Physics / mechanism
Spatial transcriptomics maps gene expression while preserving the physical coordinates of cells within tissue. Sequencing-based methods (10x Genomics Visium, Slide-seq) capture mRNA by hybridising transcripts to spatially barcoded arrays; imaging-based methods (MERFISH, seqFISH+, Xenium) use iterative fluorescent in-situ hybridisation cycles to resolve individual transcripts optically. Key parameters: spatial resolution (Visium ~55 µm spots vs. Xenium sub-cellular ~200 nm), gene panel size (targeted panels 300–5,000 genes vs. whole-transcriptome sequencing), and throughput (tissue area per run, cost per mm²). Current frontier: single-cell resolution across cm²-scale tissue sections, with multiplexed protein co-detection emerging.
Competitive landscape
Sequencing-based and imaging-based platforms compete directly on resolution vs. throughput trade-off. Adjacent: single-cell RNA-seq (no spatial context), multiplexed immunofluorescence (protein-level, not transcriptomic), and spatial proteomics (e.g., Deep Visual Proteomics). CRISPR spatial screens are an emerging orthogonal approach.
Companies using
Connected ideas
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Frontier (open questions)
- To be added.