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The HUDSEN Atlas: a three-dimensional (3D) spatial framework for studying gene expression in the developing human brain

Lookup NU author(s): Dr Janet Kerwin, Dr Subrot Sarma, Emerita Professor Susan Lindsay


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We are developing a three-dimensional (3D) atlas of the human embryonic brain using anatomical landmarks and gene expression data to define major subdivisions through 12 stages of development [Carnegie Stages (CS) 12-23; approximately 26-56 days post conception (dpc)]. Virtual 3D anatomical models are generated from intact specimens using optical projection tomography (OPT). Using mapaint software, selected gene expression data, gathered using standard methods of in situ hybridization and immunohistochemistry, are mapped to a representative 3D model for each chosen Carnegie stage. In these models, anatomical domains, defined on the basis of morphological landmarks and comparative knowledge of expression patterns in vertebrates, are linked to a developmental neuroanatomic ontology. Human gene expression patterns for genes with characteristic expression in different vertebrates (e.g. PAX6, GAD65 and OLIG2) are being used to confirm and/or refine the human anatomical domain boundaries. We have also developed interpolation software that digitally generates a full domain from partial data. Currently, the 3D models and a preliminary set of anatomical domains and ontology are available on the atlas pages along with gene expression data from approximately 100 genes in the HUDSEN Human Spatial Gene Expression Database ( The aim is that full 3D data will be generated from expression data used to define a more detailed set of anatomical domains linked to a more advanced anatomy ontology and all of these will be available online, contributing to the long-term goal of the atlas, which is to help maximize the effective use and dissemination of data wherever it is generated.

Publication metadata

Author(s): Kerwin J, Yang YY, Merchan P, Sarma S, Thompson J, Wang XX, Sandoval J, Puelles L, Baldock R, Lindsay S

Publication type: Article

Publication status: Published

Journal: Journal of Anatomy

Year: 2010

Volume: 217

Issue: 4

Pages: 289-299

Print publication date: 01/10/2010

ISSN (print): 0021-8782

ISSN (electronic): 1469-7580

Publisher: Wiley-Blackwell Publishing


DOI: 10.1111/j.1469-7580.2010.01290.x


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Funder referenceFunder name
04548/GERM/06-10891SENECA Foundation
5RO1MH070370US National Institutes of Health
BFU2008-04156Spanish Ministry of Science and Innovation