OpenFISH enables same-section spatial transcriptomics and MALDI-MSI integration.

OpenFISH achieves simultaneous, cell-type-aware mapping of transcripts and metabolites within the same tissue section, revealing metabolic heterogeneity and zonation in the CNS.

• Why it matters: Linking cellular identity to metabolic state at high resolution is crucial for understanding tissue function and disease mechanisms, but current methods face technical limitations in substrate compatibility and imaging.
• What they did: OpenFISH is an open-source, low-cost platform that integrates optimized tissue handling, a guided registration pipeline, and MALDI-MSI-compatible workflows to enable co-mapping of transcripts and metabolites in single tissue sections.
• The result: This approach uncovers cell-type-specific metabolic differences, such as phospholipid shifts in microglia and excitatory neurons, and identifies molecular changes associated with disease models and immune challenges, advancing spatial multi-omics research.