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Chris Glasbey

BioSS Associate (ex Head of Research)

Biomathematics and Statistics Scotland
JCMB, The King's Buildings,
Peter Guthrie Tait Road,
EDINBURGH, EH9 3FD, Scotland, UK.

Tel: +44 (0)131 650 4899 (or 4900)
Fax: +44 (0)131 650 4901

Email: Chris Glasbey

I took early retirement in August 2013 and am now working for BioSS on a contract basis.

My area of research is spatial and temporal models, including image analysis and bioinformatic applications. I held honorary/visiting professorships at Heriot-Watt and Edinburgh Universities, SRUC and Queensland University of Technology, Australia. In 2009 I was elected to Fellowship of The Royal Society of Edinburgh. Also I'm on Google Street: the man wearing sunhat, sunspecs and blue fleece, queuing for ticket to Isle of May (May 2009).

A book on image analysis, most of my more recent methodological papers and slides of some talks are available as pdf files:

Image warping and stochastic templates

• Automatic fruit recognition and counting from multiple images - Song, Y., Glasbey C.A., Horgan, G.W., Polder, G., Dieleman, J.A. and van der Heijden, G.W.A.M, 2014 (Biosystems Engineering, 118, 203-215).
• Non-destructive automatic leaf area measurements by combining stereo and Time-of-Flight images - Song, Y., Glasbey C.A., Polder, G. and van der Heijden, G.W.A.M., 2014 (IET Computer Vision, 8, 391-403).
• Automatic phenotyping: estimating fruit numbers by clustering repeated, incomplete observations - Glasbey C.A., Song, Y., Horgan, G.W., van der Heijden, G.W.A.M. and Polder, G. (slides from IBS Channel Network Conference, St Andrews, June 2013).
• Dynamic programming versus graph cut algorithms for phenotyping by image analysis - Glasbey C.A. (slides from ANZIAM'13, Newcastle, Australia, February 2013).
• SPICY: towards automated phenotyping of large pepper plants in the greenhouse - van der Heijden, G., Song, Y., Horgan, G., Polder, G., Dieleman, A., Bink, M., Palloix, A., van Eeuwijk, F. and Glasbey, C., 2012 (Functional Plant Biology, 39, 870-877).
• Semi-automatic 3D segmentation - Glasbey C.A (slides from presentation at FAIM1, Dublin, September 2012).
• Image analysis for automatic phenotyping - Glasbey C.A., Horgan, G.W., Song Y., van der Heijden G.W.A.M. and Polder G. (slides from presentation at symposium 'Improving yield prediction by combining statistics, genetics, physiology and phenotyping: the EU SPICY project in pepper', Wageningen, The Netherlands, March 2012).
• Combining stereo and Time-of-Flight images with application to automatic plant phenotyping - Song Y., Glasbey C.A., van der Heijden G.W.A.M., Polder G. and Dieleman J.A. 2011 (Image Analysis: 17th Scandinavian Conference, SCIA2011 (A. Heyden and F. Kahl, eds.). Lecture Notes in Computer Science 6688, Springer: Berlin, ISBN: 9783642212260, pp467-478).
• Algorithms for fitting non-parametric models to image data: Part 1, Part 2 - Glasbey, C.A (Slides from workshop at QUT, Brisbane, May 2011).
• Dynamic programming versus graph cut algorithms for fitting non-parametric models to image data - Glasbey, C.A 2010 (Proceedings of the 25th International Workshop on Statistical Modelling, A.W. Bowman, ed., University of Glasgow Printing Unit) and slides from seminar at Stochastic Centre, Chalmers University, Gothenburg, Sweden, June 2011.
• Two-dimensional generalisations of dynamic programming for image analysis - Glasbey, C.A. 2009 (Statistics and Computing, 19, 49-56).
• A statistical approach to image warping - Glasbey, C.A. 2008. (Slides from IV Workshop de Laser e Optica na Agricultura, Universidade Federal de Lavras, Brazil, October.)
• Alignment and sub-pixel interpolation of images using Fourier methods - Glasbey, C.A. and van der Heijden, G.W.A.M. 2007 (Journal of Applied Statistics, 34, 217-230).
• Maximum a posteriori estimation of image boundaries by dynamic programming - Glasbey, C.A. and Young, M.J., 2002 (Applied Statistics, 51, 209-221).
• A penalized likelihood approach to image warping - Glasbey, C.A.and Mardia, K.V., 2001 (Journal of the Royal Statistical Society, Series B, 63, 465-514). The data used in the paper are also available at ftp://ftp.bioss.sari.ac.uk/pub/chris/warping/
• A review of image warping methods - Glasbey, C.A. and Mardia, K.V., 1998 (Journal of Applied Statistics, 25, 155-171).
• Ultrasound image segmentation using stochastic templates - Glasbey, C.A., 1998 (Journal of Computing and Information Technology, 6, 107-116).
• SAR image registration and segmentation using an estimated DEM - Glasbey, C.A., 1997. In "Energy Minimization Methods in Computer Vision and Pattern Recognition" (M. Pelillo and E.R. Hancock, eds.). Lecture Notes in Computer Science 1223, Springer: Berlin, 507-520.

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Spatial, temporal and latent Gaussian models

• Tobit models for multivariate, spatio-temporal and compositional data - Glasbey, C.A., Allcroft, D.J. and Butler, A. (Slides from CoDaWork 2013, Austria, June 2013).
• Tobit models for analysing data with a preponderance of zeros - Glasbey, C.A. (Slides from Theme 6 workshop on "Health & Welfare", October 2011).
• Confidence intervals for Cavalieri sampling - Glasbey, C.A. (Slides from XXVth International Biometric Conference, Florianopolis, Brazil, December 2010).
• Spatio-temporal weather models - Glasbey, C.A. and Allcroft, D.J. (Slides from talk at PASCAL2 workshop "Spatiotemporal Modelling", University of Edinburgh, October 2009).
• Standard errors in systematic sampling - Glasbey, C.A. and Bierman, S. 2008. (Slides from seminar at Departamento de Ciencias Exatas, Universidade Federal de Lavras, Brazil, October.)
• A latent Gaussian model for compositional data with zeros - Butler, A. and Glasbey, C.A. 2008 (Applied Statistics, 57, 505-520).
• A spatiotemporal auto-regressive moving average model for solar radiation - Glasbey, C.A. and Allcroft, D.J. 2008 (Applied Statistics, 57, 343-355), and slides from talk at RSS'08.
• A latent Gaussian model for multivariate consumption data - Allcroft, D.J., Glasbey, C.A., and Paulo, M.J. 2007 (Food Quality and Preference, 18, 508-516).
• The importance of `memory' in statistical models for animal feeding behaviour - Allcroft, D.J., Tolkamp, B.J., Glasbey, C.A. and Kyriazakis, I. 2004 (Behavioural Processes, 67, 99-109).
• Analysis of crop lodging using a latent variable model - Allcroft, D.J. and Glasbey, C.A., 2003 (Journal of Agricultural Science, 140, 383-393).
• A latent Gaussian Markov random field model for spatio-temporal rainfall disaggregation - Allcroft, D.J. and Glasbey, C.A., 2003 (Applied Statistics, 52, 487-498).
• A simulation-based method for model evaluation - Allcroft, D.J. and Glasbey, C.A., 2003 (Statistical Modelling, 3, 1-13).
• A spectral estimator of ARMA parameters from thresholded data - Allcroft, D.J. and Glasbey, C.A., 2002 (Statistics and Computing, 12 369-376).
• Spatial disaggregation of rainfall using a latent Gaussian Markov random field - Allcroft, D.J. and Glasbey, C.A., 2002. (Proceedings of the 17th International Workshop on Statistical Modelling, 85-93).
• Modelling weather data - Allcroft, D.J., Glasbey, C.A. and Durban, M. (SCRI Annual Report 2001, 192-195).
• Weather modelling using a multivariate latent Gaussian model - Durban, M. and Glasbey, C.A., 2001 (Agricultural and Forest Meteorology, 109, 187-201).
• Nonlinear autoregressive times series with multivariate Gaussian mixtures as marginal distributions - Glasbey, C.A., 2001 (Applied Statistics, 50, 143-154). Data available at ftp://ftp.bioss.sari.ac.uk/pub/chris/solardata.zip
• Estimation of latent Gaussian ARMA models for categorical behaviour data - Allcroft, D.J. and Glasbey, C.A., 2000. In "Statistical Modelling: Proceedings of the 15th International Workshop on Statistical Modelling" (V. Nunez-Anton and E. Ferreira, eds.). Universidad del Pais Vasco: Bilbao, Spain, 294-299.
• Parameter estimators for Gaussian models with censored time series and spatio-temporal data - Glasbey, C.A., Nevison, I.M., and Hunter, A.G.M., 1998. In "COMPSTAT98 Proceedings in Computational Statistics" (R. Payne and P. Green, eds.). Physica-Verlag: Heidelberg, 323-328.
• Rainfall modelling using a latent Gaussian variable - Glasbey, C.A. and Nevison, I.M., 1997. In "Modelling Longitudinal and Spatially Correlated Data: Methods, Applications, and Future Directions" (T.G. Gregoire, D.R. Brillinger, P.J. Diggle, E. Russek-Cohen, W.G. Warren and R.D. Wolfinger, eds.). Lecture Notes in Statistics 122, Springer: New York, 233-242.

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Bioinformatics

• Efficiency of functional regression estimators for combining multiple laser scans of cDNA microarrays - Glasbey, C.A. and Khondoker, M.R. 2009 (Biometrical Journal, 51, 45-55) and slides from talk given to RSS Bioinformatics Study Group, Edinburgh, July 2007.
• A comparison of parametric and nonparametric methods for normalising cDNA microarray data - Khondoker, M.R., Glasbey, C.A. and Worton, B.J. 2007 (Biometrical Journal, 49, 815-823).
• Estimation of expression levels in spotted microarrays with saturated pixels - Glasbey, C.A., Forster, T. and Ghazal, P. 2007 (Statistical Applications in Genetics and Molecular Biology, 6, article 34). Fortran90 subroutines implementing these methods are also available.
• Warping of electrophoresis gels using generalisations of dynamic programming - Glasbey, C.A. (Workshop on Interdisciplinary Statistics and Bioinformatics, Leeds, July 2006), and slides.
• The challenge of bioinformatics - Glasbey, C.A. (Slides from a talk at a joint meeting of Rothamsted Research and the British and Irish Region of the International Biometric Society, Rothamsted, January 2006.)
• Statistical estimation of gene expression using multiple laser scans of microarrays - Khondoker, M.R., Glasbey, C.A. and Worton, B.J. 2006 (Bioinformatics, 22, 215-219). Software implementing this method is available either via a BioSS web interface MultiScan or within Bioconductor as the multiscan package.
• A statistical model for unwarping of 1-D electrophoresis gels - Glasbey, C.A., Vali, L. and Gustafsson, J.S. 2005 (Electrophoresis, 26, 4237-4242).
• Correction for pixel censoring in cDNA microarrays - Glasbey, C.A. and Khondoker, M.R., 2005 (In "Statistical Solutions to Modern Problems: Proceedings of the 20th International Workshop on Statistical Modelling", eds. A.R. Francis, K.M. Matawie, A. Oshlack, G.K. Smyth, 17-31.)
• Combinatorial image analysis of DNA microarray features - Glasbey, C.A. and Ghazal, P., 2003 (Bioinformatics, 19, 194-203). Fortran90 subroutines implementing these methods are also available.
• Identification of differential gene expression from DNA microarrays - Glasbey, C.A., 2001 (workshop on Functional and Spatial Data Analysis, Leeds, 15-17).

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Digital microscopy

• Colour displays for categorical images - Glasbey, C.A., van der Heijden, G.W.A.M., Toh, V.F.K. and Gray, A.J. 2007 (Color Research and Application, 32, 304-309).
• Estimation of centres and radial intensity profiles of spherical nano-particles in digital microscopy - Kvarnstrom, M. and Glasbey, C.A. 2007 (Biometrical Journal, 49, 300-311).
• The application of multivariate statistical methods to NMR imaging - Glasbey, C.A. and Glidewell, S.M., 2001 (Computers and Electronics in Agriculture, 32, 85-100).
• Towards automatic cell identification in DIC microscopy - Young, D., Glasbey, C.A., Gray, A.J. and Martin, N.J., 1998 (Journal of Microscopy, 192, 186-193).
• Recovery of depth information from optical microscope images by constrained deconvolution - Glasbey, C.A. and Perkins, M.G. (Scandinavian Image Analysis Conference - 97SCIA, Lappeenranta, Finland, June 1997)
• Statistical analysis of the distribution of gold particles over antigen sites after immunogold labelling - Glasbey, C.A. and Roberts, I.M., 1997 (Journal of Microscopy, 186, 258-262).
• Problems in digital microscopy - Glasbey, C.A., 1996 (Invited Paper at XVIIIth International Biometric Conference, Amsterdam, 183-200).
• Multimodality microscopy by digital image processing - Glasbey, C.A. and Martin, N.J., 1996 (Journal of Microscopy, 181, 225-237).

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Other image analysis

• Plant phenotyping in SPICY - Glasbey C.A. (slides from presentation at Eucarpia satellite meeting, Hohenheim, Germany, September 2012).
• Seeing is believing? - Glasbey, C.A. (Inaugural professorial lecture, SAC,April 2005).
• Estimators of tissue proportions from X-ray CT images - Glasbey, C.A. and Robinson, C.D., 2002 (Biometrics, 58, 928-936).
• Nonparametric estimators of 2D spectra beyond the Nyquist frequency - Glasbey, C.A., 2001 (workshop on "Functional and Spatial Data Analysis", Leeds, 131-135).
• Optimal linear interpolation of images with known point spread function - Glasbey, C.A., 2001 (Scandinavian Image Analysis Conference - SCIA2001, 161-168).
• Image analysis in agricultural research - Glasbey, C.A. and Horgan, G.W., 2001 (Quantitative Approaches in Systems Analysis, 23, 43-54).
• Image analysis: Encyclopaedia of Environmetrics - Glasbey, C.A. and Horgan, G.W., 2001 (Encyclopaedia of Environmetrics, 2, 1023-1025).
• Estimation of tissue proportions in X-ray CT images using a new mixed pixel distribution - Glasbey, C.A. and Robinson, C.D., 1999 (Task Quarterly, 3, 409-418).
• Inference from X-ray CT images of sheep - Glasbey, C.A.and Robinson, C.D., 1999 (Invited presentation at 52nd ISI Session, Helsinki, Finland).
• Image analysis and tomography: Encyclopaedia of Biostatistics - Glasbey, C.A., Berman, M. and Hudson, H.M., 1998. In Encyclopaedia of Biostatistics, (P. Armitage and T. Colton, eds.). Wiley: Chichester, pp 1980-1998.
• Fast computation of moving average and related filters in octagonal windows - Glasbey, C.A. and Jones, R., 1997 (Pattern Recognition Letters, 18, 555-565).
• Binary image restoration at subpixel resolution - Hitchcock, D. and Glasbey, C.A., 1997 (Biometrics, 53, 1040-1053).
• Inference on binary images from binary data - Glasbey, C.A., 1996 (Advances in Applied Probability, 28, 627-640).
• Towards automatic interpretation of sheep ultrasound scans - Glasbey, C.A., Abdalla, I. and Simm, G., 1996 (Animal Science, 62, 309-315).

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Image Analysis for the Biological Sciences - Glasbey, C.A. and Horgan, G.W. (published by Wiley in 1995, but now out of print)

• Chapter 1: Introduction
• Chapter 2: Display
• Chapter 3: Filters
• Chapter 4: Segmentation
• Chapter 5: Mathematical morphology
• Chapter 6: Measurement
• Chapter 7: Summary of results
• Appendix: Hardware and software
• Reference list

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