Andrew French

Contact

• workRoom B70 Computer Science
  Jubilee Campus
  Wollaton Road
  Nottingham
  NG8 1BB
  UK
• andrew.p.french@nottingham.ac.uk
• https://www.nottingham.ac.uk/research/groups/cvl/people/andrew.p.french

Biography

I am interested in Artifical Intelligence (AI) research, particularly related to understanding images. Building an understanding of AI within other disciplines, especially within the biological sciences, has been a focus in recent years, and is increasingly important as AI tools become more powerful.

Research interests include:

· Image analysis of plants and other complex structures

· Developing novel AI software tools to aid biologists

· Deep machine learning approaches

· Artificial intelligence for computer vision

· Automating image capture approaches (e.g. with robotics)

Expertise Summary

Image analysis and computer vision

Biological image analysis

Artificial intelligence methods for computer vision

Deep machine learning

High-throughput plant phenotyping

Experience with a variety of dataset modalities (colour, 3D volumetric, x-ray. MRI, confocal, LSFM etc.)

Data science training provision (via free courses and consultancy)

Teaching Summary

I mainly teach Computer Vision and Schools Experience in Computer Science, and Computer Modelling in Science (Introduction and Applications) in Biosciences. I do supervise final year projects: if you… read more

Research Summary

My research involves developing novel computer science approaches to solve imaging challenges, particularly in bioscience applications. This includes machine learning approaches as well as image… read more

Selected Publications

• MICHAEL POUND, JONATHAN ATKINSON, ALEXANDRA TOWNSEND, MICHAEL WILSON, MARCUS GRIFFITHS, AARON JACKSON, ADRIAN BULAT, GEORGIOS TZIMIROPOULOS, DARREN WELLS, ERIK MURCHIE, TONY PRIDMORE and ANDREW FRENCH, 2017. Deep Machine Learning provides state-of-the-art performance in image-based plant phenotyping Gigascience. gix083
• FRENCH, A.P., MILLS, S., SWARUP, R., BENNETT, M.J. and PRIDMORE, T.P., 2008. Colocalization of fluorescent markers in confocal microscope images of plant cells Nature Protocols. 3(4), 619-628
• IMANOL LUENGO, MARK BASHAM and ANDREW P. FRENCH, 2016. SMURFS: Superpixels from Multi-scale Refinement of Super-regions In: Proceedings of the British Machine Vision Conference 2016.
• FRENCH, A., UBEDA-TOMÁS, S., HOLMAN, T.J., BENNETT, M.J. and PRIDMORE, T., 2009. High throughput quantification of root growth using a novel image analysis tool Plant Physiology. 150(4), 1784-1795

• View all publications

I have offices on Sutton Bonington and Jubilee campuses.

On SB, you can find me in Plant Sciences, C08a. My office in Computer Science is B80. You are welcome to try dropping by, but it is best to email me first for an appointment.

I mainly teach Computer Vision and Schools Experience in Computer Science, and Computer Modelling in Science (Introduction and Applications) in Biosciences. I do supervise final year projects: if you are interested in image analysis, do email me with project ideas.

Current Research

My research involves developing novel computer science approaches to solve imaging challenges, particularly in bioscience applications. This includes machine learning approaches as well as image analysis development.

Research interests include:

· Image analysis of plants and other complex structures

· Developing novel software tools to aid biologists and mathematical modellers

· Deep machine learning approaches

· Automating image capture approaches (e.g. with robotics)

Past Research

Tracking algorithm development: how to track objects in video sequences.

Future Research

Developing deep learning approaches to image analysis.

Phenotyping - automating the characterization of plants using imaging, robotics and automation software to speed up the number of plants we can measure in an experiment.

Segmentation methods, including superpixel approaches.

Hyperspectral imaging

Generating 3D models

MRI segmentation and interpretation.

• GIBBS, JONATHON A., POUND, MICHAEL, FRENCH, ANDREW P., WELLS, DARREN M., MURCHIE, ERIK and PRIDMORE, TONY, 2017. Approaches to three-dimensional reconstruction of plant shoot topology and geometry FUNCTIONAL PLANT BIOLOGY. 44(1), 62-75
• POUND, MICHAEL P., FOZARD, SUSAN, TORRES, MERCEDES TORRES, FORDE, BRIAN G. and FRENCH, ANDREW P., 2017. AutoRoot: open-source software employing a novel image analysis approach to support fully-automated plant phenotyping PLANT METHODS. 13(12),
• BURRELL T, FOZARD S, HOLROYD GH, FRENCH AP, POUND MP, BIGLEY CJ, JAMES TAYLOR C and FORDE BG, 2017. The Microphenotron: a robotic miniaturized plant phenotyping platform with diverse applications in chemical biology. Plant methods. 13, 10
• LUENGO, IMANOL, DARROW, MICHELE C., SPINK, MATTHEW C., SUN, YING, DAI, WEI, HE, CYNTHIA Y., CHIU, WAH, PRIDMORE, TONY, ASHTON, ALUN W., DUKE, ELIZABETH M. H., BASHAM, MARK and FRENCH, ANDREW P., 2017. SuRVoS: Super-Region Volume Segmentation workbench JOURNAL OF STRUCTURAL BIOLOGY. 198(1), 43-53
• MICHAEL POUND, JONATHAN ATKINSON, ALEXANDRA TOWNSEND, MICHAEL WILSON, MARCUS GRIFFITHS, AARON JACKSON, ADRIAN BULAT, GEORGIOS TZIMIROPOULOS, DARREN WELLS, ERIK MURCHIE, TONY PRIDMORE and ANDREW FRENCH, 2017. Deep Machine Learning provides state-of-the-art performance in image-based plant phenotyping Gigascience. gix083
• POUND, MICHAEL P., ATKINSON, JONATHAN A., WELLS, DARREN M., PRIDMORE, TONY P. and FRENCH, ANDREW P., 2017. Deep Learning for Multi-task Plant Phenotyping 2017 IEEE INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW 2017). 2055-2063
• POUND, MICHAEL P.AND FRENCH, ANDREW P.AND FOZARD, JOHN A.AND MURCHIE, ERIK H.AND PRIDMORE, TONY P., 2016. A patch-based approach to 3D plant shoot phenotyping Machine Vision and Applications. 1-13
• MICHAEL POUND, ALEXANDRA J BURGESS, MICHAEL H WILSON, JONATHAN A ATKINSON, MARCUS GRIFFITHS, AARON S JACKSON, ADRIAN BULAT, GEORGIOS TZIMIROPOULOS, DARREN M WELLS, ERIK H MURCHIE, TONY P PRIDMORE and ANDREW P FRENCH, 2016. Deep Machine Learning provides state-of-the-art performance in image-based plant phenotyping Biorxiv. Available at: <http://biorxiv.org/content/early/2016/05/12/053033>
• HANNO SCHARR, MASSIMO MINERVINI, ANDREW P. FRENCH, CHRISTIAN KLUKAS, DAVID M. KRAMER, XIAOMING LIU, IMANOL LUENGO, JEAN-MICHEL PAPE, GERRIT POLDER, DANIJELA VUKADINOVIC, XI YIN and SOTIRIOS A. TSAFTARIS, 2016. Leaf segmentation in plant phenotyping: a collation study Machine Vision and Applications. 27(4), 585-606
• IMANOL LUENGO, MARK BASHAM and ANDREW P FRENCH, 2016. Fast global interactive volume segmentation with regional supervoxel descriptors In: Proc. SPIE 9784, Medical Imaging 2016: Image Processing, 97842D (March 21, 2016). 9784.
• LUENGO, IMANOL, BASHAM, MARK and FRENCH, ANDREW P, 2016. Hierarchical Piecewise-Constant Super-regions arXiv preprint arXiv:1605.05937.
• IMANOL LUENGO, MARK BASHAM and ANDREW P. FRENCH, 2016. SMURFS: Superpixels from Multi-scale Refinement of Super-regions In: Proceedings of the British Machine Vision Conference 2016.
• POUND, MICHAEL, FRENCH, ANDREW and FORDE, BRIAN, 2016. AutoRoot: fully-automated plant root phenotyping Zenodo.
• LUENGO, IMANOL, BASHAM, MARK and FRENCH, ANDREW P., 2016. Selective Labeling: Identifying Representative Sub-volumes for Interactive Segmentation PATCH-BASED TECHNIQUES IN MEDICAL IMAGING, PATCH-MI 2016. 9993, 17-24
• SCHARR, HANNO, DEE, HANNAH, FRENCH, ANDREW P. and TSAFTARIS, SOTIRIOS A., 2016. Special issue on computer vision and image analysis in plant phenotyping MACHINE VISION AND APPLICATIONS. 27(5), 607-609
• POUND, MICHAEL, FRENCH, ANDREW P. and WELLS, DARREN M., 2015. Quantification of Fluorescent Reporters in Plant Cells PLANT CELL EXPANSION: METHODS AND PROTOCOLS. 1242, 123-131
• DEE, HANNAH and FRENCH, ANDREW, 2015. From image processing to computer vision: plant imaging grows up Foreword FUNCTIONAL PLANT BIOLOGY. 42(5), III-V
• LARRIEU AP, FRENCH AP, PRIDMORE TP, BENNETT MJ and WELLS DM, 2014. Time-profiling fluorescent reporters in the Arabidopsis root. Methods in molecular biology (Clifton, N.J.). 1056, 11-17
• BAND L, WELLS DM, FOZARD JA, GHETIU T, FRENCH AP, POUND MP, WILSON MH, YU L, LI W, HIJAZI H, OH J, PEARCE S, PEREZ-AMADOR MA, YUN J, KRAMER E, ALONSO JM, GODIN G, VERNOUX T, HODGMAN TC, PRIDMORE TP, SWARUP R, KING JR and BENNETT MJ, 2014. Systems Analysis of auxin transport in the Arabidopsis root apex Plant Cell.
• MIGUEL-PACHECO, GIULIANA G., KALER, JASMEET, REMNANT, JOHN, CHEYNE, LYDIA, ABBOTT, CAROLINE, FRENCH, ANDREW P., PRIDMORE, TONY P. and HUXLEY, JONATHAN N., 2014. Behavioural changes in dairy cows with lameness in an automatic milking system Applied Animal Behaviour Science. 150(0), 1-8
• LARRIEU, ANTOINE P., FRENCH, ANDREW P., PRIDMORE, TONY P., BENNETT, MALCOLM J. and WELLS, DARREN M., 2014. Time-Profiling Fluorescent Reporters in the Arabidopsis Root PLANT CHEMICAL GENOMICS: METHODS AND PROTOCOLS. 1056, 11-17
• POUND, MICHAEL P., FRENCH, ANDREW P., MURCHIE, ERIK H. and PRIDMORE, TONY P., 2014. Automated Recovery of Three-Dimensional Models of Plant Shoots from Multiple Color Images PLANT PHYSIOLOGY. 166(4), 1688-U801
• BAND, LEAH R., WELLS, DARREN M., FOZARD, JOHN A., GHETIU, TEODOR, FRENCH, ANDREW P., POUND, MICHAEL P., WILSON, MICHAEL H., YU, LEI, LI, WENDA, HIJAZI, HUSSEIN I., OH, JAESUNG, PEARCE, SIMON P., PEREZ-AMADOR, MIGUEL A., YUN, JEONGA, KRAMER, ERIC, ALONSO, JOSE M., GODIN, CHRISTOPHE, VERNOUX, TEVA, HODGMAN, T. CHARLIE, PRIDMORE, TONY P., SWARUP, RANJAN, KING, JOHN R. and BENNETT, MALCOLM J., 2014. Systems Analysis of Auxin Transport in the Arabidopsis Root Apex PLANT CELL. 26(3), 862-875
• ANDREW P FRENCH and MICHAEL P POUND, 2014. Analysis of Root Growth Using Image Analysis. In: S DUTTA GUPTA and YASUOMI IBARAKI, eds., Plant Image Analysis: Fundamentals and Applications CRC Press / Taoylor and Francis. 279-289
• MICHAEL P POUND and ANDREW P FRENCH, 2014. An Introduction to Images and Image Analysis. In: S DUTTA GUPTA and YASUOMI IBARAKI, eds., Plant Image Analysis: Fundamentals and Applications CRC Press / Taylor and Francis.
• POUND MP, FRENCH AP, MURCHIE E and PRIDMORE TP, 2014. Surface reconstruction of plant shoots from multiple views In: European Conference on Computer Vision (ECCV) Workshop on Computer Vision Problems in Plant Phenotyping.
• MICHAEL P POUND, ANDREW P FRENCH, JONATHAN ATKINSON, DARREN M WELLS, MALCOLM J BENNETT and TONY P PRIDMORE, 2013. RootNav: Navigating images of complex root architectures: http://www.plantphysiol.org/content/162/4/1802.long Plant Physiology.
• POUND, M.P., FRENCH, A.P., ATKINSON, J.A., WELLS, D.M., BENNETT, M.J. and PRIDMORE, T., 2013. RootNav: navigating images of complex root architectures Plant Physiology. 162(4), 1802-1814
• PÉRET B, MIDDLETON AM, FRENCH AP, LARRIEU A, BISHOPP A, NJO M, WELLS DM, PORCO S, MELLOR N, BAND LR, CASIMIRO I, KLEINE-VEHN J, VANNESTE S, SAIRANEN I, MALLET R, SANDBERG G, LJUNG K, BEECKMAN T, BENKOVA E, FRIML J, KRAMER E, KING JR, DE SMET I, PRIDMORE T, OWEN M and BENNETT MJ, 2013. Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Molecular systems biology. 9, 699
• PERET, BENJAMIN, MIDDLETON, ALISTAIR M., FRENCH, ANDREW P., LARRIEU, ANTOINE, BISHOPP, ANTHONY, NJO, MARIA, WELLS, DARREN M., PORCO, SILVANA, MELLOR, NATHAN, BAND, LEAH R., CASIMIRO, ILDA, KLEINE-VEHN, JUERGEN, VANNESTE, STEFFEN, SAIRANEN, ILKKA, MALLET, ROMAIN, SANDBERG, GORAN, LJUNG, KARIN, BEECKMAN, TOM, BENKOVA, EVA, FRIML, JIRI, KRAMER, ERIC, KING, JOHN R., DE SMET, IVE, PRIDMORE, TONY, OWEN, MARKUS and BENNETT, MALCOLM J., 2013. Sequential induction of auxin efflux and influx carriers regulates lateral root emergence MOLECULAR SYSTEMS BIOLOGY. 9,
• FRENCH AP, WELLS DM, EVERITT N and PRIDMORE TP, 2012. High-Throughput Quantification of Root Growth. In: MANCUSO, S, ed., Measuring Roots: An Updated Approach Heidelberg. xiii, 382 p.
• BAND. L.R., WELLS, D.M., LARRIEU, A., SUN, J., MIDDLETON, A.M., FRENCH, A.P., BRUNOUD, G., SATO, E.M., WILSON, M.H., PÉRET, B., OLIVA, M., SWARUP, R., SAIRANEN, I., PARRY, G., LJUNG, K., BEECKMAN, T., GARIBALDI, J.M., ESTELLE, M., OWEN, M.R., VISSENBERG, K., HODGMAN, T.C., PRIDMORE, T.P., KING, J.R., VERNOUX, T. and BENNETT, M.J., 2012. Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism Proceedings of the National Academy of Sciences of the United States of America. 109(12), 4668-4673
• WELLS, D.M., FRENCH, A.P., NAEEM, A., ISHAQ, O., TRAINI, R., HIJAZI, H., BENNETT, M.J. and PRIDMORE, T.P., 2012. Recovering the dynamics of root growth and development using novel image acquisition and analysis methods Philosophical Transactions of the Royal Society B: Biological Sciences. 367(1595), 1517-1524
• POUND, M.P., FRENCH, A.P., WELLS, D.M., BENNETT, M.J. and PRIDMORE, T.P., 2012. CellSeT: novel software to extract and analyze structured networks of plant cells from confocal images Plant Cell. 24(4), 1353-1361
• TONY P. PRIDMORE, ANDREW P. FRENCH and MICHAEL P. POUND, 2012. What lies beneath: underlying assumptions in bioimage analysis Trends in Plant Science. 17(12), 688-692
• SETHURAMAN, V., FRENCH, A., WELLS, D., KENOBI, K. and PRIDMORE, T., 2012. Tissue-level segmentation and tracking of cells in growing plant roots Machine Vision and Applications. 23(4), 639-658
• FRENCH AP, WILSON MH, KENOBI K, DIETRICH D, VOß U, UBEDA-TOMÁS S, PRIDMORE TP and WELLS DM, 2012. Identifying biological landmarks using a novel cell measuring image analysis tool: Cell-o-Tape. Plant methods. 8, 7
• NAEEM, A., FRENCH, A.P., WELLS, D.M. and PRIDMORE, T.P., 2011. High-throughput feature counting and measurement of roots Bioinformatics. 27(9), 1337-1338
• HODGMAN, TC, FRENCH, A and WESTHEAD, DR, 2010. Instant Notes in Bioinformatics 2nd ed.. Abingdon.
• FRENCH, A., UBEDA-TOMÁS, S., HOLMAN, T.J., BENNETT, M.J. and PRIDMORE, T., 2009. High throughput quantification of root growth using a novel image analysis tool Plant Physiology. 150(4), 1784-1795
• WRIGHT, EF, WELLS, DM, FRENCH, AP, HOWELLS, C and EVERITT, NM, 2009. A Low-Cost Automated Focusing System For Time-Lapse Microscopy Measurement Science & Technology. 20(2), 027003
• SETHURAMAN VS, TAYLOR S, PRIDMORE TP, FRENCH AP and WELLS DM, 2009. Segmentation and Tracking of Confocal Images of Arabidopsis thaliana Root Cells using Automatically-Initialized Network Snakes In: 3rd International Conference on Bioinformatics and Biomedical Engineering, Beijing, China.
• FRENCH, A.P., MILLS, S., SWARUP, R., BENNETT, M.J. and PRIDMORE, T.P., 2008. Colocalization of fluorescent markers in confocal microscope images of plant cells Nature Protocols. 3(4), 619-628
• FRENCH AP, BENNETT MJ, HOWELLS C, PATEL D and PRIDMORE TP, 2008. Probablilistic Tracking Approach to Root measurement in Images In: Biosignals 2008 - International Conference on Bio-inspired Systems and Signal Processing - Madeira, Portugal.
• GREENHALGH, C., FRENCH, A., HUMBLE, J. and TENNENT, P., 2007. Engineering a replay application based on RDF and OWL In: Online Proceedings of the UK e-Science All Hands Meeting 2007, September 10-13, Nottingham. (In Press.)
• GREENHALGH, C., FRENCH, A., TENNENT, P., HUMBLE, J. and CRABTREE, A., 2007. From ReplayTool to Digital Replay System In: Online Proceedings of the 3rd International Conference on e-Social Science, October 7-9, Ann Arbor, Michigan: ESRC/NSF.. (In Press.)
• FRENCH, A, NAEEM, A. DRYDEN, I and T. PRIDMORE, 2007. Using Social Effects to Guide Tracking in Complex Scenes In: IEEE Int. Conference on Advanced Video and Signal-based Surveillance. 217--217
• WALKER, B., SCHNÄDELBACH, H., RENNICK EGGLESTONE, S., CLARK, A., ORBACH, T., WRIGHT, M., NG, K., FRENCH, A., RODDEN, T. and BENFORD, S., 2007. Augmenting amusement rides with telemetry In: Advances in Computer Entertainment Technology. 115-122
• POUND M, NAEEM A, FRENCH A and PRIDMORE T, 2007. Quantitative and Qualitative Evaluation of Visual Tracking Algorithms using Statistical Tests In: 10th IEEE International Workshop on Performance Evaluation of Tracking and Surveillance.
• CRABTREE, A., FRENCH, A., GREENHALGH, C., BENFORD, S., CHEVERST, K., FITTON, D., ROUNCEFIELD, M. and GRAHAM, C., 2006. Developing digital records: early experiences of record and replay Computer Supported Cooperative Work. 15(4), 281-319
• FRENCH, A., GREENHALGH, C., CRABTREE, A., WRIGHT, M., BRUNDELL, P., HAMPSHIRE, A. and RODDEN, T., 2006. Software Replay Tools for Time-Based Social Science Data In: Second International Conference on e-Social Science.
• CRABTREE, A, GREENHALGH, C, FRENCH, A, RODDEN, T and BENFORD, S., 2006. Exploiting digital records: new resources and tools for qualitative research in contemporary social science In: Words Instead of Numbers: The Status of Software in the Qualitative Research World.
• CRABTREE, A, FRENCH, A, GREENHALGH, C and RODDEN, T. BENFORD, S., 2006. Working with digital records: developing tool support In: The 2nd International Conference on e-Social Science.
• FROST,A., FRENCH,A., TILLETT,R., PRIDMORE,T.P. and WELCH,T.R., 2004. A vision guided robot for tracking a live, loosely constrained pig Computers and Electronics in Agriculture,. 44(2), 93-106
• FRENCH,A., PRIDMORE,T.P. and MILLS,S., 2004. Condensation Tracking Through a Hough Space In: Proceedings of the 17th International Conference on Pattern Recognition, 2004 (ICPR 2004). 195- 198
• FRENCH, A., PRIDMORE, T.P., TILLETT, R. and FROST, A., 2003. An Image Analysis System to Guide a Sensor Placement Robot onto a Feeding Pig In: Proceedings of the Irish Machine Vision Conference.