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Combining spatial transcriptomics with tissue morphology

Author

Listed:
  • Eduard Chelebian

    (Uppsala University)

  • Christophe Avenel

    (Uppsala University)

  • Carolina Wählby

    (Uppsala University)

Abstract

Spatial transcriptomics has transformed our understanding of tissue architecture by preserving the spatial context of gene expression patterns. Simultaneously, advances in imaging AI have enabled extraction of morphological features describing the tissue. This review introduces a framework for categorizing methods that combine spatial transcriptomics with tissue morphology, focusing on either translating or integrating morphological features into spatial transcriptomics. Translation involves using morphology to predict gene expression, creating super-resolution maps or inferring genetic information from H&E-stained samples. Integration enriches spatial transcriptomics by identifying morphological features that complement gene expression. We also explore learning strategies and future directions for this emerging field.

Suggested Citation

  • Eduard Chelebian & Christophe Avenel & Carolina Wählby, 2025. "Combining spatial transcriptomics with tissue morphology," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-58989-8
    DOI: 10.1038/s41467-025-58989-8
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