorer

A napari plugin for interactive visualization of decoded spots from spatial transcriptomic data stored as CSV

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This napari plugin was generated with Cookiecutter using with @napari's cookiecutter-napari-plugin template.

The plugin code was written by Sebastian Gonzalez-Tirado.

Reader hookspec¶

napari-spacetx-explorer allows the user to open and visualize CSV files that have point-data stored in a given format. The main target is for users who want to analyze decoded spot maps from spatial omics experiments but it can used as well for any other type of coordinate data where each point has assigned a label (e. g. a gene) as a string and the x and y-coordinates of the point's center. The header for these data must be 'target', 'xc', and 'yc', respectively.

Selecting genes¶

After loading the gene/target maps it is possible to select specific groups for better visualization. This creates a new "Points" layer in napari with the selected groups displayed in different colors.

Loading data in OME.ZARR format¶

The plugin napari-ome-zarr can be used to display whole-tissue images in addition to the spot maps produced with the napari-spacetx-explorer plugin.

Installation¶

The easiest installation is via the "Install/Uninstall Plugins..." under the Plugins menu in napari.
Another way is through pip

pip install napari-spacetx-explorer

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-spacetx-explorer" is free and open source software

Issues¶

If you encounter any problems or would like some support, please file an issue along with a detailed description.