Xenium to QuPath

This repository contains a Python script designed to facilitate the conversion of Xenium data into a geoJSON format compatible with QuPath.

Features

• Converts Xenium output data into geoJSON formats.
• Streamlines the integration of spatial transcriptomics data into QuPath workflows.

Requirements

• Python 3.7 or higher
• Required Python libraries (see requirements.txt)

Installation

1. Clone this repository:

   git clone https://github.com/your-repo/xenium_to_qupath.git

Usage

Modify the script to use the appropiated pixel size and paht the the cells.zarr file from the Xenium Ranger output.

# Path to the Zarr directory (adjust the path accordingly)
zarr_dir = 'cells.zarr'

# pixel size
psize = 0.2125

Run the script with the following command:

python xenium_to_qupath.py 

Output

Output file will be a geojson file named 'exported_cells.geojson'.

Example

python xenium_to_qupath.py 

Contact

For questions or issues, please contact [gascui@lji.org].