Article
Soil Science
Lei (Helen) Hou, Wei Gao, Frederik der Bom van, Zhe (Han) Weng, Casey L. Doolette, Anton Maksimenko, Daniel Hausermann, Yunyun Zheng, Caixian Tang, Enzo Lombi, Peter M. Kopittke
Summary: This review discusses the use of X-ray CT technology to examine root distribution in soils and its importance. With the development of high-end X-ray CT systems and image processing algorithms, this method can be used to study various factors such as root system architecture and soil-root interactions.
Article
Agronomy
Top Bahadur Pun, Arjun Neupane, Richard Koech
Summary: This study developed a semi-automated method to quantify root-knot nematodes (RKN) based on size using image analysis, with three novel approaches showing good performance in detecting and quantifying RKN length, with the SG method being the most suitable for this purpose.
Article
Agriculture, Multidisciplinary
Liang Gong, Xiaofeng Du, Kai Zhu, Chenghui Lin, Ke Lin, Tao Wang, Qiaojun Lou, Zheng Yuan, Guoqiang Huang, Chengliang Liu
Summary: The study of plant growth state relies on root architecture parameters, with root segmentation being crucial to measuring these parameters. A new method based on a convolutional neural network was proposed for pixel-level segmentation of rice roots under strong noise, achieving an intersection over union (IoU) of 87.4%. This approach provides an automatic and fast pixel-level root segmentation method, essential for root morphology analysis.
COMPUTERS AND ELECTRONICS IN AGRICULTURE
(2021)
Article
Biochemical Research Methods
Shota Teramoto, Yusaku Uga
Summary: In this study, we developed a semi-automatic workflow that tracks individual root growth by vectorizing root system architecture (RSA) from time-series 3D images. This workflow can be applied to the time-series analysis of RSA development and plasticity.
Review
Plant Sciences
Pooja Tripathi, Sangita Subedi, Abdul Latif Khan, Yong-Suk Chung, Yoonha Kim
Summary: Silicon is a common element in soil that enhances root morphological traits in various crop species, promoting plant growth. Advanced image analysis methods utilizing machine learning technologies allow for comprehensive study of root functions and the effects of Si application on roots.
Article
Biology
Nicolas Gaggion, Federico Ariel, Vladimir Daric, Eric Lambert, Simon Legendre, Thomas Roule, Alejandra Camoirano, Diego H. Milone, Martin Crespi, Thomas Blein, Enzo Ferrante
Summary: This study introduces the ChronoRoot system, combining 3D printing and deep learning techniques for high temporal resolution phenotyping of plant roots in agarized medium. A novel deep learning-based root extraction method was developed, incorporating temporal consistency into root system architecture reconstruction, allowing automatic extraction of phenotypic parameters and derivation of novel time-related parameters from spectral features of temporal signals. The combination of machine intelligence methods and a 3D-printed device expands the possibilities of root high-throughput phenotyping for genetic and natural variation studies.
Article
Biochemical Research Methods
Maxime Phalempin, Eva Lippold, Doris Vetterlein, Steffen Schlueter
Summary: X-ray computed tomography is a powerful tool for studying plant root system architecture. This paper presents the improved root segmentation algorithm Rootine v.2, which outperforms its predecessor in root recovery accuracy. The new features in Rootine v.2 include pot wall detection, root average gray value calculation, automatic threshold calculation, and false negatives recovery based on shape criteria, showing improved usability and potential for high-throughput root phenotyping procedures.
Article
Computer Science, Artificial Intelligence
Guanke Chen, Kun Hao, Beibei Wang, Zhisheng Li, Xiaofang Zhao
Summary: This paper proposes an improved power line segmentation model based on Deeplabv3+ (PL-Deeplab), which addresses the problems of complex background interference and thin structure of power lines in aerial images. The model utilizes a multibranch concatenation network (MCNet), a one-shot aggregation feature pyramid (OSAFP), and a feature fusion module (FFM) to accurately segment the power lines. Experimental results on a public dataset demonstrate the superiority of the proposed model in completing the power line inspection task and ensuring security for UAV power line inspection.
EXPERT SYSTEMS WITH APPLICATIONS
(2023)
Article
Computer Science, Artificial Intelligence
Aocheng Li, Jie Guo, Yanwen Guo
Summary: A new image stitching method is proposed in this paper, which aligns a set of matched dominant semantic planar regions to improve the precision and accuracy of image stitching, utilizing semantic information and deep Convolutional Neural Network.
IEEE TRANSACTIONS ON IMAGE PROCESSING
(2021)
Article
Computer Science, Information Systems
Xinbo Yang, Yan Zhang
Summary: Multi-atlas segmentation is widely accepted as an essential image segmentation approach, and a deep learning-based approach integrating feature extraction and label fusion has been proposed to enhance accuracy. Experimental results demonstrate that this approach outperforms existing techniques in efficiency and effectiveness.
MULTIMEDIA TOOLS AND APPLICATIONS
(2021)
Article
Multidisciplinary Sciences
Narendra Narisetti, Michael Henke, Christiane Seiler, Astrid Junker, Joern Ostermann, Thomas Altmann, Evgeny Gladilin
Summary: Our study developed a GUI-based tool for automated quantitative analysis of soil-root images using a pre-trained CNN model, achieving a Dice coefficient of 0.87 and outperforming existing tools.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Joshua Peeples, Weihuang Xu, Romain Gloaguen, Diane Rowland, Alina Zare, Zachary Brym
Summary: This article proposes a new method called STARSEED, which incorporates spatial information through the Earth Mover's Distance (EMD) to compare root system distributions. The approach captures the response of sesame root systems for different genotypes and soil moisture levels. STARSEED can be generalized to other plants and provides valuable insights into root system architecture development and response to varying growth conditions. The code and data for the experiments are publicly available at: https://github.com/GatorSense/STARSEED.
Article
Plant Sciences
Md. Parvez Islam, Yuka Nakano, Unseok Lee, Keinichi Tokuda, Nobuo Kochi
Summary: The real challenge in separating leaf pixels from background pixels in thermal images lies in factors such as emitted and reflected thermal radiation from the plant, absorption of reflected radiation by greenhouse humidity, and external environment. The proposed TheLNet270v1 achieved 91% accuracy in distinguishing canopy pixels from background pixels and segmenting the image into leaf and background classes. Through evaluation with over 13,766 images, training and validation accuracies of 95.75% and 95.23% were achieved, without overfitting. This research focuses on developing a deep learning technique for automatically segmenting thermal images to monitor canopy surface temperature in greenhouses continuously.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Takudzwa Mandizvo, Alfred Oduor Odindo, Jacob Mashilo, Julia Sibiya, Sascha Lynn Beck-Pay
Summary: This study compared the root system architecture of drought-tolerant citron watermelon under water-stress conditions. The results showed significant positive correlations between root dry mass and other root system architecture traits under water stress. Principal component analysis identified key root system architecture traits that could be useful for improving drought adaptation and yield performance in citron watermelon genotypes.
Article
Computer Science, Information Systems
Song-Toan Tran, Minh-Hoa Nguyen, Huu-Phuc Dang, Thanh-Tan Nguyen
Summary: The study introduces a modified Residual Recurrent Unet architecture model with a smaller size and superior performance for segmenting polyps in colonoscopy images. Experimental results show that the proposed model performs better on three public colonoscopy image datasets compared to recent related studies.
Article
Agronomy
Merlijn Morisse, Darren M. Wells, Emilie J. Millet, Morten Lillemo, Sven Fahrner, Francesco Cellini, Peter Lootens, Onno Muller, Juan M. Herrera, Alison R. Bentley, Michela Janni
Summary: To address the challenges of future food security, innovative technologies are needed to accelerate crop production. Plant phenotyping methods have advanced significantly, and field-based phenotyping plays a crucial role in capturing plant responses to the environment for breeding and selection requirements.
FIELD CROPS RESEARCH
(2022)
Article
Plant Sciences
Britta M. C. Kumpers, Jingyi Han, John Vaughan-Hirsch, Nicholas Redman, Alexander Ware, Jonathan A. Atkinson, Nicola Leftley, George Janes, Giuseppe Castiglione, Paul T. Tarr, Kevin Pyke, Ute Voss, Darren M. Wells, Anthony Bishopp
Summary: The study developed dual expression anatomy lines to track gene expression and anatomy changes in plant organs, which can be applied at different growth stages.
Article
Plant Sciences
Jerome De Pessemier, Taraka Ramji Moturu, Philippe Nacry, Rebecca Ebert, Hugues De Gernier, Pascal Tillard, Kamal Swarup, Darren M. Wells, Jim Haseloff, Seth C. Murray, Malcolm J. Bennett, Dirk Inze, Christopher Vincent, Christian Hermans
Summary: A positive correlation was found between root system size and high-affinity nitrate uptake in a core set of Arabidopsis natural accessions, highlighting the beneficial role of exploratory root organ in plant nitrogen acquisition. The study evaluated the role of root phenes in nitrogen acquisition and biomass production in different accessions of Arabidopsis thaliana. The low nitrogen treatment resulted in increased root to shoot biomass ratio and enhanced proliferation of lateral roots and root hairs. Greater biomass production could be achieved through increased root length or specific root hair characteristics.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Biochemistry & Molecular Biology
Nathan L. Mellor, Ute Voss, Alexander Ware, George Janes, Duncan Barrack, Anthony Bishopp, Malcolm J. Bennett, Markus Geisler, Darren M. Wells, Leah R. Band
Summary: Members of the B family of membrane-bound ATP-binding cassette (ABC) transporters play important roles in auxin efflux in plants. This study integrates ABCB localization data into a multicellular model to predict the impact of ABCB-mediated auxin transport on organ-scale distribution. The results suggest that ABCBs enable auxin efflux independently of PINs, but PINs predominantly mediate auxin efflux when co-localized with ABCBs.
Article
Agriculture, Multidisciplinary
Marcus Griffiths, Jonathan A. Atkinson, Laura-Jayne Gardiner, Ranjan Swarup, Michael P. Pound, Michael H. Wilson, Malcolm J. Bennett, Darren M. Wells
Summary: The genetic basis of root system architecture and resource adaptive responses in wheat was studied using a high-throughput germination paper-based plant phenotyping system and quantitative trait locus (QTL) analysis. Significant genotypic and nitrate-N treatment variation was found for seedling traits, and a total of 59 seedling trait QTLs were identified. Transcriptomic analysis revealed gene enrichment in N-related biological processes and differentially expressed genes related to root angle response. These findings provide genetic insight into root system architecture and plant adaptive responses, and offer targets for improving nitrogen capture in wheat.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2022)
Article
Agriculture, Multidisciplinary
Jacqueline L. Stroud, Iain Dummett, Simon J. Kemp, Craig J. Sturrock
Summary: The conversion from conventional tillage to no-tillage soil management practices improves aggregate stability and earthworm populations. UK farmers found that middened soil, which accounts for up to 42% of the soil surface, has significantly more earthworms than general soil. In a recent experimental field trial, middened areas covering 13% of the trial showed improved aggregate stability and porosity compared to general soil. These findings emphasize the importance of considering middens in assessing soil quality and health in arable systems.
ANNALS OF APPLIED BIOLOGY
(2023)
Article
Soil Science
Samuel W. Booth, Benedikt Kurtz, Martine I. de Heer, Sacha J. Mooney, Craig J. Sturrock
Summary: In this study, X-ray CT was used to visualize and quantify wireworms, their burrow networks, and the root architecture of maize, barley, and bare soil. The study found that the presence of root structures caused behavioral differences in wireworms, leading to variations in the volume and structure of burrow networks.
APPLIED SOIL ECOLOGY
(2022)
Article
Multidisciplinary Sciences
Guoqiang Huang, Azad Kilic, Michal Karady, Jiao Zhang, Poonam Mehra, Xiaoyun Song, Craig J. Sturrock, Wanwan Zhu, Hua Qin, Sjon Hartman, Hannah M. Schneider, Rahul Bhosale, Ian C. Dodd, Robert E. Sharp, Rongfeng Huang, Sacha J. Mooney, Wanqi Liang, Malcolm J. Bennett, Dabing Zhang, Bipin K. Pandey
Summary: Soil compaction poses a significant challenge to agriculture, inhibiting root elongation and affecting crop productivity. This study reveals that ethylene regulates the synthesis of auxin and abscisic acid, as well as cortical cell radial expansion, thereby impacting the ability of rice roots to penetrate compacted soil.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Riccardo Fusi, Serena Rosignoli, Haoyu Lou, Giuseppe Sangiorgi, Riccardo Bovina, Jacob K. Pattem, Aditi N. Borkar, Marco Lombardi, Cristian Forestan, Sara G. Milner, Jayne L. Davis, Aneesh Lale, Gwendolyn K. Kirschner, Ranjan Swarup, Alberto Tassinari, Bipin K. Pandey, Larry M. York, Brian S. Atkinson, Craig J. Sturrock, Sacha J. Mooney, Frank Hochholdinger, Matthew R. Tucker, Axel Himmelbach, Nils Stein, Martin Mascher, Kerstin A. Nagel, Laura De Gara, James Simmonds, Cristobal Uauy, Roberto Tuberosa, Jonathan P. Lynch, Gleb E. Yakubov, Malcolm J. Bennet, Rahul Bhosale, Silvio Salvi
Summary: Root angle in crops is an important trait for efficient utilization of soil resources. This study identifies a regulatory gene called EGT1 that controls root angle by affecting cell wall stiffness in elongating root cortical tissue. Mutations in the EGT1 gene result in a striking root phenotype with steeper growth angles in barley and wheat. These findings suggest that EGT1 plays a crucial role in exerting an antigravitropic mechanism to control root angle in cereal crops.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Anatomy & Morphology
Adam Best, Monika Egerbacher, Sophia Swaine, William Perez, Aziza Alibhai, Paul Rutland, Valentina Kubale, Samir A. A. El-Gendy, Mohamed A. M. Alsafy, Kerstin Baiker, Craig J. Sturrock, Catrin Sian Rutland
Summary: This systematic review compares the prevalence, histology, and anatomical location of Ossa cordis in different veterinary species and humans. It also discusses the associated factors, such as aging and cardiovascular disease, and the potential functions and formation mechanisms of Ossa cordis.
ANATOMIA HISTOLOGIA EMBRYOLOGIA
(2022)
Article
Agronomy
Shadia H. S. Kareem, Malcolm J. Hawkesford, Jayalath DeSilva, Minuka Weerasinghe, Darren M. Wells, Michael P. Pound, Jonathan A. Atkinson, M. John Foulkes
Summary: The study demonstrates genetic variation in seedling RSA traits in landrace-derived wheat lines above the elite parental cultivar Paragon, which could potentially be used to enhance nitrogen use efficiency in breeding programs.
EUROPEAN JOURNAL OF AGRONOMY
(2022)
Review
Soil Science
D. Luke R. Wardak, Faheem N. Padia, Martine I. de Heer, Craig J. Sturrock, Sacha J. Mooney
Summary: This paper reviews 34 studies that demonstrate the influence of zero-tillage (ZT) on porosity, depending on soil texture, pore size class, and depth. ZT can also affect important transport mechanisms that impact the fate of agrochemicals in soils, although the effects on hydraulic transport are less clear.
Article
Plant Sciences
Yi Xiao, Jen Sloan, Chris Hepworth, Marc Fradera-Soler, Andrew Mathers, Rachel Thorley, Alice Baillie, Hannah Jones, Tiangen Chang, Xingyuan Chen, Nazmin Yaapar, Colin P. Osborne, Craig Sturrock, Sacha. J. J. Mooney, Andrew. J. J. Fleming, Xin-Guang Zhu
Summary: Leaf structure plays a crucial role in photosynthesis, but the relationship between a single structural parameter and the overall photosynthetic performance is still debated. In this study, a mechanistic model called eLeaf was developed to capture the photosynthetic performance of rice leaves under various environmental conditions. The model successfully quantified the importance of different elements by analyzing imaging data and biochemical measurements. The results showed that photosynthetic metabolism was the major driver of increased carbon assimilation under elevated CO2 levels, and various structural elements made positive and negative contributions. The findings provide theoretical support for experimental data and highlight the significance of leaf structural plasticity in improving crop photosynthesis.
Article
Plant Sciences
Jordan K. Robson, John N. Ferguson, Lorna McAusland, Jonathan A. Atkinson, Christine Tranchant-Dubreuil, Phillipe Cubry, Francois Sabot, Darren M. Wells, Adam H. Price, Zoe A. Wilson, Erik H. Murchie
Summary: Rising temperatures and extreme heat events threaten rice production. Developing heat-tolerant rice is essential for food security. Researchers have developed a high-throughput chlorophyll fluorescence-based screen for photosynthetic heat tolerance, which has identified candidate genes for improving rice's heat tolerance.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Alison Tidy, Norliza Abu Bakar, David Carrier, Ian D. Kerr, Charlie Hodgman, Malcolm J. Bennett, Ranjan Swarup
Summary: AXR4 is an endoplasmic reticulum accessory protein that regulates the trafficking of auxin influx carriers AUXIN1 and LIKE-AUX2.
