All Outputs (39)

Quantification of root water uptake in soil using X-ray Computed Tomography and image based modelling (2017)
Journal Article
Daly, K. R., Tracy, S. R., Crout, N. M., Mairhofer, S., Pridmore, T. P., Mooney, S. J., & Roose, T. (2018). Quantification of root water uptake in soil using X-ray Computed Tomography and image based modelling. Plant, Cell and Environment, 41(1), 121-133. https://doi.org/10.1111/pce.12983

Spatially averaged models of root-soil interactions are often used to calculate plant water uptake. Using a combination of X-ray Computed Tomography (CT) and image based modelling we tested the accuracy of this spatial averaging by directly calculati... Read More about Quantification of root water uptake in soil using X-ray Computed Tomography and image based modelling.

SuRVoS: Super-Region Volume Segmentation workbench (2017)
Journal Article
Luengo, I., Darrow, M. C., Spink, M. C., Sun, Y., Dai, W., He, C. Y., …French, A. P. (2017). SuRVoS: Super-Region Volume Segmentation workbench. Journal of Structural Biology, 198(1), 43-53. https://doi.org/10.1016/j.jsb.2017.02.007

Segmentation of biological volumes is a crucial step needed to fully analyse their scientific content. Not having access to convenient tools with which to segment or annotate the data means many biological volumes remain under-utilised. Automatic seg... Read More about SuRVoS: Super-Region Volume Segmentation workbench.

Approaches to three-dimensional reconstruction of plant shoot topology and geometry (2016)
Journal Article
Gibbs, J., Pound, M. P., French, A. P., Wells, D. M., Murchie, E. H., & Pridmore, T. P. (2016). Approaches to three-dimensional reconstruction of plant shoot topology and geometry. Functional Plant Biology, 44(1), 62-75. https://doi.org/10.1071/FP16167

There are currently 805 million people classified as chronically undernourished, and yet the World’s population is still increasing. At the same time, global warming is causing more frequent and severe flooding and drought, thus destroying crops and... Read More about Approaches to three-dimensional reconstruction of plant shoot topology and geometry.

A patch-based approach to 3D plant shoot phenotyping (2016)
Journal Article
Pound, M. P., French, A. P., Fozard, J. A., Murchie, E. H., & Pridmore, T. P. (2016). A patch-based approach to 3D plant shoot phenotyping. Machine Vision and Applications, 27(5), 767-779. https://doi.org/10.1007/s00138-016-0756-8

The emerging discipline of plant phenomics aims to measure key plant characteristics, or traits, though as yet the set of plant traits that should be measured by automated systems is not well defined. Methods capable of recovering generic representat... Read More about A patch-based approach to 3D plant shoot phenotyping.

Three-dimensional reconstruction of plant shoots from multiple images using an active vision system (2015)
Journal Article
Gibbs, J., Pound, M. P., Wells, D. M., Murchie, E. H., French, A. P., & Pridmore, T. P. (2015). Three-dimensional reconstruction of plant shoots from multiple images using an active vision system

The reconstruction of 3D models of plant shoots is a challenging problem central to the emerging discipline of plant phenomics – the quantitative measurement of plant structure and function. Current approaches are, however, often limited by the use o... Read More about Three-dimensional reconstruction of plant shoots from multiple images using an active vision system.

High-Resolution Three-Dimensional Structural Data Quantify the Impact of Photoinhibition on Long-Term Carbon Gain in Wheat Canopies in the Field (2015)
Journal Article
Burgess, A. J., Retkute, R., Pound, M. P., Foulkes, J., Preston, S. P., Jensen, O. E., …Murchie, E. H. (2015). High-Resolution Three-Dimensional Structural Data Quantify the Impact of Photoinhibition on Long-Term Carbon Gain in Wheat Canopies in the Field. Plant Physiology, 169(2), 1192-1204. https://doi.org/10.1104/pp.15.00722

Photoinhibition reduces photosynthetic productivity; however, it is difficult to quantify accurately in complex canopies partly because of a lack of high-resolution structural data on plant canopy architecture, which determines complex fluctuations o... Read More about High-Resolution Three-Dimensional Structural Data Quantify the Impact of Photoinhibition on Long-Term Carbon Gain in Wheat Canopies in the Field.

Root system markup language: Toward a unified root architecture description language (2015)
Journal Article
Meunier, F., Lobet, G., Pound, M. P., Diener, J., Pradal, C., Draye, X., …Schnepf, A. (2015). Root system markup language: Toward a unified root architecture description language. Plant Physiology, 167(3), 617-627. https://doi.org/10.1104/pp.114.253625

© 2015 American Society of Plant Biologists. All rights reserved. The number of image analysis tools supporting the extraction of architectural features of root systems has increased in recent years. These tools offer a handy set of complementary fac... Read More about Root system markup language: Toward a unified root architecture description language.

Automated recovery of 3D models of plant shoots from multiple colour images (2014)
Journal Article
Pound, M. P., French, A. P., Murchie, E. H., & Pridmore, T. P. (2014). Automated recovery of 3D models of plant shoots from multiple colour images. Plant Physiology, 166(4), https://doi.org/10.1104/pp.114.248971

Increased adoption of the systems approach to biological research has focussed attention on the use of quantitative models of biological objects. This includes a need for realistic 3D representations of plant shoots for quantification and modelling.... Read More about Automated recovery of 3D models of plant shoots from multiple colour images.

Systems Analysis of Auxin Transport in the Arabidopsis Root Apex (2014)
Journal Article
Band, L. R., Wells, D. M., Fozard, J. A., Ghetiu, T., French, A. P., Pound, M. P., …Bennett, M. J. (2014). Systems Analysis of Auxin Transport in the Arabidopsis Root Apex. Plant Cell, 26(3), 862-875. https://doi.org/10.1105/tpc.113.119495

Auxin is a key regulator of plant growth and development. Within the root tip, auxin distribution plays a crucial role specifying developmental zones and coordinating tropic responses. Determining how the organ-scale auxin pattern is regulated at the... Read More about Systems Analysis of Auxin Transport in the Arabidopsis Root Apex.

Mechanical modelling quantifies the functional importance of outer tissue layers during root elongation and bending (2014)
Journal Article
Dyson, R. J., Vizcay-Barrena, G., Band, L. R., Fernandes, A. N., French, A. P., Fozard, J. A., …Jensen, O. E. (2014). Mechanical modelling quantifies the functional importance of outer tissue layers during root elongation and bending. New Phytologist, 202(4), 1212-1222. https://doi.org/10.1111/nph.12764

Root elongation and bending require the coordinated expansion of multiple cells of different types. These processes are regulated by the action of hormones that can target distinct cell layers. We use a mathematical model to characterise the influenc... Read More about Mechanical modelling quantifies the functional importance of outer tissue layers during root elongation and bending.

Time-Profiling Fluorescent Reporters in the Arabidopsis Root (2013)
Book Chapter
Larrieu, A. P., French, A. P., Pridmore, T. P., Bennett, M. J., & Wells, D. M. (2014). Time-Profiling Fluorescent Reporters in the Arabidopsis Root. In Plant chemical genomics : methods and protocols (11-17). Springer. https://doi.org/10.1007/978-1-62703-592-7_2

Confocal laser scanning microscopy is a useful nondestructive approach for the visualization of fluorescent reporters in planta. Samples are usually placed between a slide and a cover slip which, although suited to single time-point imaging, does not... Read More about Time-Profiling Fluorescent Reporters in the Arabidopsis Root.

Behavioural changes in dairy cows with lameness in an automatic milking system (2013)
Journal Article
Miguel-Pacheco, G., Kaler, J., Remnant, J., Cheyne, L., Abbott, C., French, A. P., …Huxley, J. N. (2014). Behavioural changes in dairy cows with lameness in an automatic milking system. Applied Animal Behaviour Science, 150, 1-8. https://doi.org/10.1016/j.applanim.2013.11.003

There is a tendency worldwide for the automation of farms; this has included the introduction of automatic milking systems (AMS) in the dairy industry. Lameness in dairy cows is highly prevalent and painful. These impacts potentially affect not only... Read More about Behavioural changes in dairy cows with lameness in an automatic milking system.

Sequential induction of auxin efflux and influx carriers regulates lateral root emergence (2013)
Journal Article
Peret, B., Middleton, A. M., French, A. P., Larrieu, A., Bishopp, A., Njo, M., …Bennett, M. J. (2013). Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Molecular Systems Biology, 9(1), Article 699. https://doi.org/10.1038/msb.2013.43

In Arabidopsis, lateral roots originate from pericycle cells deep within the primary root. New lateral root primordia (LRP) have to emerge through several overlaying tissues. Here, we report that auxin produced in new LRP is transported towards the o... Read More about Sequential induction of auxin efflux and influx carriers regulates lateral root emergence.

Effects of X-ray dose on rhizosphere studies using X-ray computed tomography (2013)
Journal Article
Zappala, S., Helliwell, J. R., Tracy, S., Mairhofer, S., Sturrock, C., Pridmore, T., Bennett, M. J., & Mooney, S. J. (2013). Effects of X-ray dose on rhizosphere studies using X-ray computed tomography. PLoS ONE, 8(6), Article e67250. https://doi.org/10.1371/journal.pone.0067250

X-ray Computed Tomography (CT) is a non-destructive imaging technique originally designed for diagnostic medicine, which was adopted for rhizosphere and soil science applications in the early 1980s. X-ray CT enables researchers to simultaneously visu... Read More about Effects of X-ray dose on rhizosphere studies using X-ray computed tomography.

RootNav: navigating images of complex root architectures (2013)
Journal Article
Pound, M. P., French, A. P., Atkinson, J. A., Wells, D. M., Bennett, M. J., & Pridmore, T. (2013). RootNav: navigating images of complex root architectures. Plant Physiology, 162(4), 1802-1814. https://doi.org/10.1104/pp.113.221531

We present a novel image analysis tool that allows the semiautomated quantification of complex root system architectures in a range of plant species grown and imaged in a variety of ways. The automatic component of RootNav takes a top-down approach,... Read More about RootNav: navigating images of complex root architectures.

The spatial character of sensor technology (2006)
Presentation / Conference Contribution
Reeves, S., Pridmore, T., Crabtree, A., Green, J., Benford, S., & O'Malley, C. (2006). The spatial character of sensor technology.

By considering the spatial character of sensor-based interactive systems, this paper investigates how discussions of seams and seamlessness in ubiquitous computing neglect the complex spatial character that is constructed as a side-effect of deployin... Read More about The spatial character of sensor technology.

Expected, sensed, and desired: A framework for designing sensing-based interaction (2005)
Journal Article
Benford, S., Schnädelbach, H., Koleva, B., Anastasi, R., Greenhalgh, C., Rodden, T., …Steed, A. (2005). Expected, sensed, and desired: A framework for designing sensing-based interaction. ACM Transactions on Computer-Human Interaction, 12(1), 3-30. https://doi.org/10.1145/1057237.1057239

Movements of interfaces can be analyzed in terms of whether they are expected, sensed, and desired. Expected movements are those that users naturally perform; sensed are those that can be measured by a computer; and desired movements are those that a... Read More about Expected, sensed, and desired: A framework for designing sensing-based interaction.

Camping in the digital wilderness: Tents and flashlights as interfaces to virtual worlds (2001)
Presentation / Conference Contribution
Green, J., Schnädelbach, H., Koleva, B., Benford, S., Pridmore, T., Medina, K., …Smith, H. (2001, April). Camping in the digital wilderness: Tents and flashlights as interfaces to virtual worlds. Paper presented at Conference on Human Factors in Computing Systems - Proceedings

A projection screen in the shape of a tent provides children with a shared immersive experience of a virtual world based on the metaphor of camping. RFID aerials at its entrances sense tagged children and objects as they enter and leave. Video tracki... Read More about Camping in the digital wilderness: Tents and flashlights as interfaces to virtual worlds.

TRIC-track: tracking by regression with incrementally learned cascades
Presentation / Conference Contribution
Wang, X., Valstar, M. F., Martinez, B., Khan, M. H., & Pridmore, T. (2015, December). TRIC-track: tracking by regression with incrementally learned cascades. Presented at 2015 IEEE International Conference on Computer Vision (ICCV), Santiago, Chile

This paper proposes a novel approach to part-based track- ing by replacing local matching of an appearance model by direct prediction of the displacement between local image patches and part locations. We propose to use cascaded regression with incre... Read More about TRIC-track: tracking by regression with incrementally learned cascades.