Share Email Print

Proceedings Paper

Gene expression based mouse brain parcellation using Markov random field regularized non-negative matrix factorization
Author(s): Sayan D. Pathak; David R. Haynor; Carol L. Thompson; Ed Lein; Michael Hawrylycz
Format Member Price Non-Member Price
PDF $17.00 $21.00

Paper Abstract

Understanding the geography of genetic expression in the mouse brain has opened previously unexplored avenues in neuroinformatics. The Allen Brain Atlas ( (ABA) provides genome-wide colorimetric in situ hybridization (ISH) gene expression images at high spatial resolution, all mapped to a common three-dimensional 200μm3 spatial framework defined by the Allen Reference Atlas (ARA) and is a unique data set for studying expression based structural and functional organization of the brain. The goal of this study was to facilitate an unbiased data-driven structural partitioning of the major structures in the mouse brain. We have developed an algorithm that uses nonnegative matrix factorization (NMF) to perform parts based analysis of ISH gene expression images. The standard NMF approach and its variants are limited in their ability to flexibly integrate prior knowledge, in the context of spatial data. In this paper, we introduce spatial connectivity as an additional regularization in NMF decomposition via the use of Markov Random Fields (mNMF). The mNMF algorithm alternates neighborhood updates with iterations of the standard NMF algorithm to exploit spatial correlations in the data. We present the algorithm and show the sub-divisions of hippocampus and somatosensory-cortex obtained via this approach. The results are compared with established neuroanatomic knowledge. We also highlight novel gene expression based sub divisions of the hippocampus identified by using the mNMF algorithm.

Paper Details

Date Published: 27 February 2009
PDF: 12 pages
Proc. SPIE 7262, Medical Imaging 2009: Biomedical Applications in Molecular, Structural, and Functional Imaging, 726212 (27 February 2009); doi: 10.1117/12.813437
Show Author Affiliations
Sayan D. Pathak, Microsoft Imaging R&D (United States)
Univ. of Washington (United States)
David R. Haynor, Univ. of Washington (United States)
Carol L. Thompson, Allen Institute for Brain Science (United States)
Ed Lein, Allen Institute for Brain Science (United States)
Michael Hawrylycz, Allen Institute for Brain Science (United States)

Published in SPIE Proceedings Vol. 7262:
Medical Imaging 2009: Biomedical Applications in Molecular, Structural, and Functional Imaging
Xiaoping P. Hu; Anne V. Clough, Editor(s)

© SPIE. Terms of Use
Back to Top
Sign in to read the full article
Create a free SPIE account to get access to
premium articles and original research
Forgot your username?