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Identifying 3D signal overlaps in spatial transcriptomics data with ovrlpy

Imaging-based spatially resolved transcriptomics can localize transcripts within tissue sections in three dimensions. However, cell segmentation, which assigns transcripts to cells, is usually performed in two dimensions and spatial doublets in the vertical dimension result in segmented cells contai...

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Autori principali: Tiesmeyer, Sebastian (Autore) , Müller-Bötticher, Niklas (Autore) , Malt, Alexander (Autore) , Ma, Leyao (Autore) , Marco-Salas, Sergio (Autore) , Kiessling, Paul (Autore) , Horn, Paul (Autore) , Guillot, Adrien (Autore) , Kuemmerle, Louis B. (Autore) , Tacke, Frank (Autore) , Theis, Fabian J. (Autore) , Kuppe, Christoph (Autore) , Nilsson, Mats (Autore) , Eils, Roland (Autore) , Long, Brian (Autore) , Ishaque, Naveed (Autore)
Natura: Article (Journal)
Lingua:inglese
Pubblicazione: 10 February 2026
In: Nature biotechnology

ISSN:1546-1696
DOI:10.1038/s41587-026-03004-8
Accesso online:Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1038/s41587-026-03004-8
Verlag, lizenzpflichtig, Volltext: https://www.nature.com/articles/s41587-026-03004-8
Testo
Note sull'autore:Sebastian Tiesmeyer, Niklas Müller-Bötticher, Alexander Malt, Leyao Ma, Sergio Marco-Salas, Paul Kiessling, Paul Horn, Adrien Guillot, Louis B. Kuemmerle, Frank Tacke, Fabian J. Theis, Christoph Kuppe, Mats Nilsson, Roland Eils, Brian Long, and Naveed Ishaque
Descrizione
Riassunto:Imaging-based spatially resolved transcriptomics can localize transcripts within tissue sections in three dimensions. However, cell segmentation, which assigns transcripts to cells, is usually performed in two dimensions and spatial doublets in the vertical dimension result in segmented cells containing transcripts originating from multiple cell types. Here we present a computational tool called ovrlpy that identifies overlapping cells, tissue folds and inaccurate cell segmentation by analyzing transcript localization in three dimensions.
Descrizione del documento:Gesehen am 10.06.2026
Descrizione fisica:Online Resource
ISSN:1546-1696
DOI:10.1038/s41587-026-03004-8

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