Visium spatial transcriptomics (heart sections)
Training materials for the 2026 V4SDB Student Summer School
Instructor:
Raphaël Mauron (KTH Royal Institute of Technology, Stockholm)
raphael.mauron@scilifelab.se
Workshop Overview
In developmental biology, spatial transcriptomics allows researchers to measure gene expression while preserving the tissue’s spatial organization, revealing how cell types and gene programs are arranged across an organ as it forms. However, working with spatial data introduces challenges not present in standard single-cell analysis: each measurement reflects a mixture of cells at a fixed position, and deciding what signal to keep versus filter out is a central part of the analysis. This workshop aims to demonstrate the effective utilization of 10x Genomics Visium data through hands-on analysis of embryonic heart sections. Participants will work step by step through loading, filtering, processing, and clustering spatial transcriptomics data in R using the semla and Seurat packages, first on a single tissue section and then across three sections spanning different developmental ages, drawing on data from a published atlas of the developing human heart.
By the end of this workshop, participants will be familiar with loading and visualizing Visium data, will have filtered and clustered spots into biologically meaningful groups and mapped them onto tissue anatomy, and will know how to identify cluster-defining genes, correct for batch effects across multiple sections, and explore how gene expression changes across developmental stages.