Abstract
A primary objective of the eMouseAtlas Project is to enable 3D spatial mapping of whole embryo gene expression data to capture complex 3D patterns for indexing, visualization, cross-comparison and analysis. For this we have developed a spatio-temporal framework based on 3D models of embryos at different stages of development coupled with an anatomical ontology. Here we introduce a method of defining coordinate axes that correspond to the anatomical or biologically relevant anterior–posterior (A–P), dorsal–ventral (D–V) and left–right (L–R) directions. These enable more sophisticated query and analysis of the data with biologically relevant associations, and provide novel data visualizations that can reveal patterns that are otherwise difficult to detect in the standard 3D coordinate space. These anatomical coordinates are defined using the concept of a ‘straight mouse-embryo’ within which the anatomical coordinates are Cartesian. The straight embryo model has been mapped via a complex non-linear transform onto the standard embryo model. We explore the utility of this anatomical coordinate system in elucidating the spatial relationship of spatially mapped embryonic ‘Fibroblast growth factor’ gene expression patterns, and we discuss the importance of this technology in summarizing complex multimodal mouse embryo image data from gene expression and anatomy studies. Database URL: www.emouseatlas.org
Highlights
The concept of using coordinate systems to understand embryo development has a long history and was pioneered by D’Arcy Thompson in his seminal work On Growth andForm [1]
The Sonic hedgehog (Shh) expression pattern in the midline of the A–P axis is clearly visible in the dorsal views of the original and straightened embryo models; Shh is expressed in the zone of polarizing activity (ZPA) in the posterior region of the limb buds [11], and this enabled accurate identification of the A–P axis in the developing forelimb and hindlimb buds
The anatomical coordinate system that we have outlined here—‘the straight mouse’—has allowed us to define the major axes of the embryo such that we are able to computationally define the midline, and to define patterns in relation to the midline in terms of A–P, dorsal– ventral (D–V) and L–R coordinates
Summary
The concept of using coordinate systems to understand embryo development has a long history and was pioneered by D’Arcy Thompson in his seminal work On Growth andForm [1]. Despite the proven utility of coordinate systems in allowing us to record data such as injections sites or understand the developing and regenerating limb, there has not been an equivalent coordinate space introduced into 3D models of vertebrate embryo development. The reasons for this are inherent in the complexity of the developing embryo, with the mammalian embryo being variable in visual presentation and pose
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callMore From: Database : the journal of biological databases and curation
Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
