NDLI: Automated segmentation of the actively-stained mouse brain using multi-spectral MR microscopy

Content Provider	PubMed Central
Author	Sharief, Anjum A. Badea, Alexandra Dale, Anders M. Johnson, G. Allan
Abstract	Magnetic Resonance Microscopy (MRM) has created new approaches for high-throughput morphological phenotyping of mouse models of diseases. Transgenic and knockout mice serve as a test bed for validating hypotheses that link genotype to the phenotype of diseases, as well as developing and tracking treatments. We describe here a Markov Random Fields based segmentation of the actively-stained mouse brain, as a prerequisite for morphological phenotyping. Active staining achieves higher signal to noise ratio (SNR) thereby enabling higher resolution imaging per unit time than obtained in previous formalin-fixed mouse brain studies. The segmentation algorithm was trained on isotropic 43-micron T1- and T2-weighted MRM images. The mouse brain was segmented into 33 structures, including the hippocampus, amygdala, hypothalamus, thalamus, as well as fiber tracts and ventricles. Probabilistic information used in the segmentation consisted of a) intensity distributions in the T1- and T2-weighted data, b) location, and c) contextual priors for incorporating spatial information. Validation using standard morphometric indices showed excellent consistency between automatically- and manually-segmented data. The algorithm has been tested on the widely used C57BL/6J strain, as well as on a selection of six recombinant inbred BXD strains, chosen especially for their largely-variant hippocampus.
Related Links	http://dx.doi.org/10.1016/j.neuroimage.2007.08.028
Ending Page	145
Page Count	10
Starting Page	136
File Format	PDF
ISSN	10538119
e-ISSN	10959572
Journal	NeuroImage
Issue Number	1
Volume Number	39
Language	English
Publisher Date	2008-01-01
Access Restriction	Open
Subject Keyword	Cognitive Neuroscience Neurology Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Neurology Cognitive Neuroscience

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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