EMAP and EMAGE: A Framework for Understanding Spatially Organized Data

Abstract

The Edinburgh MouseAtlas Project (EMAP) is a time-series of mouse-embryo volumetric models. The models provide a context-free spatial framework onto which structural interpretations and experimental data can be mapped. This enables collation, comparison, and query of complex spatial patterns with respect to each other and with respect to known or hypothesized structure. The atlas also includes a time-dependent anatomical ontology and mapping between the ontology and the spatial models in the form of delineated anatomical regions or tissues. The models provide a natural, graphical context for browsing and visualizing complex data. The Edinburgh Mouse Atlas Gene-Expression Database (EMAGE) is one of the first applications of the EMAP framework and provides a spatially mapped gene-expression database with associated tools for data mapping, submission, and query. In this article, we describe the underlying principles of the Atlas and the gene-expression database, and provide a practical introduction to the use of the EMAP and EMAGE tools, including use of new techniques for whole body gene-expression data capture and mapping.

A high-resolution anatomical ontology of the developing murine genitourinary tract

“…A descriptive anatomical ontology was developed to define these domains. This combination of three dimensional models and text-based anatomical nomenclature has been exploited in the Edinburgh Mouse Atlas of Gene Expression (EMAGE; http://genex.hgu.mrc.ac.uk/Emage/database/emageIntro.html) (Baldock et al, 2003) in which gene expressions are painted onto the models. The EMAP anatomical ontology has been adopted by the Gene Expression Database (GXD) at the Jackson Laboratory (http://www.informatics.jax.org/mgihome/GXD/aboutGXD.shtml) and has provided an invaluable resource for the developmental biology community both for the teaching of developmental anatomy and the broad description of gene and protein expression patterns.…”

Assembling models of embryo development: Image analysis and the construction of digital atlases

“…2G). This strategy has been used for vertebrates at late developmental stages ("Developmental stages" section) when the specimen's size and lack of optical transparency do not allow imaging with resolution at the single cell level (Baldock et al, 2003;Ruffinsetal., 2007;Rittscher etal., 2011).…”

“…After following an annotation procedure for anatomy and gene expression data with a controlled, standard vocabulary, the mapping procedure is reduced to just linking names to positions or domains (Baldock et al, 2003;Boline et al, 2008). Given the difficulty of geometric registration across greatly variable resources, this strategy is useful to guarantee interoperability and can bring together data coming from different laboratories, resources, developmental stages, or even different species.…”

Live optical projection tomography

“…The range of species successfully imaged now includes human, 9 mouse, 10,11 chick, 12 reptile species, 13 zebrafish, 14 Drosophila 15 and Arabidopsis. 16 Mouse embryos are routinely imaged at E9.5 up to E12.5, 17 and, for older specimens, organs in isolation are scanned, for example, the developing limb 18 or brain 19 at E14.5. The Edinburgh Mouse Atlas Project (EMAP) has also performed purely anatomical scanning (of autofluorescence) for a few whole embryos up to an age of ∼E15.…”

“…The Edinburgh Mouse Atlas Project (EMAP) has also performed purely anatomical scanning (of autofluorescence) for a few whole embryos up to an age of ∼E15. 17 Thus, all the organogenesis stages of mouse development have been imaged with OPT. Younger and smaller embryos can also be imaged by OPT, but because previous techniques (such as confocal microscopy) were already able to capture these smaller specimens, they have not been considered an important application for OPT itself.…”