Selected Recent Publications:


WILLIAMSON H, BRETTSCHNEIDER J, CACCAMO M, DAVEY R, GOBLE C, KERSEY P, MAY S, MORRIS R, OSTLER R, PRIDMORE T, RAWLINGS C, STUDHOLME D, TSAFTARIS S, and LEONELLI S, Data management challenges for artificial intelligence in plant and agricultural research, F1000Research, 10, 324.

BELLOS D, BASHAM M, PRIDMORE T and FRENCH A, A stacked dense denoising–segmentation network for undersampled tomograms and knowledge transfer using synthetic tomograms, Machine Vision and Applications volume 32, Article number: 75 (2021)

T and MOONEY SJ,Hydrodynamic Characterization Of Soil Compaction Using Integrated Electrical Resistivity And X-ray Computed Tomography, Vadose Zone Journal,


BAGLEY S, ATKINSON J, HUNT H, WILSON M, PRIDMORE T and WELLS D, Low-cost Automated Vectors and Modular Environmental Sensors for Plant Phenotyping, Sensors 20(11), 3319;

T and MOONEY SJ, A Pedophysical Relationship between X-ray Computed Tomography and Electrical Resistivity Data, Journal of Environmental and Engineering Geophysics 25 (2), 181-187.

GAO J, FRENCH A, POUND M, HE Y, PRIDMORE T and PIETERS JG, Deep convolutional neural networks for image-based Convolvulus sepium detection in sugar beet fields, Plant Methods 16 (1), 1-12

SOLTANINEJAD M, STURROCK C, GRIFFITHS M, PRIDMORE T and POUND M, Three Dimensional Root CT Segmentation using Multi-Resolution Encoder-Decoder Networks, IEEE Transactions on Image Processing (Early Access), DOI: 10.1109/TIP.2020.2992893.

ATANBORI J, FRENCH A, and PRIDMORE T, Towards infield, live plant phenotyping using a reduced-parameter CNN, Machine Vision and Applications, 31, 1, 2.

CIMPOIASU M, KURAS O, PRIDMORE T and MOONEY S, Potential of geoelectrical methods to monitor root zone processes and structure: A review, Geoderma 365, 114232


GIBBS J, POUND M, FRENCH A, WELLS D, MURCHIE E and PRIDMORE T Active vision and surface reconstruction for 3D plant shoot modelling, IEEE/ACM Transactions on Computational Biology and Bioinformatics, DOI: 10.1109/TCBB.2019.2896908.

BELLOS D, BASHAM M, PRIDMORE T and FRENCH A, A convolutional neural network for fast upsampling of undersampled tomograms in X-ray CT time-series using a representative highly sampled tomogram, Journal of Synchrotron Radiation, 26, 3.

GIBBS J, BURGESS A, POUND M, PRIDMORE T and MURCHIE E, Recovering Wind-Induced Plant Motion in Dense Field Environments via Deep Learning and Multiple Object Tracking, Plant Physiology, 181, 1, pp 28-42.

CIMPOIASU M, KURAS O, PRIDMORE T and MOONEY S, Enhancing Time-Lapse Geoelectrical Models of Soil Moisture Dynamics with a-priori X-Ray CT Derived Information, 25th European Meeting of Environmental and Engineering Geophysics, 2019, 1, pp1-5.

ATANBORI J, MONTOYA-P, M, SELVARAJ GOMEZ M, FRENCH A, and PRIDMORE T. Convolutional Neural Net-Based Cassava Storage Root Counting Using Real and Synthetic Images, Frontiers in Plant Science, 10,

CIMPOIASU M, KURAS O, PRIDMORE T and MOONEY S, Combining X-ray and electrical resistivity tomography methods towards a new methodology of soil hydraulics properties assessment. Geophysical Research Abstracts 21.

SELVARAJ GOMEZ M, MONTOYA-P, M, ATANBORI J, FRENCH A, and PRIDMORE T. A low-cost aeroponic phenotyping system for storage root development: unravelling the below-ground secrets of cassava (Manihot esculenta). Plant Methods. 15:131 1-15.

YASRAB R, ATKINSON J, WELLS D, FRENCH A, PRIDMORE T and POUND M, RootNav 2.0: Deep learning for automatic navigation of complex plant root architectures, GigaScience 8, 11.


GIBBS, JONATHON A., POUND, MICHAEL, FRENCH, ANDREW P., WELLS, DARREN M., MURCHIE, ERIK and PRIDMORE, TONY, 2018. An Active Vision Cell for Three-Dimensional Plant Shoot Reconstruction. Plant Physiology, Published online August 2018. DOI:

BENSON E, POUND M, FRENCH, A, JACKSON A, and PRIDMORE T, 2019, Deep Hourglass for Brain Tumor Segmentation, 4th International Workshop, BrainLes 2018, Held in Conjunction with MICCAI 2018, Granada, Spain, September 16, 2018, Revised Selected Papers, Part II.

ATANBORI, JOHN, CHEN, FENG, FRENCH, ANDREW P., and PRIDMORE, TONY, 2018, Towards Low-Cost Image-based Plant Phenotyping using Reduced-Parameter CNN, Proceedings Computer Vision Problems in Plant Phenotyping Workshop (CVPPP 2018), BMVC 2018 Workshop Proceedings.

ZHOU J, TARDIEU F, PRIDMORE T, DOONAN J, REYNOLDS D, HALL N, GRIFFITHS S, CHENG T, ZHU Y, WANG X, JIANG D and DING Y, 2018. Plant phenomics: history,present status and challenges. Journal of Nanjing Agricultural University, 41(4):580-588.



MAIRHOFER, S., PRIDMORE, T., BENNETT, M., MOONEY, S., STURROCK, C., GRIFFITHS, M., ATKINSON, J. ATKINSON, B. 2017. Particle Level Set Tracking for Low Resolution X-ray CT Image Data of Plant Root Systems in Soil. Computer Vision Problems in Plant Phenotyping (CVPPP), ICCV Workshop, Venice.

POUND, M. ATKINSON, J. WELLS, D. PRIDMORE, T. And FRENCH, A. Deep Learning for Multi-task Plant Phenotyping. Computer Vision Problems in Plant Phenotyping (CVPPP), ICCV Workshop, Venice.

MAIRHOFER, S., PRIDMORE, T., JOHNSON, J., WELLS, D.M., BENNETT, M.J., MOONEY, S.J. and STURROCK, C.J., 2017. X‐Ray Computed Tomography of Crop Plant Root Systems Grown in Soil. Current Protocols in Plant Biology, 2(4), pp.270-286

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

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

DALY, KEITH R, TRACY, SAOIRSE R, CROUT, NEIL M J, MAIRHOFER, STEFAN, PRIDMORE, TONY P, MOONEY, SACHA J and ROOSE, TIINA, 2017. Quantification of root water uptake in soil using X-ray computed tomography and image-based modelling, Plant, cell & environment

TARDIEU F, CABRERA-BOQUET L, PRIDMORE T and BENNETT MJ, 2017. Plant Phenomics, From Sensors to Knowledge, Current Biology. 27, 770-783


GIRI, J., BHOSALE, R., HUANG, G., PANDEY, B.K., PARKER, H., ZAPPALA, S., YANG, J., DIEVART, A., BUREAU, C., LJUNG, K., PRICE, A., ROSE, T., LARRIEU, A., MAIRHOFER, S., STURROCK C., WHITE, P., DUPUY, L., HAWKESFORD, M., PERIN, C., LIANG, W., PERET, B., HODGEMAN, C., LYNCH, J., WISSUWA, M., ZHANG, D., PRIDMORE, T., MOONEY, S., GUIDERONI, E., SWARUP R., and BENNETT M.J., 2018. Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate. Nature communications, 9(1), p.1408


BURGESS, ALEXANDRA J., RETKUTE, RENATA, PRESTON, SIMON P., JENSEN, OLIVER E., POUND, MICHAEL P., PRIDMORE, TONY P. and MURCHIE, ERIK H., 2016. The 4-Dimensional Plant: Effects of Wind-Induced Canopy Movement on Light Fluctuations and Photosynthesis Frontiers in Plant Science. 7, 1392

KRISTAN et al, 2016. The Visual Object Tracking VOT2016 Challenge Results COMPUTER VISION - ECCV 2016 WORKSHOPS, PT II. 9914, 777-823

POUND M, BURGESS A, WILSON M, ATKINSON J, GRIFFITHS A, JACKSON A, BULAT A, TZIMIROPOLOUS G, WELLS D, MURCHIE E, PRIDMORE T, FRENCH A, Deep Machine Learning provides state-of-the-art performance in image-based plant phenotyping, bioRxiv doi:

POUND M, FRENCH A, FOZARD J, MURCHIE E and PRIDMORE T, A patch-based approach to 3D plant shoot phenotyping, Machine Vision and Applications, published online 1st march 2016


MAIRHOFER S, STURROCK C, BENNETT M, MOONEY S and PRIDMORE T, Visual Tracking for the Recovery of Multiple Interacting Plant Root Systems from X-ray µCT Images. Machine Vision and Applications. Accepted October 2015

WANG X, VALSTAR MF, MARTINEZ B, KHAN MH and PRIDMORE T, TRIC-track: Tracking by Regression with Incrementally Learned Cascades, in IEEE Int’l Conf. on Computer Vision (ICCV), 2015

GIBBS JA, POUND MP, WELLS DM, MURCHIE E, FRENCH A, and PRIDMORE T, Three-dimensional Reconstruction of Plant Shoots from Multiple Images using an Active Vision System, IEEE IROS workshop on Agri-Food Robotics, Hamburg, October 2015

MAIRHOFER S, STURROCK C, BENNETT M, MOONEY S and PRIDMORE T, Extracting Multiple Interacting Root Systems using X-ray Micro Computed Tomography. The Plant Journal. Accepted manuscript online: 13 OCT 2015 09:57AM EST | DOI: 10.1111/tpj.13047

BURGESS A, RETKUTE R, POUND MP, FOULKES J. PRESTON SP, JENSEN OE, PRIDMORE TP and MURCHIE EH, High-resolution 3D structural data quantifies the impact of photo inhibition on long term carbon gain in wheat canopies in the field, Plant Physiology, published online before print, August 2015.

ROUSSEAU D, DEE, H and PRIDMORE TP, Imaging methods for phenotyping of plant traits, in Phenomics of Crop Plants: Trends, Options, Limitations, Eds. J Kumar, A Pratap and S Kumar, Springer 2015.

ABDELRAOUF A, HIGGINS C A, PRIDMORE TP and KHALIL MI, Arabic character recognition using a Haar-Cascade Classifier approach. Pattern Analysis and Applications, accepted for publication.

LOBET G, POUND M, DIENER J, PRADAL C, DRAYE X, GODIN C, JAVAUX M, LEITNER D, MEUNIER F, NACRY P, PRIDMORE T and SCHNEPF A, Root system markup language: towards a unified root architecture description language. Plant Physiology 167 (3), 617-27, 2015.

NGUYEN T and PRIDMORE TP, 2015. Adaptive tracking via multiple appearance models and multiple linear searches. Proc. 10th International Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications (VISAPP 2015), Berlin 2015.


POUND M, FRENCH A, MURCHIE E and PRIDMORE TP, Automated recovery of three-dimensional models of plant shoots from multiple colour images,Plant Physiology 166(4) , December 2014.

MAIRHOFER S, STURROCK C, WELLS, D, BENNETT M, MOONEY S and PRIDMORE TP 2014. On the evaluation of methods for the recovery of plant root systems from X-ray computed tomography images. Functional Plant Biology, Published online 2nd December 2014.

MAIRHOFER S, STURROCK C, BENNETT M, MOONEY S and PRIDMORE TP, Visual object tracking for the extraction of multiple interacting plant root systems, ECCV Workshop on Computer Vision Problems in Plant Phenotyping, Zurich, September 2014. To appear in Lecture Notes in Computer Science.

POUND M, FRENCH A, MURCHIE E and PRIDMORE TP, Surface reconstruction of plant shoots from multiple views. ECCV Workshop on Computer Vision Problems in Plant Phenotyping, Zurich, September 2014. To appear in Lecture Notes in Computer Science.

KHAN MH, VALSTAR MF and PRIDMORE TP, 2014. MTS: A multiple temporal scale tracker handling occlusion and abrupt motion variations, Proc Asian Computer Vision Conference (ACCV 2014), Singapore, November 2014.

NGUYEN T and PRIDMORE TP, 2014. Tracking using multiple linear searches and motion direction sampling. Proc. International Conference on Pattern Recognition (ICPR 2014), Stockholm 2014

KHAN MH, VALSTAR MF and PRIDMORE TP, 2014. A generalised search method for multiple competing hypotheses in visual tracking. Proc. International Conference on Pattern Recognition (ICPR 2014), Stockholm 2014

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. The Plant Cell, March 2014 tpc.113.119495.

R.J. DYSON, G. VIZCAY-BARRENA, L.R. BAND, A.N. FERNANDES, A.P. FRENCH, J.A. FOZARD, T.C. HODGMAN, K. KENOBI, T. PRIDMORE, M. STOUT, D.M. WELLS, M. WILSON, M.J. BENNETT & O.E. JENSEN., 2014, Mechanical modelling quantifies the functional importance of outer tissues during root elongation and bending. New Phytologist, 202(4): 1212-22.

GREEN, JONATHAN, PRIDMORE, TONY and BENFORD, STEVE, 2014. Exploring attractions and exhibits with interactive flashlights Personal and Ubiquitous Computing. 18(1), 239-251

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, 1-8


ZAPPALA S, HELLIWELL J, TRACY S, MAIRHOFER S, STURROCK C J, PRIDMORE T, BENNETT M J and MOONEY S, 2013. Effects of X-ray dose on rhizosphere studies using X-ray computed tomography Plos One. 8(6)

MURARO D, MELLOR N, POUND MP, HELP H, LUCAS M, CHOPARD J, BYRNE HM, GODIN C, HODGMAN TC, KING JR, PRIDMORE TP, HELARIUTTA Y, BENNETT MJ and BISHOPP A, 2013. Integration of hormonal signaling networks and mobile microRNAs is required for vascular patterning in Arabidopsis roots. Proceedings of the National Academy of Sciences of the United States of America. published ahead of print December 31, 2013, doi:10.1073/pnas.1221766111

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

DADASHI N, STEDMON A and PRIDMORE T, 2013. Semi-automated CCTV surveillance: The effects of system confidence, system accuracy and task complexity on operator vigilance, reliance and workload Applied Ergonomics. 44(5), 730-738

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

ABDELRAOUF, ASHRAF, HIGGINS, COLIN A., PRIDMORE, TONY P. and KHALIL, MAHMOUD I., 2013. Arabic Corpus Enhancement using a New Lexicon/Stemming Algorithm. In: ICPRAM. 435-440

MEESE, R., ALI, S., THORNE, E., BENFORD, S., QUINN, A., MORTIER, R., KOLEVA, B., PRIDMORE, T. and BAURLEY, S., 2013. From codes to patterns: designing interactive decoration for tableware In: CHI '13: Proceedings of the SIGCHI Conference on Human Factors in Computing Systems. 931-940

SUSAN ZAPPALA, STEFAN MAIRHOFER, SAOIRSE TRACY, CRAIG STURROCK, MALCOLM BENNETT, TONY PRIDMORE and SACHA MOONEY, 2013. Quantifying the effect of soil moisture content on segmenting root system architecture in X-ray computed tomography images Plant and Soil. 370(1-2), 35-45

STEFAN MAIRHOFER, SUSAN ZAPPALA, SAOIRSE TRACY, CRAIG STURROCK, MALCOLM BENNETT, SACHA MOONEY and TONY PRIDMORE, 2013. Recovering complete plant root system architectures from soil via X-ray mu-Computed Tomography Plant Methods. 9(8)


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

BAND L, J. FOZARD, C. GODIN, O. JENSEN, T. PRIDMORE, M. BENNETT and J. KING, 2012. Multiscale systems analysis of root growth and development: modelling beyond the network and cellular scales Plant Cell. 24(10), 3892-906

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.

MAIRHOFER S, ZAPPALA S, TRACY S, STURROCK C, BENNETT MJ, MOONEY S and PRIDMORE T, 2012. RooTrak: Automated recovery of 3D plant root architecture in soil from X-ray Micro computed Tomography using visual tracking Plant Physiology. 158(2), 561-569

BAND LR, WELLS DM, LARRIEU A, SUN J, MIDDLETON AM, FRENCH AP, BRUNOUD G, SATO EM, WILSON MH, PÉRET B, OLIVA M, SWARUP R, SAIRANEN I, PARRY G, LJUNG K, BEECKMAN T, GARIBALDI JM, ESTELLE M, OWEN MR, VISSENBERG K, HODGMAN TC, PRIDMORE TP, KING JR, VERNOUX T and BENNETT MJ, 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

SETHURAMAN, VIJAYA, FRENCH, ANDREW, WELLS, DARREN, KENOBI, KIM and PRIDMORE, TONY, 2012. Tissue-level segmentation and tracking of cells in growing plant roots Machine Vision and Applications. 23, 639-658

WELLS, DARREN M., FRENCH, ANDREW P., NAEEM, ASAD, ISHAQ, OMER, TRAINI, RICHARD, HIJAZI, HUSSEIN, BENNETT, MALCOLM J. and PRIDMORE, TONY 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, MICHAEL P., FRENCH, ANDREW P., WELLS, DARREN M., BENNETT, MALCOLM J. and PRIDMORE, TONY P., 2012. CellSeT: Novel Software to Extract and Analyze Structured Networks of Plant Cells from Confocal Images Plant Cell 2012 Apr;24(4):1353-61. doi: 10.1105/tpc.112.096289. Epub 2012 Apr 3.

MOONEY, S., PRIDMORE, T., HELLIWELL, J. and BENNETT, M., 2012. Developing X-ray Computed Tomography to non-invasively image 3-D root systems architecture in soil Plant and Soil. 352, 1-22


LUCAS, M, SWARUP, R, PAPONOV, IA, SWARUP, K, CASIMIRO, I, LAKE, D, PERET, B, ZAPPALA, S, MAIRHOFER, S, WHITWORTH, M, WANG, JH, LJUNG, K, MARCHANT, A, SANDBERG, G, HOLDSWORTH, MJ, PALME, K, PRIDMORE, T, MOONEY, S and BENNETT, MJ, 2011. Short-Root Regulates Primary, Lateral, And Adventitious Root Development In Arabidopsis Plant Physiology. 155(1), 384-398

NAEEM A, FRENCH AP, WELLS DM and PRIDMORE TP, 2011. High-Throughput Feature Counting And Measurement Of Roots. Bioinformatics (Oxford, England). 27(9), 1337-8

BAYOUMI, SAHAR, PRIDMORE, TONY and KOLEVA, BORIANA, 2010. Exploiting ambient illumination to locate and recognise user behaviour in enclosed environments Personal and Ubiquitous Computing. 14, 335-345

TOMLINSON, M, A. NAEEM, K. JAYAPRAKASAN, R, JAYARAKASAN, T. SIMPSON, T. NEWTON, K. POOLEY, J. HOPKISSON and T. PRIDMORE, 2010. Validation of a novel computer assisted sperm analysis (CASA) system employing multi-target tracking algorithms Fertility and Sterility. 93(6), 1911-1920

GUO, SIYU, PRIDMORE, TONY, KONG, YAGUANG and ZHANG, XUFANG, 2009. An improved Hough transform voting scheme utilizing surround suppression Pattern Recogn. Lett.. 30(13), 1241-1252

FRENCH, A., UBEDA-TOMAS, 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. 10, 1104

CHANDESA T, PRIDMORE T and BARGIELA A, 2009. Detecting occlusion and camouflage during visual tracking In: Proc. Int. Conf. on Signal and Image Processing Applications, ICSIPA09.

FRENCH A, MILLS S, SWARUP R, BENNNETT M and PRIDMORE T, 2008. Colocalization of fluorescent markers in confocal microscope images of plant cells Nature Protocols. 3, 619-628

NAEEM, A., PRIDMORE, T and MILLS, S., 2007. Managing particle spread via hybrid particle filter/kernel mean shift tracking In: British Machine Vision Conference 2007, University of Warwick, UK, 10-13 September, 2007

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

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.