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Cell segmentation-free inference of cell types from in situ transcriptomics data

Multiplexed fluorescence in situ hybridization techniques have enabled cell-type identification, linking transcriptional heterogeneity with spatial heterogeneity of cells. However, inaccurate cell segmentation reduces the efficacy of cell-type identification and tissue characterization. Here, we pre...

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Hauptverfasser: Park, Jeongbin (VerfasserIn) , Choi, Wonyl (VerfasserIn) , Tiesmeyer, Sebastian (VerfasserIn) , Long, Brian (VerfasserIn) , Borm, Lars E. (VerfasserIn) , Garren, Emma (VerfasserIn) , Nguyen, Thuc Nghi (VerfasserIn) , Tasic, Bosiljka (VerfasserIn) , Codeluppi, Simone (VerfasserIn) , Graf, Tobias (VerfasserIn) , Schlesner, Matthias (VerfasserIn) , Stegle, Oliver (VerfasserIn) , Eils, Roland (VerfasserIn) , Ishaque, Naveed (VerfasserIn)
Dokumenttyp: Article (Journal)
Sprache:Englisch
Veröffentlicht: 10 June 2021
In: Nature Communications
Year: 2021, Jahrgang: 12, Pages: 1-13
ISSN:2041-1723
DOI:10.1038/s41467-021-23807-4
Online-Zugang:Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1038/s41467-021-23807-4
Verlag, lizenzpflichtig, Volltext: https://www.nature.com/articles/s41467-021-23807-4
Volltext
Verfasserangaben:Jeongbin Park, Wonyl Choi, Sebastian Tiesmeyer, Brian Long, Lars E. Borm, Emma Garren, Thuc Nghi Nguyen, Bosiljka Tasic, Simone Codeluppi, Tobias Graf, Matthias Schlesner, Oliver Stegle, Roland Eils & Naveed Ishaque
Beschreibung
Zusammenfassung:Multiplexed fluorescence in situ hybridization techniques have enabled cell-type identification, linking transcriptional heterogeneity with spatial heterogeneity of cells. However, inaccurate cell segmentation reduces the efficacy of cell-type identification and tissue characterization. Here, we present a method called Spot-based Spatial cell-type Analysis by Multidimensional mRNA density estimation (SSAM), a robust cell segmentation-free computational framework for identifying cell-types and tissue domains in 2D and 3D. SSAM is applicable to a variety of in situ transcriptomics techniques and capable of integrating prior knowledge of cell types. We apply SSAM to three mouse brain tissue images: the somatosensory cortex imaged by osmFISH, the hypothalamic preoptic region by MERFISH, and the visual cortex by multiplexed smFISH. Here, we show that SSAM detects regions occupied by known cell types that were previously missed and discovers new cell types.
Beschreibung:Gesehen am 27.07.2021
Beschreibung:Online Resource
ISSN:2041-1723
DOI:10.1038/s41467-021-23807-4

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