Spatial Transcriptomics Pipeline

Spatially-resolved gene expression analysis

Overview

Spatial transcriptomics preserves the spatial context of gene expression, enabling analysis of tissue architecture and microenvironments.

flowchart LR
    subgraph Visium
        A1[Gene Expression and Spots Coordinates] --> B1[Cell Type Deconvolution]
        B1 --> C1[Integration and Batch Correction]
        C1 --> D1[Spatial Clustering]
        D1 --> E1[Domain Identification]
    end

    subgraph Xenium
        A2[Transcripts Coordinates] --> B2[Segmentation]
        B2 --> C2[Integration and Batch Correction]
        C2 --> D2[Cell Type Annotation]
    end

    E1 --> D[Spatial Analysis]
    D2 --> D
    D --> E[Visualization]

    style A1 fill:#e74c3c,stroke:#c0392b,color:#fff
    style B1 fill:#f39c12,stroke:#d68910,color:#fff
    style C1 fill:#3498db,stroke:#2980b9,color:#fff
    style D1 fill:#9b59b6,stroke:#8e44ad,color:#fff
    style E1 fill:#1abc9c,stroke:#16a085,color:#fff

    style A2 fill:#e67e22,stroke:#ca6f1e,color:#fff
    style B2 fill:#16a085,stroke:#117a65,color:#fff
    style C2 fill:#3498db,stroke:#2980b9,color:#fff
    style D2 fill:#8e44ad,stroke:#76448a,color:#fff

    style D fill:#27ae60,stroke:#1e8449,color:#fff
    style E fill:#2c3e50,stroke:#1b2631,color:#fff

    style Visium fill:none,stroke:#3498db,stroke-width:2px,color:#3498db
    style Xenium fill:none,stroke:#9b59b6,stroke-width:2px,color:#9b59b6

Platforms Covered

10x Genomics Visium Read More→

Capture areas with ~5,000 spots, each containing 1-10 cells. Genome-wide gene expression with spatial coordinates.

10x Genomics Xenium Read More→

In situ hybridization-based platform with subcellular resolution. Targeted panel of genes (~300-5000).

Resources