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Prof J. Andrew Bangham

J. Andrew Bangham
Job Title Contact Location
Emeritus Professor  A dot Bangham at uea dot ac dot uk
Tel: +44 (0)1603 59 2245   		Environmental 2.16 
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Biography

Recently the Head of Computing Science, Bangham has returned to the interface between biology and computing and founded the UEA D’Arcy Thompson Centre for computational biology.
 
One goal of which is to understand the algorithms underpinning the evolution and growth of plants. In a  collaboration with Prof. Enrico Coen (in the neighbouring John Innes Centre), he leads the computing science behind an integrated plant biology and computing science project to model the growing leaf and meristem. Fluorescent probes are incorporated into plants and imaged in two and three dimensions using optical projection tomography and confocal microscopy. Our visualisation tools include haptics and automatic methods for analysing finite element and cell-based models.This work highlights the importance of hierarchies of spatio-temporally separated gene expression patterns.
 
Previously Bangham founded the UEA Computing Science computer vision laboratory where he contributed to non-linear mathematical morphology. The laboratory continues to use the scale-space conserving algorithms, sieves, to find and exploit what are sometimes termed maximally stable, extremal, regions and salient contours. Sieves are also used to generate robust features for characterising images and image sequences, for example, for lip-reading.
 
Having trained at University College London, it was work on integrating computing methods with the electrophysiology of the giant axon, insulin secreting beta-cells and patch clamping lens cells that provoked a need for robust signal filtering and led to the new, patented, mathematical morphology algorithms and it was to study these that he moved from UEA Biology to the School of Computing. On the way he also founded Fo2PiX, a software company based in Cambridge that exploited the intellectual property to create tools for making pictures from digital photographs.

Career

University College London Physiology/Biophysics, University of East Anglia Biology, University of East Anglia Computing Sciences.

Key Research Interests

Andrew Bangham is part of the Computational Biology Group

Computational biology. Starting in the 1990’s but particularly since 2000 Bangham has collaborated with Enrico Coen (John Innes Centre) introducing a computational approach to the analysis and modelling of plant growth. Image analysis methods are applied to three dimensional images of growing plant organs and provide new perspectives on the hierarchy of genetic factors that affect growth and the evolution of plants.

Computer vision.  Our algorithms that transform images into scale-space preserving, segmentation, hierarchies namely sieves are being improved. They provide robust visual features for characterising points and regions, sometimes known as maximally stable extremal regions and salient contours. The computer vision laboratory is extending early work using these features for lipreading and for finding images.

Some of the papers are collaborations with biologists and in these Bangham leads the computational aspects of the research.

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Selected Publications

  1. Kennaway R, Coen E, Green A, Bangham A, Generation of Diverse Biological Forms through Combinatorial Interactions between Tissue Polarity and Growth. 2011 PLoS Comput Biol 7(6): e1002071. doi:10.1371
  2. Green AA, Kennaway JR, Hanna AI, Bangham JA, Coen E, Genetic Control of Organ Shape and Tissue Polarity. 2010 PLoS Biol 8(11): e1000537.
  3. Cui M-L, Copsey L, Green AA, Bangham JA, Coen E, Quantitative Control of Organ Shape by Combinatorial Gene Activity. 2010 PLoS Biol 8(11): e1000538. doi:10.1371
  4. Xianzhong Feng, Yvette Wilson, Jennifer Bowers, Richard Kennaway, Andrew Bangham, Andrew Hannah, Enrico Coen and Andrew Hudson Evolution of Allometry in Antirrhinum 2009 The Plant Cell 21:2999-3007
  5. Whibley, A. C., Langlade, N. B., Andalo, C., Hanna, A. I., Bangham, A., Thebaud, C. & Coen, E., Evolutionary Paths Underlying Flower Color Variation in Antirrhinum. Science, 2006. 313(5789): p. 963 - 966.
  6. Lee, K., J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, A. Bangham, and E. Coen, Visualizing Plant Development and Gene Expression in Three Dimensions Using   Optical Projection Tomography. Plant Cell, 2006: p. tpc.106.043042.
  7. Bangham, A.J., B.d.l. Iglesia, G. Buratti, and D. Montesi, Data Model and Query Languages for Biological Databases. Multimedia Communications E-Letter of the IEEE Communications Society, 2005. 2(2): p. 7-10.
  8. Nicolas B. Langlade , X.F., Tracy Dransfield, Lucy Copsey, Andrew I. Hanna , Christophe Thébaud, Andrew Bangham , Andrew Hudson and Enrico Coen, Evolution through genetically controlled allometry space. Proceedings of the National Academy of Sciences of the United States of America, 2005. 102(29): p. 10221-10226.
  9. Rolland-Lagen, A.-G., E. Coen, S. Impey, and J.A. Bangham, A computational method for inferring growth parameters and shape changes during development based on clonal analysis. Journal of Theoretical Biology, 2005. 232: p. 157-177. 
  10. Theobald, B., J.A. Bangham, I. Matthews, and G.C. Cawley, Near-videorealistic synthetic talking faces: Implementation and evaluation. Speech Communication, 2004. 44(1-4): p. 127-140.
  11. Rolland-Lagan, A.-G., A.J. Bangham, and E. Coen, Growth dynamics underlying petal shape and asymmetry. Nature, 2003. 422: p. 161-163. 
  12. Matthews, I.A., T. Cootes, J.A. Bangham, S.J. Cox, and R.W. Harvey, Extraction of Visual Features for Lipreading. IEEE Trans. on Pattern Analysis and Machine Intelligence, 2002. 24(2): p. 198--213.
  13. Bangham, J.A., P. Ling, and R. Young, Multiscale recursive medians, scale-space, and transforms with applications to image processing. IEEE Trans. on Image Processing, 1996. 5(6): p. 1043-1048. 
  14. Impey, S. and J.A. Bangham. Improvements to the 'top hat' transform used for analysing pigmented patches on flower petals. in Signal Processing VII, 'Theories and applications. 1994.
  15. Bangham, J.A., Properties of a Series of Nested Median Filters, Namely the Data Sieve. IEEE Trans. on Signal Processing, 1993. 41(1): p. 31-42 
 
Selected software publications
  1. (Avondo, J. (2006) OPTView Bioptonics Edinburgh, written by gradiate student Jerome Avondo, see [2]).
  2. Courtenay, A. and Bangham, J.A., (2005) ArtMaster Fo2PiX, Cambridge (a family of software applications for PC and Mac, currently sold over 60,000 licences). 
  3. J. Andrew Bangham, (1984) StatsStream Elsevier Cambridge (a statistical package for the Apple II.

List all publications by Professor Andrew Bangham (Eprints)


Research Group Members

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Post Docs

Dr. Andy Hanna, image analysis

Dr. Richard Kennaway, finite element modelling

Dr. Pierre Barbier de Reuille (Jointly with J.I.C.)

Students

Johann Strasser, three dimensional image analysis and haptics

Alberto Pastrana Palma, image retrieval

Jerome Avondo, three dimensional image rendering

Recent Alumni

Dr. Iain Matthews

Dr. Lilian Blot

Collaborators

Laboratories of Enrico Coen (John Innes Centre) and Richard Harvey


Current Research Projects and Grants

Project Title Start Date End Date Funding Body Project Members
A Multiscale Approach to Genes, Growth and Geometry 1/3/2008 28/2/2013 BBSRC Andrew Bangham


Past Research Projects and Grants

Project Title Start Date End Date Funding Body Project Members
Modelling growth and gene regulation in floral organs 1/6/2008 31/5/2011 BBSRC Andrew Bangham
Spatio-temporal modeling network on plant systems (STEMN) 1/11/2007 31/10/2010 BBSRC Andrew Bangham
Renishaw Plc and DTI Knowledge Transfer Partnership 1/6/2006 31/5/2008 Renishaw Plc. Rudy Lapeer, Andrew Bangham
Developmental genetics of allometric variation between species 1/1/2006 31/12/2008 BBSRC Andrew Bangham
Dynamic growth maps of development 16/2/2004 15/2/2007 BBSRC Andrew Bangham
Closed-signing for broadcast 1/10/2003 30/9/2005 Department of Trade and Industry Andrew Bangham, John Glauert
Virtual Signing: Capture, Animation, Storage and Transmission (VISICAST) 1/1/2000 31/12/2002 CEC (Framework 1-5) Ralph Elliott, Stephen Cox, Andrew Bangham, John Glauert

Jump to: Article | Book Section | Conference or Workshop Item | Patent | Software
Number of items: 49.

Article

Kennaway, R, Coen, E, Green, A and Bangham, A (2011) Generation of diverse biological forms through combinatorial interactions between tissue polarity growth. PLoS Computational Biology, 7 (6). p. 22.

Leyser, O, Green, AA, Kennaway, R, Hanna, AI, Bangham, JA and Coen, E (2010) Genetic Control of Organ Shape and Tissue Polarity. PLoS Biology, 8 (11). e1000537. ISSN 1545-7885

Feng, X, Wilson, Y, Bowers, J, Kennaway, R, Bangham, A, Hannah, A, Coen, E and Hudson, A (2009) Evolution of Allometry in Antirrhinum. Plant Cell, 21. pp. 2999-3007.

Lee, K, Strasser, J, Avondo, J, Southam, P, Bangham, A and Coen, E (2009) Visualising plant growth and shape in 3D using optical projection tomography. Mechanisms of Development, 126 (1). S93.

Bensmihen, S, Hanna, AI, Langlade, NB, Bangham, A and Coen, ES (2008) Mutational spaces for leaf shape and size. HFSP Journal, 2 (2). pp. 110-120.

Lee, K, Avondo, J, Morrison, H, Blot, L, Stark, M, Sharpe, J, Bangham, A and Coen, E (2006) Visualizing Plant Development and Gene Expression in Three Dimensions Using Optical Projection Tomography. The Plant Cell, 18 (9). pp. 2145-2156. ISSN 1040-4651

Whibley, AC, Langlade, NB, Andalo, C, Hanna, A, Bangham, A, Thébaud, C and Coen, E (2006) Evolutionary Paths Underlying Flower Color Variation in Antirrhinum. Science, 313 (5789). 963 - 966. ISSN 0036-8075

Langlade, N, Feng, Z, Dransfield, T, Copsey, L, Hanna, A, Thébaud, C, Bangham, JA, Hudson, A and Coen, E (2005) Evolution through genetically controlled allometry space. Proceedings of the National Academy of Sciences of the United States of America, 102 (29). pp. 10221-10226. ISSN 1091-6490

Rolland-Lagan, A-G, Coen, E, Impey, SJ and Bangham, JA (2005) A computational method for inferring growth parameters and shape changes during development based on clonal analysis. Journal of Theoretical Biology, 232 (2). pp. 157-177. ISSN 0022-5193

Bangham, JA, de la Iglesia, B, Buratti, G and Montesi, D (2005) Data Model and Query Languages for Biological Databases. Multimedia Communications E-Letter of the IEEE Communications Society (2). pp. 7-10.

Theobald, B, Bangham, JA, Matthews, I and Cawley, GC (2004) Near-videorealistic synthetic talking faces: Implementation and evaluation. Speech Communication, 44 (1-4). pp. 127-140. ISSN 0167-6393

Coen, E, Rolland-Lagen, A-G, Matthews, M, Bangham, JA and Prusinkiewicz, P (2004) The genetics of geometry. Proceedings of the National Academy of Sciences USA, 101 (14). pp. 4728-4735. ISSN 0027-8424

Theobald, BJ, Kruse, SM, Bangham, JA and Cawley, GC (2003) Towards a low bandwidth talking face using appearance models. Image and Vision Computing, 21 (13-14). pp. 1117-1124. ISSN 0262-8856

Rolland-Lagan, A-G, Bangham, JA and Coen, E (2003) Growth dynamics underlying petal shape and asymmetry. Nature, 422. pp. 161-163. ISSN 0028-0836

Matthews, I, Cootes, TF, Bangham, JA, Cox, SJ and Harvey, RW (2002) Extraction of Visual Features for Lipreading. IEEE Transactions on Pattern Analysis and Machine Intelligence, 24 (2). pp. 198-213. ISSN 0162-8828

Yli-Harja, O, Koivisto, P, Bangham, JA, Cawley, GC, Harvey, RW and Shmulevich, I (2001) Simplified implementation of the recursive median sieve. Signal Processing, 81 (7). pp. 1565-1570. ISSN 0165-1684

Moravec, K, Harvey, RW and Bangham, JA (2000) Scale trees for stereo vision. IEE Proceedings: Vision, Image and Signal Processing, 147 (4). pp. 363-370. ISSN 1350-245X

Bangham, JA, Harvey, RW, Ling, PD and Aldridge, RV (1996) Morphological scale-space preserving transforms in many dimensions. The Journal of Electronic Imaging (JEI), 5 (3). pp. 283-299.

Bangham, JA, Chardaire, P, Pye, CJ and Ling, PD (1996) Multiscale nonlinear decomposition: The sieve decomposition theorem. IEEE Transactions on Pattern Analysis and Machine Intelligence, 18 (5). pp. 529-539. ISSN 0162-8828

Bangham, JA, Ling, PD and Harvey, RW (1996) Scale-space from nonlinear filters. IEEE Trans. Pattern Analysis and Machine Intelligence, 18 (5). pp. 520-528.

Bangham, JA, Ling, P and Young, R (1996) Multiscale recursive medians, scale-space, and transforms with applications to image processing. IEEE Transactions on Image Processing, 5 (6). pp. 1043-1048. ISSN 1057-7149

Bangham, JA, Campbell, TG and Aldridge, RV (1994) Multiscale Median and Morphological Filters for 2D Pattern Recognition. Signal Processing, 38 (3). pp. 387-415.

Bangham, JA (1993) Properties of a Series of Nested Median Filters, Namely the Data Sieve. IEEE Transactions on Signal Processing, 41 (1). pp. 31-42. ISSN 1053-587X

Book Section

Theobald, B, Bangham, JA, Kruse, S, Cawley, GC and Matthews, I (2001) Towards videorealistic synthetic visual speech. In: Uncertainty in Geometric Computations. The Kluwer International Series in Engineering and Computer Science, 704 . Kluwer Academic Publishers, pp. 175-184. ISBN 978-0-7923-7309-4

Bangham, JA, Harvey, RW, Ling, PD and Aldridge, RV (1996) Nonlinear scale space from n-dimensional sieves. In: 4th European Conference on Computer Vision (ECCV '96). Lecture Notes in Computer Science, 1064 . Springer, Berlin / Heidelberg, pp. 189-198. ISBN 3-540-61122-3

Bangham, JA (1990) Linking Real-Time Measurement with Cal. In: Computer Assisted Learning. Lecture Notes in Computer Science, 438 . Springer, Berlin / Heidelberg, pp. 225-234.

Conference or Workshop Item

Southam, P, Strasser, J, Lee, K, Avondo, J and Bangham, A (2009) UFEEL: using haptics and stereo to place landmarks in three-dimensional volumetric images. In: IEEE.

Theobald, B, Cawley, G, Bangham, A and Matthews, I (2008) Comparing text-driven and speech-driven visual speech synthesisers. In: Interspeech.

Bangham, JA, Gibson, SE and Harvey, RW (2003) The Art of Scale-Space. In: British Machine Vision Conference, 9th-11th September 2003, University of East Anglia, Norwich, UK.

Theobald, B-J, Bangham, JA, Matthews, I and Cawley, GC (2003) Evaluating talking heads based on appearance models. In: Proceedings of the International Conference on Auditory-Visual Speech Processing (AVSP-2003), September 4-7, 2003, St. Jorioz, France.

Theobald, BJ, Cawley, GC, Matthews, I and Bangham, JA (2003) Near-videorealistic synthetic visual speech using non-rigid appearance models. In: Proceedings of the IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP '03), 6-10 April 2003, Hong Kong, China.

Theobald, B, Bangham, JA, Matthews, I and Cawley, GC (2002) Towards video realistic synthetic visual speech. In: IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP- 2002), 13-17 May 2002, Orlando, Florida.

Theobald, B, Bangham, JA, Matthews, I and Cawley, GC (2001) Visual speech synthesis using statistical models of shape and appearance. In: International Conference on Auditory-Visual Speech Processing (AVSP-2001), September 7-9, 2001, Aalborg, Denmark.

Bangham, JA, Cox, SJ, Elliott, R, Glauert, JRW, Marshall, I, Rankov, S and Wells, M (2000) Virtual Signing: Capture, Animation, Storage and Transmission - an overview of the ViSiCAST Project. In: IEE Colloquium on Speech and Language Processing for the Disabled and Elderly, 4 April 2000, London, UK.

Bangham, JA, Cox, SJ, Lincoln, M, Marshall, I, Tutt, M and Wells, M (2000) Signing for the deaf using virtual humans. In: IEE Colloquium on Speech and Language processing for Disabled and Elderly.

Chan, Y, Harvey, RW and Bangham, JA (2000) Using colour features to block dubious images. In: European Signal Processing Conference (Eusipco).

Fisher, MH, Mandic, DP, Bangham, JA and Harvey, RW (2000) Visualising error surfaces for adaptive filters and other purposes. In: IEEE International Conference Acoustics Speech and Signal Processing, ICASSP2000, 05 Jun 2000 - 09 Jun 2000, Istanbul, Turkey.

Pezeshkpour, F, Marshall, I, Elliott, R and Bangham, JA (1999) Development of a Legible Deaf Signing Virtual Human. In: IEEE International Conference on Multimedia Computing and Systems '99 (IEEE ICMCS '99), 07 Jun 1999 - 11 Jun 1999, Florence, Italy.

Bangham, JA, Harvey, RW and Tattersall, G (1998) Recognition of image patterns generated by a stochastic object-replacement model. In: IEEE Conference on Image Processing, 4-7 Oct 1998 , Chicago, IL .

Bangham, JA, Ling, PD and Harvey, RW (1995) Scale space from Nonlinear filters. In: Fifth Internation Conference on Computer Vision, 20 Jun 1995 - 23 Jun 1995, Cambridge, MA, USA.

Chardaire, P, Bangham, JA, Pye, CJ and Wu, DQ (1994) Properties of multiscale morphological filters namely the morphology decomposition theorem. In: SPIE Nonlinear signal processing.

Pye, CJ and Bangham, JA (1994) 2D pattern recognition using 1D sieves based on alternating sequential, root median and self-dual filters. In: Signal Processing VII, 'Theories and applications' (EUSIPCO-94), 13-16 Sept 1994, Edinburgh, UK.

Bangham, JA and Aldridge, RV (1993) Multiscale decomposition using median and morphological filters. In: IEEE Winter Workshop on Nonlinear Digital Signal Processing, Jan. 17-20, 1993.

Aldridge, RV, Bangham, JA and Campbell, TG (1993) Decomposition of signals by scale using non-linear filters. In: A workshop on the applications of wavelet transforms in image processing, IEE.

Bangham, JA and Campbell, TG (1993) Sieves and wavelets: multiscale transforms for pattern recognition. In: IEEE Winter Workshop on Nonlinear Digital Signal Processing, Jan. 17-20, 1993.

Patent

Cambridge Consultants Limited (2000) Data processing method and apparatus. 6081617.

Cambridge Consultants Limited (1999) Pulse analysis using ordinal value filtering. 5917733.

Cambridge Consultants Limited (1999) Data processing method and apparatus. 5912826.

Software

Courtenay, A and Bangham, JA (2004) ArtMaster. [Software]

This list was generated on Thu Feb 9 08:03:29 2012 GMT.

External Activities and Indicators of Esteem

  • External Faculty Member of the John Innes Centre

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