# Project II - 3D Quantitative Analysis of Mouse Models of Structural Birth Defects Through Computational Anatomy

> **NIH NIH P01** · SEATTLE CHILDREN'S HOSPITAL · 2021 · $328,199

## Abstract

PROJECT SUMMARY
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.

## Key facts

- **NIH application ID:** 10154929
- **Project number:** 1P01HD104435-01
- **Recipient organization:** SEATTLE CHILDREN'S HOSPITAL
- **Principal Investigator:** Ali Murat Maga
- **Activity code:** P01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $328,199
- **Award type:** 1
- **Project period:** 2021-01-11 → 2025-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10154929

## Citation

> US National Institutes of Health, RePORTER application 10154929, Project II - 3D Quantitative Analysis of Mouse Models of Structural Birth Defects Through Computational Anatomy (1P01HD104435-01). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10154929. Licensed CC0.

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