spatialdata_xenium_explorer 0.1.3

Converting any SpatialData object into files that can be open by the Xenium Explorer

SpatialData to Xenium Explorer

Converting any SpatialData object into files that can be open by the Xenium Explorer.

Xenium Explorer is a registered trademark of 10x Genomics

Installation

Requirement: python>=3.9

pip install spatialdata_xenium_explorer

Usage

You can use our CLI or API, see examples below. It will create up to 6 files, among which a file called experiment.xenium. Double-click on this file to open it on the Xenium Explorer (make sure you have the latest version of the software).

CLI

spatialdata_xenium_explorer write /path/to/sdata.zarr

Check our documentation for more details.

API

import spatialdata
import spatialdata_xenium_explorer

sdata = spatialdata.read_zarr("...")

spatialdata_xenium_explorer.write("/path/to/directory", sdata, image_key, shapes_key, points_key, gene_column)

Check our documentation for more details.

Contributing

This package is still in early development. Contributions are welcome (new issues, pull requests, ...).