Open AccessBuilding quantitative, three‐dimensional atlases of gene expression and morphology at cellular resolution
Author(s) -
Knowles David W.,
Biggin Mark D.
Publication year - 2013
Publication title -
wiley interdisciplinary reviews: developmental biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.779
H-Index - 45
eISSN - 1759-7692
pISSN - 1759-7684
DOI - 10.1002/wdev.107
Subject(s) - computational biology , computer science , transcriptome , quantitative analysis (chemistry) , focus (optics) , visualization , biology , gene expression , morphogenesis , expression (computer science) , data mining , gene , genetics , chemistry , physics , chromatography , optics , programming language
Animals comprise dynamic three‐dimensional arrays of cells that express gene products in intricate spatial and temporal patterns that determine cellular differentiation and morphogenesis. A rigorous understanding of these developmental processes requires automated methods that quantitatively record and analyze complex morphologies and their associated patterns of gene expression at cellular resolution. Here we summarize light microscopy‐based approaches to establish permanent, quantitative datasets—atlases—that record this information. We focus on experiments that capture data for whole embryos or large areas of tissue in three dimensions, often at multiple time points. We compare and contrast the advantages and limitations of different methods and highlight some of the discoveries made. We emphasize the need for interdisciplinary collaborations and integrated experimental pipelines that link sample preparation, image acquisition, image analysis, database design, visualization, and quantitative analysis. WIREs Dev Biol 2013, 2:767–779. doi: 10.1002/wdev.107 This article is categorized under: Gene Expression and Transcriptional Hierarchies > Quantitative Methods and Models Technologies > Analysis of Cell, Tissue, and Animal Phenotypes Technologies > Analysis of the Transcriptome