Bayesian Segmentation of Spatial Transcriptomics Data

a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challenge of accurately segmenting individual cells in complex imaging datasets, leveraging a unique approach based on graph neural networks (GNNs).

A Julia package for single cell and spatial data analysis

R-based Xenium Spatial Analysis Toolkit to assess gene expression gradients

Code companion to the publication "High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spatial and in situ analysis of FFPE tissue"

A Julia package for single cell and spatial data analysis

Analysis workflow for 10x Genomics Xenium spatial transcriptomics data. Includes scripts to unpack raw Xenium outputs, convert them into AnnData objects, and perform downstream analyses.

End-to-end pipeline for spinal-cord microscopy segmentation with Cellpose, tiling, and mask stitching.

Spatial transcriptomics analysis for Bangs et al., 2025

Xenium liver cancer data analysis