A novel 3D mouse embryo atlas based on micro-CT

Abstract

SUMMARYThe goal of the International Mouse Phenotyping Consortium (IMPC) is to phenotype targeted knockout mouse strains throughout the whole mouse genome (23,000 genes) by 2021. A significant percentage of the generated mice will be embryonic lethal; therefore, phenotyping methods tuned to the mouse embryo are needed. Methods that are robust, quantitative, automated and high-throughput are attractive owing to the numbers of mice involved. Three-dimensional (3D) imaging is a useful method for characterizing morphological phenotypes. However, tools to automatically quantify morphological information of mouse embryos from 3D imaging have not been fully developed. We present a representative mouse embryo average 3D atlas comprising micro-CT images of 35 individual C57BL/6J mouse embryos at 15.5 days post-coitum. The 35 micro-CT images were registered into a consensus average image with our automated image registration software and 48 anatomical structures were segmented manually. We report the mean and variation in volumes for each of the 48 segmented structures. Mouse organ volumes vary by 2.6-4.2% on a linear scale when normalized to whole body volume. A power analysis of the volume data reports that a 9-14% volume difference can be detected between two classes of mice with sample sizes of eight. This resource will be crucial in establishing baseline anatomical phenotypic measurements for the assessment of mutant mouse phenotypes, as any future mutant embryo image can be registered to the atlas and subsequent organ volumes calculated automatically.

Behavioral and Neuroanatomical Phenotypes in Mouse Models of Autism

“…There are several different 3D imaging techniques that can be used to examine the mouse brain at the mesoscopic scale. Computed tomography is one example, which is often used to examine high-density structures like bone or vascular trees (filled with X-ray opaque contrast agents) [94][95][96], and, more recently, examine mouse embryos, which relies on the use of an iodine contrast agent to enhance the soft tissue contrast [97][98][99]. Ultrasound biomicroscopy, commonly used for cardiac imaging in the mouse [100][101][102], is also useful for studying embryonic development [103].…”

4D atlas of the mouse embryo for precise morphological staging

“…The ability to stage individual whole organs at the structural level is more valuable than analyzing the stages of each of the thousands of voxels within those structures. A 3D segmented atlas of individual organs, such as the one previously described in Development (Wong et al, 2012), can be used to calculate the average stage over all the voxels in the segmented structure of interest. Unfortunately, the 3D segmented atlas previously described (E15.5) cannot be used for the time points within the 4D atlas (E11.5-E14.0).…”

“…Extending the 4D atlas into late gestation would require another imaging modality. Micro-computed tomography (CT) imaging has been successful in capturing 3D anatomy, both external and internal including a variety of soft, nonmineralized tissues, of late gestation mouse embryos that are stained with iodine (Degenhardt et al, 2010;Metscher, 2009a,b;Wong et al, 2012). A micro-CT late gestation 4D atlas would be much easier to generate because morphological differences in organs during late gestation are mostly due to growth.…”

“…Previously, we have presented methods to identify where mutant anatomical phenotypes are found in knockout mouse embryo images (Wong et al, 2012(Wong et al, , 2014. Image registration methods were used to localize, in a mutant mouse population, statistical differences in volume, shape, and image intensity.…”

“…Image registration Group-wise registration: generation of image models Group-wise image registration was performed as previously described (Boehm et al, 2011;Kovacevic, 2004;Wong et al, 2012Wong et al, , 2014. Briefly, each mouse embryo image was subjected to a six-parameter, rigid registration (three translations, three rotations) towards a model embryo such that every image was identically oriented and positioned in 3D image space.…”