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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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Main Authors: Tiesmeyer, Sebastian (Author) , Müller-Bötticher, Niklas (Author) , Malt, Alexander (Author) , Ma, Leyao (Author) , Marco-Salas, Sergio (Author) , Kiessling, Paul (Author) , Horn, Paul (Author) , Guillot, Adrien (Author) , Kuemmerle, Louis B. (Author) , Tacke, Frank (Author) , Theis, Fabian J. (Author) , Kuppe, Christoph (Author) , Nilsson, Mats (Author) , Eils, Roland (Author) , Long, Brian (Author) , Ishaque, Naveed (Author)
Format: Article (Journal)
Language:English
Published: 10 February 2026
In: Nature biotechnology

ISSN:1546-1696
DOI:10.1038/s41587-026-03004-8
Online Access:Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1038/s41587-026-03004-8
Verlag, lizenzpflichtig, Volltext: https://www.nature.com/articles/s41587-026-03004-8
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Author Notes: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
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Summary: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.
Item Description:Gesehen am 10.06.2026
Physical Description:Online Resource
ISSN:1546-1696
DOI:10.1038/s41587-026-03004-8

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