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

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

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

1. Clone this repository:

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

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

Before Running script, extract the cells.zarr.zip file.

unzip cells.zarr.zip -d cells.zarr

Define the zarr_dir and the pixel size in the scripts.

# 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 cellsegmentationvectors.py --zarr_dir /path/to/cells.zarr --output_dir /path/to/output/directory

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

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