Metadata-Version: 2.1
Name: spatialdata_xenium_explorer
Version: 0.1.3
Summary: Converting any SpatialData object into files that can be open by the Xenium Explorer
Home-page: https://quentinblampey.github.io/spatialdata_xenium_explorer/
License: BSD-3-Clause
Author: Quentin Blampey
Author-email: quentin.blampey@gmail.com
Requires-Python: >=3.9,<3.11
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering
Requires-Dist: botocore (>=1.31.47,<2.0.0)
Requires-Dist: spatialdata (>=0.0.12,<0.0.13)
Requires-Dist: typer (>=0.9.0,<0.10.0)
Project-URL: Documentation, https://quentinblampey.github.io/spatialdata_xenium_explorer/
Project-URL: Repository, https://github.com/quentinblampey/spatialdata_xenium_explorer
Description-Content-Type: text/markdown

# SpatialData to Xenium Explorer

[![PyPI](https://img.shields.io/pypi/v/spatialdata_xenium_explorer.svg)](https://pypi.org/project/spatialdata_xenium_explorer)
[![Downloads](https://static.pepy.tech/badge/spatialdata_xenium_explorer)](https://pepy.tech/project/spatialdata_xenium_explorer)
[![Docs](https://img.shields.io/badge/docs-mkdocs-blue)](https://quentinblampey.github.io/spatialdata_xenium_explorer/)
![Build](https://github.com/quentinblampey/spatialdata_xenium_explorer/workflows/ci/badge.svg)
[![Code Style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
[![License](https://img.shields.io/pypi/l/spatialdata_xenium_explorer.svg)](https://github.com/quentinblampey/spatialdata_xenium_explorer/blob/master/LICENSE)
[![Imports: isort](https://img.shields.io/badge/imports-isort-blueviolet)](https://pycqa.github.io/isort/)

Converting any [`SpatialData`](https://github.com/scverse/spatialdata) object into files that can be open by the [Xenium Explorer](https://www.10xgenomics.com/support/software/xenium-explorer).

> *Xenium Explorer* is a registered trademark of 10x Genomics

## Installation

Requirement: `python>=3.9`

```sh
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](https://www.10xgenomics.com/support/software/xenium-explorer/downloads) (make sure you have the latest version of the software).

### CLI

```sh
spatialdata_xenium_explorer write /path/to/sdata.zarr
```

Check [our documentation](https://quentinblampey.github.io/spatialdata_xenium_explorer/cli) for more details.

### API

```python
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](https://quentinblampey.github.io/spatialdata_xenium_explorer/api) for more details.

## Contributing

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