ArticleNature communications2024
Pianno: a probabilistic framework automating semantic annotation for spatial transcriptomics.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- PromptSTG: prototype-guided prompting for few-shot spatial transcriptomics annotation.Briefings in bioinformatics · 2026Article
- Neurogenesis drives hippocampal formation-wide spatial transcription alterations in health and Alzheimer's disease.Frontiers in dementia · 2025Article
- SELF-Former: multi-scale gene filtration transformer for single-cell spatial reconstruction.Briefings in bioinformatics · 2024Article
- Pianno: a probabilistic framework automating semantic annotation for spatial transcriptomics.Nature communications · 2024Article
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Authors and funding
4 authors.
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Abstract
Spatial transcriptomics has revolutionized the study of gene expression within tissues, while preserving spatial context. However, annotating spatial spots' biological identity remains a challenge. To tackle this, we introduce Pianno, a Bayesian framework automating structural semantics annotation based on marker genes. Comprehensive evaluations underscore Pianno's remarkable prowess in precisely annotating a wide array of spatial semantics, ranging from diverse anatomical structures to intricate tumor microenvironments, as well as in estimating cell type distributions, across data generated from various spatial transcriptomics platforms. Furthermore, Pianno, in conjunction with clustering approaches, uncovers a region- and species-specific excitatory neuron subtype in the deep layer 3 of the human neocortex, shedding light on cellular evolution in the human neocortex. Overall, Pianno equips researchers with a robust and efficient tool for annotating diverse biological structures, offering new perspectives on spatial transcriptomics data.
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Registered trials
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