visium

Visium: Spatial Transcriptomics

Overview

10X Visium is a spatial transcriptomics platform that captures gene expression data with spatial coordinates from tissue sections. This skill provides guidance on analyzing Visium data using available tools.

When to Use This Skill

This skill should be used when:

• Analyzing 10X Visium spatial transcriptomics data
• Understanding tissue spatial gene expression patterns
• Creating spatial maps of gene expression
• Identifying spatially variable genes
• Characterizing tissue architecture

Data Structure

Visium Output

After running SpaceRanger:

• filtered_feature_bc_matrix/: Expression matrix
• spatial/: Tissue image and coordinates
• analysis/: Pre-computed clustering

Key Files

sample/
├── filtered_feature_bc_matrix/
│   ├── barcodes.tsv.gz
│   ├── features.tsv.gz
│   └── matrix.mtx.gz
├── spatial/
│   ├── tissue_positions.csv
│   ├── tissue_lowres_image.png
│   └── tissue_hires_image.png
└── spatial.csv

Quick Start

With Scanpy/Squidpy

import scanpy as sc
import squidpy as sq

# Load Visium data
adata = sc.read_visium("path/to/spaceranger/output/")

# Preprocess
sc.pp.filter_genes(adata, min_cells=3)
sc.pp.normalize_total(adata, target_sum=1e4)
sc.pp.log1p(adata)
sc.pp.highly_variable_genes(adata, n_top_genes=2000)

# Dimensionality reduction
sc.pp.pca(adata, n_comps=50)
sc.pp.neighbors(adata, n_neighbors=15, n_pcs=50)

# Clustering
sc.tl.leiden(adata, resolution=0.5)
sc.tl.umap(adata)

# Spatial analysis
sq.gr.spatial_neighbors(adata)
sq.gr.centrality_scores(adata, cluster_key="leiden")

# Visualization
sq.pl.spatial_scatter(adata, color="leiden")

With Seurat

# Load Visium data
visium <- Load10X_Spatial("path/to/spaceranger/output/")

# Standard Seurat workflow
visium <- NormalizeData(visium)
visium <- FindVariableFeatures(visium)
visium <- ScaleData(visium)
visium <- RunPCA(visium)
visium <- RunUMAP(visium, dims = 1:30)
visium <- FindNeighbors(visium, dims = 1:30)
visium <- FindClusters(visium, resolution = 0.5)

# Spatial visualization
SpatialDimPlot(visium)
SpatialFeaturePlot(visium, features = "Gene")