title: In Silico Methods for Cell Annotation, Quantification of Gene Expression, and Cell Geometry at Single-Cell Resolution Using 3DCellAtlas.
abstract: A comprehensive understanding of plant growth and development requires the integration of the spatial and temporal dynamics of gene regulatory networks with changes in cellular geometry during 3D organ growth. 3DCellAtlas is an integrative computational pipeline that semi-automatically identifies cell type and position within radially symmetric plant organs, and simultaneously quantifies 3D cell anisotropy and reporter abundance at single-cell resolution. It is a powerful tool that generates digital single-cell cellular atlases of plant organs and enables 3D cell geometry and reporter abundance (gene/protein/biosensor) from multiple samples to be integrated at single-cell resolution across whole organs. Here we describe how to use 3DCellAtlas to process and analyze radially symmetric organs, and to identify cell types and extract geometric cell data within these 3D cellular datasets. We detail how to use two statistical tools in 3DCellAtlas to compare cellular geometries, and to analyze reporter abundance at single-cell resolution.
authors.affiliation: School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
authors.forename: Petra
authors.initials: P
authors.lastname: Stamm
authors.affiliation: Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
authors.forename: Soeren
authors.initials: S
authors.lastname: Strauss
authors.affiliation: School of Mathematics, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Montenegro-Johnson
authors.affiliation: Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany. smith@mpipz.mpg.de.
authors.forename: Richard
authors.initials: R
authors.lastname: Smith
authors.affiliation: School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK. g.w.bassel@bham.ac.uk.
authors.forename: George W
authors.initials: GW
authors.lastname: Bassel
mesh_terms: D016880:Anisotropy; D003198:Computer Simulation; D053263:Gene Regulatory Networks / Q000235:genetics*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D063245:Plant Development / Q000502:physiology*; D059010:Single-Cell Analysis / Q000379:methods*
keywords: 3D anisotropy; 3D image analysis; 3D imaging; 3DCellAtlas; Cell type identification; Digital single-cell analysis; MorphoGraphX