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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].