Cover Image

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...

Full description

Saved in:
Bibliographic Details
Main Authors: Park, Jeongbin (Author) , Choi, Wonyl (Author) , Tiesmeyer, Sebastian (Author) , Long, Brian (Author) , Borm, Lars E. (Author) , Garren, Emma (Author) , Nguyen, Thuc Nghi (Author) , Tasic, Bosiljka (Author) , Codeluppi, Simone (Author) , Graf, Tobias (Author) , Schlesner, Matthias (Author) , Stegle, Oliver (Author) , Eils, Roland (Author) , Ishaque, Naveed (Author)
Format: Article (Journal)
Language:English
Published: 10 June 2021
In: Nature Communications
Year: 2021, Volume: 12, Pages: 1-13
ISSN:2041-1723
DOI:10.1038/s41467-021-23807-4
Online Access:Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1038/s41467-021-23807-4
Verlag, lizenzpflichtig, Volltext: https://www.nature.com/articles/s41467-021-23807-4
Get full text
Author Notes: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
Description
Summary: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.
Item Description:Gesehen am 27.07.2021
Physical Description:Online Resource
ISSN:2041-1723
DOI:10.1038/s41467-021-23807-4

Similar Items