Comprehensive defect detection in mouse embryos and the heart by combining automated phenotyping with novel population averages and atlases

Micro-CT has become the standard for the assessment of malformations in mouse embryos because it allows the visualisation of internal structures in the context of the intact embryo. Statistical comparison of volume differences is possible via manual segmentation of organs of interest from micro-CT scans, but this process is slow and laborious. Automated registration-based methods now exist that make the volumetric analysis of all organs feasible. Here, we expand the available atlases for use with the LAMA registration and analysis pipeline to include high-resolution population averages derived from phosphotungstic acid-stained C57BL/6J embryos and corresponding manually segmented atlases at embryonic stage (E) 12.5, E15.5, and E17.5. We report application of these population averages and atlases with the LAMA phenotyping pipeline to Wbp11 heterozygous null embryos, identifying defects previously reported in the cervical vertebrae, brain, nasal cavity, palate, liver and kidneys as well as a right aortic arch defects missed by manual analysis, and volume differences in the eyes and spinal cord. Finally, we report a high-resolution isolated E18.5 mouse heart population average and corresponding atlas that when applied to the Wbp11 line identified significant differences. These findings highlight the advantages of unbiased, volumetric and quantitative approaches in the analysis of mouse models of human disease.