Digital Three-Dimensional Atlas of Quail Development Using High-Resolution MRI

Seth W Ruffins,Lindsey Keough,Rusty Lansford,Melanie Martin,Salina Truong,Scott E Fraser,Russell E Jacobs

doi:10.1100/tsw.2007.125

Abstract

We present an archetypal set of three-dimensional digital atlases of the quail embryo based on microscopic magnetic resonance imaging (μMRI). The atlases are composed of three modules: (1) images of fixed ex ovo quail, ranging in age from embryonic day 5 to 10 (e05 to e10); (2) a coarsely delineated anatomical atlas of the μMRI data; and (3) an organ system-based hierarchical graph linked to the anatomical delineations. The atlas is designed to be accessed using SHIVA, a free Java application. The atlas is extensible and can contain other types of information including anatomical, physiological, and functional descriptors. It can also be linked to online resources and references. This digital atlas provides a framework to place various data types, such as gene expression and cell migration data, within the normal three-dimensional anatomy of the developing quail embryo. This provides a method for the analysis and examination of the spatial relationships among the different types of information within the context of the entire embryo.

Highlights

Embryology describes the emergence of complex anatomical forms through the growth, specification, and differentiation of the primordial germ layers
We present a series of embryonic quail atlases ranging in age from embryonic day 5 through 10 (Fig. 1)
Unlike traditional atlases, which are based on histological sections, these atlases are built from μMRI, a nondestructive imaging modality that preserves the native morphology of tissues

Summary

Introduction

Embryology describes the emergence of complex anatomical forms through the growth, specification, and differentiation of the primordial germ layers. Anatomy is a primary descriptor of all organisms and represents the overt consequence of a genotype. Anatomical atlases present a precise, visual representation of the distinguishable components comprising an organism. Atlases are invaluable references for understanding the complex forms and spatial relationships of the structures that comprise organisms. Atlases are composed of photographic plates of histological sections in conjunction with descriptive text and clarifying illustrations. Much information is lost when presenting three-dimensional datasets in a two-dimensional book format. Atlas users can interact more dynamically with web-based embryo datasets and new data can be added continually once acquired

Methods

Results

Conclusion