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A Review of Imaging Techniques for Plant Phenotyping

Lei Li, Qin Zhang, Danfeng Huang
2014 Sensors  
In high-throughput phenotyping platforms, a variety of imaging methodologies are being used to collect data for quantitative studies of complex traits related to the growth, yield and adaptation to biotic  ...  The features used to apply these imaging techniques to plant phenotyping are described and discussed in this review.  ...  Conflicts of Interest The authors declare no conflict of interest.  ... 
doi:10.3390/s141120078 pmid:25347588 pmcid:PMC4279472 fatcat:o2nifgjn5fec3o5ttjbo6cszrm

Leveraging Image Analysis for High-Throughput Plant Phenotyping

Sruti Das Choudhury, Ashok Samal, Tala Awada
2019 Frontiers in Plant Science  
the state-of-the-art methods; (4) an overview of the state-of-the-art image-based high-throughput plant phenotyping methods; and (5) open problems for the advancement of this research field.  ...  The paper provides (1) a framework for plant phenotyping in a multimodal, multi-view, time-lapsed, high-throughput imaging system; (2) a taxonomy of phenotypes that may be derived by image analysis for  ...  This research was supported by the Nebraska Agricultural Experiment Station with funding from the Hatch Act capacity funding program (Accession Number 1011130) from the USDA National Institute of Food  ... 
doi:10.3389/fpls.2019.00508 pmid:31068958 pmcid:PMC6491831 fatcat:xr6pxm7kfjfl5jdmd6ls6454pi

Watching plants grow – a position paper on computer vision and Arabidopsis thaliana

Jonathan Bell, Hannah M. Dee
2017 IET Computer Vision  
As there is a close correlation between plant weight and leaf area, [4], using images to measure leaf area gives biologists a useful measure of the size of the plant and using images as the basis of measurement  ...  We present a comprehensive overview of image processing and analysis work done to support research into the model flowering plant Arabidopsis thaliana.  ...  Acknowledgements Jonathan Bell's work is funded by the EPSRC funded project "Dynamic modelling of plant growth with computer vision", project number EP/LO17253/1.  ... 
doi:10.1049/iet-cvi.2016.0127 fatcat:34hp7toydrhf7kbobwt7aq6fnq

All roads lead to growth: imaging-based and biochemical methods to measure plant growth

2019 Journal of Experimental Botany  
In this review, we summarise the cellular and molecular mechanisms underlying plant growth, highlight state-of-the-art imaging and non-imaging-based techniques to quantitatively measure growth, including  ...  a discussion of their advantages and drawbacks, and suggest a terminology for growth rates depending on the type of technique used.  ...  Key developments in measuring plant growthImaging system based on laser-scanning Dornbusch et al. (2012) used laser-scanning to obtain 3D image sequences of plants growing in 12-36 pots (each containing  ... 
doi:10.1093/jxb/erz406 pmid:31613967 pmcid:PMC6913701 fatcat:qdzze7mp6zg6lh5e253jg7lui4

High-throughput Phenotyping for Abiotic Stress Resilience in Cereals

Nusrat Ul Islam, Shabir Hussain Wani, Gowhar Ali, Zahoor Ahmad Dar, Altaf Wani, Ajaz Lone
2021 Journal of Cereal Research  
By 2050, the world's population is projected to hit 9 billion and the current production of food must be doubled to meet the needs of a rising population Langridge, 2011, Ganie et al., 2021).  ...  Currently, intermittent precipitation events, high temperatures, drought, salinity stress, etc. are more likely to occur due to global climate change, which has increased the pace of biotic and abiotic  ...  to estimate leaf greenness and ground cover, a far-infrared thermometer to assess canopy temperature, a 3D stereo imaging system to determine plant biomass.  ... 
doi:10.25174/2582-2675/2021/111256 fatcat:vu4psalqbbdqzjbvzwwmhq4m6u

Holistic and component plant phenotyping using temporal image sequence

Sruti Das Choudhury, Srinidhi Bashyam, Yumou Qiu, Ashok Samal, Tala Awada
2018 Plant Methods  
The total number of leaves are counted and the length of each leaf is measured for all images in the sequence to monitor leaf growth.  ...  Tala, "Holistic and component plant phenotyping using temporal image sequence" (2018). CSE Journal Articles. 164.  ...  Acknowledgements Authors appreciate Dipal Bhandari for his contributions in preparing the ground truth of the dataset.  ... 
doi:10.1186/s13007-018-0303-x pmid:29760766 pmcid:PMC5944015 fatcat:uw6pmangrnfijkw3kr4n7wrvom

Visual Growth Tracking for Automated Leaf Stage Monitoring Based on Image Sequence Analysis

Srinidhi Bashyam, Sruti Das Choudhury, Ashok Samal, Tala Awada
2021 Remote Sensing  
The method accepts an image sequence of a plant as the input and automatically generates a leaf status report containing the phenotypes, which are crucial in the understanding of a plant's growth, i.e.  ...  In this paper, we define a new problem domain, called visual growth tracking, to track different parts of an object that grow non-uniformly over space and time for application in image-based plant phenotyping  ...  of Nebraska-Lincoln, USA, for generating the images used in this study.  ... 
doi:10.3390/rs13050961 fatcat:dxj2dsira5dpzlm43h7uvmn7zi

Approaches to three-dimensional reconstruction of plant shoot topology and geometry

Jonathon A. Gibbs, Michael Pound, Andrew P. French, Darren M. Wells, Erik Murchie, Tony Pridmore
2017 Functional Plant Biology  
Here we review approaches to the reconstruction of 3D models of plant shoots from image data, consider current applications in plant and crop science, and identify remaining challenges.  ...  With access to 3D models of real plants it is possible to acquire detailed morphological and gross developmental data that can be used to study their ecophysiology, leading to an increase in crop yield  ...  They successfully monitored rosette and individual leaf growth in 483 Arabidopsis. 484 Challenges and opportunities 485 With accurate 3D models various traits such as the tolerance, resistance, architecture  ... 
doi:10.1071/fp16167 pmid:32480547 fatcat:e3uf4zj7jjcvpnextyf4v6ogom

Phenotyping of poplar seedling leaves based on a 3D visualization method

Chunhua Hu, Pingping Li, Zhou Pan
2018 International Journal of Agricultural and Biological Engineering  
In plant research, there is a demand for non-destructive and non-invasive trait measurement methods for phenotyping that can be used to accurately analyze various aspects of plants, such as stem length  ...  In this study, a method for measuring the leaf geometric characteristics of poplar seedlings based on 3D visualization via the use of time-of-flight (ToF) and digital cameras was proposed.  ...  Biskup [24] designed a stereo vision system with two cameras to build 3D models of soybean plant foliage and analyzed the angle of inclination of leaves and its changes over time.  ... 
doi:10.25165/j.ijabe.20181106.4110 fatcat:jpjl3k3jmnbgjar6qy4feumfyi

Future Scenarios for Plant Phenotyping

Fabio Fiorani, Ulrich Schurr
2013 Annual Review of Plant Biology  
We provide an overview of the inherently multidisciplinary research in plant phenotyping, focusing on traits that will assist in selecting genotypes with increased resource use efficiency.  ...  For personal use only.  ...  The work at the Jülich Plant Phenotyping Centre is institutionally funded by the Helmholtz Association and supported by third-party projects of the state of North Rhine-Westphalia (PhenoCrops project number  ... 
doi:10.1146/annurev-arplant-050312-120137 pmid:23451789 fatcat:ex3anila4vbzvb2ck5hzv4skv4

Arabidopsis NPF4.6 and NPF5.1 Control Leaf Stomatal Aperture by Regulating Abscisic Acid Transport

Takafumi Shimizu, Yuri Kanno, Hiromi Suzuki, Shunsuke Watanabe, Mitsunori Seo
2021 Genes  
Promoter activities of NPF5.1 were detected in several leaf cell types.  ...  Although several transmembrane ABA transporters have been identified, how the movement of ABA within plants is regulated is not fully understood.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/genes12060885 pmid:34201150 pmcid:PMC8227765 fatcat:wyyyxmkm2fcjteamukh5rn6z3u

Machine Vision System for 3D Plant Phenotyping

Ayan Chaudhury, John L. Barron
2018 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
We present an automated system for analyzing plant growth in indoor conditions. A gantry robot system is used to perform scanning tasks in an automated manner throughout the lifetime of the plant.  ...  click and get back the growth analysis results at the end of the lifetime of the plant with no intermediate intervention.  ...  ACKNOWLEDGMENTS The authors gratefully acknowledge CFI support to acquire/ build the growth chamber, the robot arm and the near infrared scanner.  ... 
doi:10.1109/tcbb.2018.2824814 pmid:29993836 fatcat:yrxfjl7345g4dmfm2nzzhmev4u

3D Laser Triangulation for Plant Phenotyping in Challenging Environments

Katrine Kjaer, Carl-Otto Ottosen
2015 Sensors  
(rapeseed), using a simple linear correlation between scanned parameters and destructive growth measurements.  ...  Secondly, we demonstrate that it is possible to estimate phenotypic variation amongst the growth pattern of ten genotypes of Brassica napus L.  ...  We further thank Jülich Research Center for providing the ten rapeseed genotypes as part of a pan European EPPN trial, Ruth Nielsen for maintenance of the plant material, and Kaj Ole Dideriksen and Jakob  ... 
doi:10.3390/s150613533 pmid:26066990 pmcid:PMC4507705 fatcat:o63tamtmxvgpjkqnhbj3gne6xu

High-Throughput Plant Phenotyping Platform (HT3P) as a Novel Tool for Estimating Agronomic Traits From the Lab to the Field

Daoliang Li, Chaoqun Quan, Zhaoyang Song, Xiang Li, Guanghui Yu, Cheng Li, Akhter Muhammad
2021 Frontiers in Bioengineering and Biotechnology  
Food scarcity, population growth, and global climate change have propelled crop yield growth driven by high-throughput phenotyping into the era of big data.  ...  Fortunately, the high-throughput plant phenotyping platform (HT3P), employing advanced sensors and data collection systems, can take full advantage of non-destructive and high-throughput methods to monitor  ...  ACKNOWLEDGMENTS The authors would like to thank the editors and reviewers for their valuable input, time, and suggestions for improving the overall quality of the manuscript.  ... 
doi:10.3389/fbioe.2020.623705 pmid:33520974 pmcid:PMC7838587 fatcat:5rfrtcrkr5bcphaaemxrvle4ym

Plant phenomics and the need for physiological phenotyping across scales to narrow the genotype-to-phenotype knowledge gap

Dominik K. Großkinsky, Jesper Svensgaard, Svend Christensen, Thomas Roitsch
2015 Journal of Experimental Botany  
assessment of responses under defined environments with advanced crop models.  ...  to be used as proxy for the underlying processes.  ...  Collinge for critical proofreading of the manuscript. We also thank the University of Copenhagen and the Promilleafgiftsfonden for landbrug for financial support.  ... 
doi:10.1093/jxb/erv345 pmid:26163702 fatcat:tdskjk4lvndm5pqztp7fuh2y5e
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