title: Automatic classification framework for ventricular septal defects: a pilot study on high-throughput mouse embryo cardiac phenotyping.
abstract: Intensive international efforts are underway toward phenotyping the entire mouse genome by modifying all its [Formula: see text] genes one-by-one for comparative studies. A workload of this scale has triggered numerous studies harnessing image informatics for the identification of morphological defects. However, existing work in this line primarily rests on abnormality detection via structural volumetrics between wild-type and gene-modified mice, which generally fails when the pathology involves no severe volume changes, such as ventricular septal defects (VSDs) in the heart. Furthermore, in embryo cardiac phenotyping, the lack of relevant work in embryonic heart segmentation, the limited availability of public atlases, and the general requirement of manual labor for the actual phenotype classification after abnormality detection, along with other limitations, have collectively restricted existing practices from meeting the high-throughput demands. This study proposes, to the best of our knowledge, the first fully automatic VSD classification framework in mouse embryo imaging. Our approach leverages a combination of atlas-based segmentation and snake evolution techniques to derive the segmentation of heart ventricles, where VSD classification is achieved by checking whether the left and right ventricles border or overlap with each other. A pilot study has validated our approach at a proof-of-concept level and achieved a classification accuracy of 100% through a series of empirical experiments on a database of 15 images.
authors.affiliation: Imperial College London, Department of Computing, South Kensington Campus, London SW7 2AZ, United Kingdom; National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430, Japan.
authors.forename: Zhongliu
authors.initials: Z
authors.lastname: Xie
authors.affiliation: National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430, Japan; University of Melbourne, Department of Computer Science and Software Engineering, Parkville Campus, Melbourne VIC 3010, Australia.
authors.forename: Xi
authors.initials: X
authors.lastname: Liang
authors.affiliation: Imperial College London , Department of Electrical and Electronic Engineering, South Kensington Campus, London SW7 2AZ, United Kingdom.
authors.forename: Liucheng
authors.initials: L
authors.lastname: Guo
authors.affiliation: National Institute of Informatics , 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430, Japan.
authors.forename: Asanobu
authors.initials: A
authors.lastname: Kitamoto
authors.affiliation: National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan; RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan.
authors.forename: Masaru
authors.initials: M
authors.lastname: Tamura
authors.affiliation: National Institute of Genetics , 1111 Yata, Mishima, Shizuoka 411-8540, Japan.
authors.forename: Toshihiko
authors.initials: T
authors.lastname: Shiroishi
authors.affiliation: Imperial College London , Department of Computing, South Kensington Campus, London SW7 2AZ, United Kingdom.
authors.forename: Duncan
authors.initials: D
authors.lastname: Gillies
keywords: atlas-based segmentation; mouse embryo phenotyping; snake evolution; ventricular septal defects
references.citation: Neuroscience. 2005;135(4):1203-15
references.pmid: 16165303
references.citation: Neuroimage. 2009 Jul 1;46(3):717-25
references.pmid: 19236923
references.citation: Neuroimage. 2011 Jan 15;54(2):769-78
references.pmid: 20656039
references.citation: Neuroimage. 2010 Nov 1;53(2):365-72
references.pmid: 20600960
references.citation: J Microsc. 2009 May;234(2):173-90
references.pmid: 19397746
references.citation: Med Phys. 2007 Nov;34(11):4098-108
references.pmid: 18072476
references.citation: Hum Mol Genet. 2013 Jun 15;22(12):2471-81
references.pmid: 23449628
references.citation: Physiol Genomics. 2010 Oct;42A(2):89-95
references.pmid: 20682847
references.citation: IEEE Trans Med Imaging. 2006 Sep;25(9):1145-57
references.pmid: 16967800
references.citation: Neuroimage. 2006 Jan 1;29(1):99-105
references.pmid: 16084741
references.citation: IEEE Trans Med Imaging. 2001 Jan;20(1):45-57
references.pmid: 11293691
references.citation: Neuroimage. 2004;23 Suppl 1:S151-60
references.pmid: 15501084
references.citation: Development. 2012 Sep;139(17 ):3248-56
references.pmid: 22872090
references.citation: Neuroimage. 2006 Jul 1;31(3):1116-28
references.pmid: 16545965
references.citation: Dis Model Mech. 2013 May;6(3):571-9
references.pmid: 23519032
references.citation: Neuroinformatics. 2013 Jan;11(1):35-45
references.pmid: 23055043
references.citation: Neuroimage. 2008 Aug 1;42(1):19-27
references.pmid: 18547819
references.citation: Nature. 2002 Dec 5;420(6915):520-62
references.pmid: 12466850
references.citation: J Am Coll Cardiol. 2002 Jun 19;39(12):1890-900
references.pmid: 12084585
references.citation: Circ Cardiovasc Imaging. 2010 May;3(3):314-22
references.pmid: 20190279
references.citation: Comput Biol Med. 2010 Jan;40(1):64-74
references.pmid: 19939358
references.citation: Neuroimage. 2005 Aug 15;27(2):425-35
references.pmid: 15908233
references.citation: Neuroimage. 2008 Aug 1;42(1):60-9
references.pmid: 18502665
references.citation: NMR Biomed. 2009 Oct;22(8):857-66
references.pmid: 19598179
references.citation: Nat Med. 2001 Oct;7(10):1086-90
references.pmid: 11590420
references.citation: Med Image Comput Comput Assist Interv. 2013;16(Pt 3):437-44
references.pmid: 24505791
references.citation: Neuroimage. 2008 Jan 1;39(1):32-9
references.pmid: 17942324
references.citation: Proc SPIE Int Soc Opt Eng. 2009 Feb 1;7259:725943-725949
references.pmid: 20640188
references.citation: Cell. 2007 Jan 12;128(1):9-13
references.pmid: 17218247
references.citation: PLoS Genet. 2006 Aug 25;2(8):e118
references.pmid: 16933996
references.citation: Dis Model Mech. 2012 May;5(3):289-92
references.pmid: 22566555
references.citation: Magn Reson Med. 2013 Mar 1;69(3):877-83
references.pmid: 22556102
references.citation: Cereb Cortex. 2005 May;15(5):639-45
references.pmid: 15342433
references.citation: J Mol Cell Cardiol. 2003 Feb;35(2):217-22
references.pmid: 12606262