1. Summary

The purpose is to create the databases of phenomes by measuring and recognizing the phenotypic information of organisms from images. Genotyping of organisims has been already organized into large-scale databases, while phenotyping is still premature for databases, and the challenge here is how well we can make the automatic measurement of phenotypes using image processing and computer vision techniques. This field is called "bioimage informatics" in the decade of the 2010s, and is attracting growing interests from researchers.

We are working with National Institute of Genetics on the following topics.

1. Mouse phenotyping
2. Zebrafish neural analysis
3. Development of tools for bioimage informatics

2. References (Complete List)

1. Sharmili Roy, Xi Liang, Asanobu KITAMOTO, Masaru Tamura, Toshihiko Shiroishi, Michael S. Brown, "Phenotype Detection in Morphological Mutant Mice using Deformation Features", 16th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI2013), Part III, LNCS 8151, K. Mori et.al. (Eds.), pp. 437-444, doi:10.1007/978-3-642-40760-4_55, 2013-9 [ Abstract ]
2. Asanobu KITAMOTO, Sharmili Roy, William Grimes, Samuel Kerjose, Xi Liang, Zhongliu Xie, Masaru Tamura, Toshihiko Shiroishi, "Mouse Phenotyping Using Registration-based Deformation Features", Bioimage Informatics Workshop 2014, 2014-6 (in Japanese) [ Abstract ]
3. Xi Liang, Zhongliu Xie, Asanobu KITAMOTO, Masaru Tamura, Toshihiko Shiroishi, Ramamohanarao Kotagiri, "A Novel Atlas-based Approach to the Detection of Mouse Embryo Ventricular Septal Defects", MICCAI Workshop on Imaging Genetics (MICGen), 2014-9 [ Abstract ]
4. Xi Liang, Zhongliu Xie, Masaru Tamura, Toshihiko Shiroishi, Asanobu KITAMOTO, "Towards high-throughput mouse embryonic phenotyping: a novel approach to classifying ventricular septal defects", Proc. SPIE 9413, Medical Imaging 2015; Image Processing, S. ourselin and M.A. Styner (Eds.), pp. 8 pages, doi:10.1117/12.2081148, 2015-3
5. Mohamed HAMED, Jonathan ODUL, Asanobu KITAMOTO, Koichi KAWAKAMI, "NAS: Neuron Analyzer Suite for automatically analyzing neuronal activities from calcium imaging data", Bioimage Informatics Workshop 2015, 2015-6 [ Abstract ]
6. Mohamed HAMED, Jonathan ODUL, Andrew Steven MILLER, Koichi KAWAKAMI, Asanobu KITAMOTO, "NAS: Neuron Analyzer Suite for Automatic Analysis of Neuronal Activities from Calcium Imaging Data", 2nd International Conference on Biomedical and Bioinformatics Engineering (ICBBE 2015), 2015-8 [ Abstract ]
7. Zhongliu Xie, Xi Liang, Liucheng Guo, Asanobu KITAMOTO, Masaru Tamura, Toshihiko Shiroishi, Duncan Gillies, "Automatic classification framework for ventricular septal defects: a pilot study on high-throughput mouse embryo cardiac phenotyping", Journal of Medical Imaging, Vol. 4, No. 2, pp. 041003, doi:10.1117/1.JMI.2.4.041003, 2015-9