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Dr Richard Beare

Dr Richard BeareDr Beare is a Senior Research Fellow in Imaging within the Department of Medicine at Monash Medical Centre (Monash University). He conducts and supervises computational image analysis within the Stroke and Ageing Research Group.
He has developed new image analysis methods for two large human brain studies (TASCOG, CDOT). He has particular expertise in semi-automated segmentation of white matter hyperintensities, structural analysis using voxel-based morphometry, spherical harmonic based shape analysis of brain structures and multivariate image analysis. Involvement in the Australian Mouse Brain Mapping Consortium has led Dr Beare to develop new tools for structural analysis and computational anatomy of animal models. A further interest is the development of imaging techniques for measuring vascular geometry and flow modeling.
As well as contributing to the Insight Toolkit, the internationally recognised, NIH funded software suite for medical image analysis, Dr Beare holds 4 patents, has contributed to a number of commercial software packages (Axon ImageXpress, Evotech high content screening platform) and products (Enterix bowel cancer screening, robotic equipment) while working for CSIRO.

 

Morphological segmantation of age-related white matter lesions

 

Current Research
Tasmanian study of cognition and gait (TASCOG) - a large, population based study of healthy aged subjects examining the relationships between brain structure and gait and cognitive function. 400 subjects are being studied longitudinally.

  • Australian Mouse Brain Mapping Consortium - construction of the next generation of mouse brain atlas. This will be a probabalistic atlas and is being built using high resolution MRI and microscopy imagery.
  • Carotid artery segmentation and modelling for improved stroke risk estimation.
  • Fatigue, depression and traumatic brain injury. This study is attempting to correlate damage resulting from traumatic brain injury to sleep and psychological disorders. My role is to develop the procedures to make automated measurements from the brain scans and carry out the statistical analysis.
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Research Interests

  • Image analysis for large studies of abnormal subjects.
  • Exploratory analysis methods for neuroimaging.
  • Computational anatomy.
  • Segmentation methods.
  • Multiple object tracking, matching and registration. Application areas include matching of 2D gels and tracking platelets.
  • Coupled tracking and segmentation.
  • Region based segmentation methods.
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Major Collaborations

  • Monash-CSIRO Collaborative Research in Carotid Flow Modelling
  • The Australian Mouse Brain Mapping Consortium (involving Monash University, Queensland Brain Institute (University of Queensland), University of New South Wales (POWMRI))
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PhD Thesis

“Image segmentation based on local motion detection”.Department of Electrical and Electronic Engineering, University of Adelaide, 1998.

Journal Publications

1.    Srikanth V, Phan TG, Chen J, Beare R, Stapleton J, Reutens DC. The location of white matter lesions and gait – a voxel-based study. Annals of Neurology 2010 Feb;67(2):265-69
2.    Beare R, Srikanth V, Phan TG, Chen J, Stapleton J, Lipshut R, Reutens DC. Development and validation of morphological segmentation of age-related cerebral white matter hyperintensities. Neuroimage 2009 Aug 1;47(1):199-203
3.    Srikanth V, Beare R, Blizzard L, Phan TG, Stapleton J, Chen J, Callisaya M, Martin K, Reutens DC. Cerebral White Matter Lesions, Gait and the Risk of Incident Falls: a prospective population-based study. Stroke , 2009 Jan 40(1) 175-80
4.    C. Sun, R. Beare, K. Cheong, B.J. Jung, and M. Kim. Stereoscopic flatbed scanner. Journal of Electronic Imaging, 2009 Jan;18(1):1-6.
5.    Y. Glickmann-Johnston, M. Saling, J. Chen, K. Cooper, R. Beare, and D. Reutens. Structural and functional correlates of unilateral mesial temporal lobe spatial memory impairment. Brain, 2008 Nov;131(Pt 11):3006-18.
6.    R. Beare, K. Richards, S. Petrou, and D. Reutens. An assessment of methods for aligning two dimensional microscope sections to create image volumes. Journal of Neuroscience Methods, 2008 May 30;170(2):332-44.
7.    M. Berman, R. Beare, D. Coward, L. Whitbourn, C. Evans, Osborne. B., P. Connor,
8.    R. Phillips, and R. Quodling. Measurement of wheat grain thickness using profilometry. Cereal Chemistry, 2007 May 84(3):282–84.
9.    R. Beare. A locally constrained watershed transform. IEEE Transactions on Pattern Analysis and Machine Intelligence, 2006 Jul;28(7):1063-74.
10.    C. Sun, R. Beare, V. Hilsenstein, and P. Jackway. Mosaicing of microscope images with global geometric and radiometric corrections. Journal of Microscopy, 2006 Nov;224(Pt 2):158-65
11.    C. Sun, R. Jones, H. Talbot, X. Wu, K. Cheong, R. Beare, M. Buckley, and M. Berman. Measuring the distance of vegetation from powerlines using stereo vision. ISPRS Journal of Photogrammetry and Remote Sensing, 2006 Jun;60(4):269–83.
12.    R. Beare and A. Bouzerdoum. Biologically inspired local motion detection architecture. Journal of the Optical Society of America, 1999;16(9):2059–68
13.    Moini, A. Bouzerdoum, K. Eshraghian, A. Yakovleff, X. T. Nguyen, A. Blanksby,
R. Beare, D. Abbott, and R. E. Bogner. An insect vision-based motion detection chip. IEEE Journal of Solid-State Circuits, 1997 Feb;32(2):279–84

Open Access Publications

1.    R. Beare. Morphology with parabolic structuring elements. The Insight Journal, May 2008.
2.    R. Beare. Grayscale morphological attribute operations. The Insight Journal, November 2007.
3.    R. Beare. Imagelineariterator - withindex removed. The Insight Journal, October 2007.
4.    R. Beare. Image mask adaptor for pixel order independent filters. The Insight Journal, August 2007.
5.    R. Beare. Label object representation and manipulation with ITK. The Insight Journal, July 2007.
6.    R. Beare. Efficient implementation of kernel filtering. The Insight Journal, August 2007.
7.    R. Beare. Some extra image logical operations. The Insight Journal, February 2007.
8.    R. Beare. Consolidated morphology. The Insight Journal, July 2006.
9.    R. Beare and G. Lehmann. The watershed transform in itk - discussion and new developments. The Insight Journal, June 2006.
10.    R. Beare. Improving performance of morphological reconstruction. The Insight Journal, February 2006.
11.    R. Beare. Optimization of connected component labelling. The Insight Journal, February 2006.
12.    R. Beare and G. Lehmann. Finding regional extrema - methods and performance. The Insight Journal, December 2005.

Books
H. Talbot and R. Beare, editors. Mathematical Morphology, Proceedings of the VIth International Symposium – ISMM 2002. CSIRO Publishing, 2002.

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List of Grants for 2002-2009

  • 2006: Grant Type – ARC Linkage, Equipment, Infrastructure, Facilities. Project – Distributed Medical Image Analysis and Visualisation Engine (MedVis). Investigators: Prof H Schmidt, Dr R Beare.
  • 2007: Grant Type – Monash-CSIRO Collaborative Research Support Scheme. Project – Geometric Model Creation for blood flow simulation. Investigators – Beare, Phan, Srikanth, Sinnott.
  • 2008: Grant Type - Victorial Partnership for Advanced Computing, e-Research Program Grant Scheme. Project – Flexible annotated medical image data store. Investigator – Beare.
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Stroke and Ageing Research