Cell segmentation in imaging-based spatial transcriptomics

V Petukhov, RJ Xu, RA Soldatov, P Cadinu… - Nature …, 2022 - nature.com
Single-molecule spatial transcriptomics protocols based on in situ sequencing or
multiplexed RNA fluorescent hybridization can reveal detailed tissue organization. However …

SCS: cell segmentation for high-resolution spatial transcriptomics

H Chen, D Li, Z Bar-Joseph - Nature methods, 2023 - nature.com
Spatial transcriptomics promises to greatly improve our understanding of tissue organization
and cell–cell interactions. While most current platforms for spatial transcriptomics only offer …

Joint cell segmentation and cell type annotation for spatial transcriptomics

R Littman, Z Hemminger, R Foreman… - Molecular systems …, 2021 - embopress.org
RNA hybridization‐based spatial transcriptomics provides unparalleled detection sensitivity.
However, inaccuracies in segmentation of image volumes into cells cause misassignment of …

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

J Park, W Choi, S Tiesmeyer, B Long, LE Borm… - Nature …, 2021 - nature.com
Multiplexed fluorescence in situ hybridization techniques have enabled cell-type
identification, linking transcriptional heterogeneity with spatial heterogeneity of cells …

Spatially resolved transcriptomics adds a new dimension to genomics

L Larsson, J Frisén, J Lundeberg - Nature methods, 2021 - nature.com
As single-cell omics continue to advance, the field of spatially resolved transcriptomics has
emerged with a set of experimental and computational methods to map out the positions of …

Spatial components of molecular tissue biology

G Palla, DS Fischer, A Regev, FJ Theis - Nature Biotechnology, 2022 - nature.com
Methods for profiling RNA and protein expression in a spatially resolved manner are rapidly
evolving, making it possible to comprehensively characterize cells and tissues in health and …

Analysis and visualization of spatial transcriptomic data

B Liu, Y Li, L Zhang - Frontiers in Genetics, 2022 - frontiersin.org
Human and animal tissues consist of heterogeneous cell types that organize and interact in
highly structured manners. Bulk and single-cell sequencing technologies remove cells from …

Spatial charting of single-cell transcriptomes in tissues

R Wei, S He, S Bai, E Sei, M Hu, A Thompson… - Nature …, 2022 - nature.com
Single-cell RNA sequencing methods can profile the transcriptomes of single cells but
cannot preserve spatial information. Conversely, spatial transcriptomics assays can profile …

Advances in spatial transcriptomic data analysis

R Dries, J Chen, N Del Rossi, MM Khan… - Genome …, 2021 - genome.cshlp.org
Spatial transcriptomics is a rapidly growing field that promises to comprehensively
characterize tissue organization and architecture at the single-cell or subcellular resolution …

Spatial transcriptomics at subspot resolution with BayesSpace

E Zhao, MR Stone, X Ren, J Guenthoer… - Nature …, 2021 - nature.com
Recent spatial gene expression technologies enable comprehensive measurement of
transcriptomic profiles while retaining spatial context. However, existing analysis methods …