Xenium Resegmentation

Here we will use Proseg (Jones et al. (2025)) for segmentation. The following script sets up a SLURM job for running Proseg on the Xenium data, then the data is converted to Bayesor format to be imported to the xenium.experiment file for viewing.

#!/bin/bash

#SBATCH --account=
#SBATCH --job-name='proseg_%a'
#SBATCH --output=logs/proseg_%a.log
#SBATCH --partition=standard
#SBATCH --mem=128G
#SBATCH --cpus-per-task=16
#SBATCH --time=24:00:00
#SBATCH --array=2-4

mkdir -p logs
ml xeniumranger

# Setting up variables
samples_manifest=data/samples_manifest.txt
sample=$(cat $samples_manifest | cut -f1 | sed -n ${SLURM_ARRAY_TASK_ID}p)
xenium_outDir=$(cat $samples_manifest | cut -f2 | sed -n ${SLURM_ARRAY_TASK_ID}p)

proseg ${xenium_outDir}/transcripts.parquet --xenium --output-path ${xenium_outDir}

proseg-to-baysor \
    ${xenium_outDir}/transcript-metadata.csv.gz \
    ${xenium_outDir}/cell-polygons.geojson.gz \
    --output-transcript-metadata ${xenium_outDir}/baysor-transcript-metadata.csv \
    --output-cell-polygons ${xenium_outDir}/baysor-cell-polygons.geojson

xeniumranger import-segmentation \
    --id ${sample} \
    --xenium-bundle ${xenium_outDir} \
    --viz-polygons ${xenium_outDir}/baysor-cell-polygons.geojson \
    --transcript-assignment ${xenium_outDir}/baysor-transcript-metadata.csv \
    --units microns

References

Jones, Daniel C, Anna E Elz, Azadeh Hadadianpour, Heeju Ryu, David R Glass, and Evan W Newell. 2025. “Cell Simulation as Cell Segmentation.” Nature Methods, 1–12.