In-utero Mouse Embryo Phenotyping with High-Frequency Ultrasound


Project Summary:
The project is aiming to phenotype early- to mid-gestational mouse embryos by segmenting select organ systems in 3D data sets acquired in-utero with high-frequency ultrasound (HFU). Around 20,000 NIH Knockout (KO) mouse strains will be generated, 30% of which are expected to be embryonic or perinatal lethal, including many important models of human structural birth defects and congenital diseases. The development of phenotyping methods for embryonic lethal mice that provide for efficient pipeline analyses of defects in embryonic growth in the KO mouse strains is a highly demanded.

We propose to develop and validate in-utero 3D HFU image acquisition protocols and image processing methods that permit noninvasive, longitudinal studies of embryonic development and, in particular, the characterization of mutant phenotypes. Volumetric HFU data will be collected in-utero from mouse embryos staged between E9.5 to 15.5 in order to establish a database of normal development. With provided HFU images of mouse embryos, the focus of our team is developing advanced image analysis and machine learning methods for analyzing brain development in mouse embryos and characterizing defects caused by mutations.


Some Initial Result:

                  Figure 1 Segmentation of Brain Ventricles


                  Figure 2 Next Step: Organ Segmentation


Sponsor:
National Institute of Health


Current Participants:
Jeffrey Ketterling, Dr. Lizzi Center for Biomedical Engineering, Riverside Research, New York
Daniel Turnbull, Professor Skirball Institute of Biomolecular Medicine, NYU School of Medicine
Yao Wang1, Professor NYU Video Lab, NYU Tandon School of Engineering
Jen-wei Kuo1, NYU Video Lab, NYU Tandon School of Engineering
Orlando Aristizabal2, Skirball Institute of Biomolecular Medicine, NYU School of Medicine
Zhongqi Wang, NYU Video Lab, NYU Tandon School of Engineering


Related Publications:

  1. Jen-wei Kuo, Yao Wang, Orlando Aristizabal, Jeffrey A. Ketterling, Jonathan Mamou"Automatic Mouse Embryo Brain Ventricle Segmentation from 3D 40-MHz Ultrasound Data", IEEE International Ultrasonics Symposium (IUS), July 2013.
  2. Jen-wei Kuo, Jonathan Mamou, Yao Wang, Emi Saegusa-Beecroft, Junji Machi, Ernest J. Feleppa "A Novel Nested Graph Cuts Method for Segmenting Human Lymph Nodes in 3D High Frequency Ultrasound Images", 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI), pp. 372-375. IEEE, 2015.
  3. Jen-wei Kuo, Jonathan Mamou, Orlando Aristiz√°bal, Xuan Zhao, Jeffrey A. Ketterling, Yao Wang "Nested Graph Cut for Automatic Segmentation of High-Frequency Ultrasound Images of the Mouse Embryo", IEEE transactions on medical imaging 35, no. 2 (2016): 427-441.
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