E15.5 fetuses of 6 homozygous mutants from each of the 85 sci-RNA-seq lines will be acquired from Project 1 to be imaged via high-resolution microCT following established diffusible iodine contrast enhanced scan protocols for fetal mice. Up to hundred fetuses of unaffected littermates will also be imaged to derive a synthetic population template of normative samples (Figure1) and will be used to assess the ?normal? phenotypic variation in mouse development at E15.
5 (Aim 1). The template will be segmented to the finest anatomical detail possible and will contain more anatomical structure and detail than the existing KOMP2 fetal atlas. Each sci-RNA-seq line will be assesses for overall phenotypic variability (Figure 3) and then be subjected to region-specific statistical (Figure 4) analysis of tissue volume and shape differences (Aim 2). We will also train a deep-learning model to achieve automated segmentation of fetal mice and compare the results to the current-state-of-the-art, template-based analysis (Aim 3). Our goal is to leverage recent advances in the 3D imaging, computer vision and machine-learning to make the 3D morphological characterization of mouse mutants to be more accurate, quantitative, reproducible and accessible. Combining molecular phenotype and anatomical phenotypes will provide a comprehensive characterization of mice with mutations relevant to human structural birth defects.
