22 results for “topic:xenium”
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).
DeepSpot: Deep learning model for predicting spatial transcriptomics from H&E histopathology images. Supports spot-level (Visium) and single-cell (Xenium) resolution.
A Julia package for single cell and spatial data analysis
Interactive spatial omics viewer in the browser for thousands of images | https://rakaia.io/
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"
No description provided.
Identifying cell-type-specific spatially variable genes
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.
Decoding the Archetypes and Ecotypes of Triple-Negative Breast Cancer in Response to Chemotherapy
No description provided.
Data-centric marker distillation for zero-shot cell-type and spatial annotation with LLMs.
Spatial transcriptomics analysis for Bangs et al., 2025
End-to-end pipeline for spinal-cord microscopy segmentation with Cellpose, tiling, and mask stitching.
Additional MultiQC report sections for 10x Genomics Xenium data.
A Flask web app for joint visualization of multimodal spatial transcriptomics data
This document describes the pipeline employed to analyze the composition and spatial organization of salivary gland tissue from a Sjögren’s syndrome patient, using a dataset generated with the Xenium platform. This project was performed at GIMM during my Masters' degree.
Xenium liver cancer data analysis
Codes associated to the analyses performed in Dauyey Velds et al., "A spatial single-cell transcriptomic atlas of metastatic breast cancer progression".
Spatial transcriptomics workflows for 10x Xenium data. Developed and maintained while at the Allen Institute as part of the analysis for Zhang et al., Nature, 2026.
single-cell RNA-seq, spatial transcriptomics, and spatial proteomics analysis skills