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HTPheno: An image analysis pipeline for high-throughput plant phenotyping

Anja Hartmann, Tobias Czauderna, Roberto Hoffmann, Nils Stein, Falk Schreiber
2011 BMC Bioinformatics  
Results: This paper presents an image analysis pipeline (HTPheno) for high-throughput plant phenotyping. HTPheno is implemented as a plugin for ImageJ, an open source image processing software.  ...  Conclusions: HTPheno, an open source image analysis pipeline, supplies a flexible and adaptable ImageJ plugin which can be used for automated image analysis in high-throughput plant phenotyping and therefore  ...  HTPheno is such a plugin and provides an adaptable image analysis pipeline for high-throughput phenotyping.  ... 
doi:10.1186/1471-2105-12-148 pmid:21569390 pmcid:PMC3113939 fatcat:tpeurxtj3veuth6yd4ljvyl5ji

Affordable Imaging Lab for Noninvasive Analysis of Biomass and Early Vigour in Cereal Crops

Rita Armoniené, Firuz Odilbekov, Vivekanand Vivekanand, Aakash Chawade
2018 BioMed Research International  
The LCP lab is an affordable alternative for analysis of cereal crops when access to a high-throughput phenotyping facility is unavailable or when the experiments require growing plants in highly controlled  ...  Plant phenotyping by imaging allows automated analysis of plants for various morphological and physiological traits.  ...  Supplementary Materials Description of the two files: Supplementary File 1: R script for preparing barcodes. Supplementary File 2: script for the software digiCamControl for imaging.  ... 
doi:10.1155/2018/5713158 pmid:29850536 pmcid:PMC5933035 fatcat:tuh6rb52kbh6rpxhzww6chel6y

Integrated Analysis Platform: An Open-Source Information System for High-Throughput Plant Phenotyping

C. Klukas, D. Chen, J.-M. Pape
2014 Plant Physiology  
Here, we present Integrated Analysis Platform (IAP), an open-source framework for high-throughput plant phenotyping.  ...  High-throughput phenotyping is emerging as an important technology to dissect phenotypic components in plants.  ...  Moses Mahugu Muraya, and Hea-Jung Jeon (Leibniz Institute of Plant Genetics and Crop Plant Research) as users of the imaging system and especially Thomas Altmann for valuable feedback and support during  ... 
doi:10.1104/pp.113.233932 pmid:24760818 pmcid:PMC4044849 fatcat:hygbj5s6kbb3rnl7h7ye6fo7om

Analysis of high-throughput plant image data with the information system IAP

Christian Klukas, Jean-Michel Pape, Alexander Entzian
2012 Journal of Integrative Bioinformatics  
This work presents a sophisticated information system, the Integrated Analysis Platform (IAP), an approach supporting large-scale image analysis for different species and imaging systems.  ...  analysis, data management for raw data and analysis results, to the automated generation of experiment reports.  ...  Building blocks of image analysis pipelines Traditionally different approaches are used to define image analysis pipelines.  ... 
doi:10.2390/biecoll-jib-2012-191 pmid:22745177 fatcat:cmwfn6vnjzbqrpc4hutx2q2s3i

Analysis of high-throughput plant image data with the information system IAP

Christian Klukas, Jean-Michel Pape, Alexander Entzian
2012 Journal of Integrative Bioinformatics  
SummaryThis work presents a sophisticated information system, the Integrated Analysis Platform (IAP), an approach supporting large-scale image analysis for different species and imaging systems.  ...  work, cover the complete end-to-end pipeline, starting with the image transfer from the imaging infrastructure, (grid distributed) image analysis, data management for raw data and analysis results, to  ...  Building blocks of image analysis pipelines Traditionally different approaches are used to define image analysis pipelines.  ... 
doi:10.1515/jib-2012-191 fatcat:v3l6l5wlpfhydhvuqk4xw3ggsy

Image-Based, Organ-Level Plant Phenotyping for Wheat Improvement

Cody S. Bekkering, Jin Huang, Li Tian
2020 Agronomy  
This review discusses challenges and advancements in image analysis platforms for wheat phenotyping at the organ level.  ...  Phenotypic information has historically been instrumental in wheat breeding for improved traits.  ...  Conveyor-assisted imaging systems that can generate images suitable for analysis with high throughput phenotyping software are constructed by companies such as Phenospex (Heerlen, Netherlands), Lemnatech  ... 
doi:10.3390/agronomy10091287 fatcat:n27usx54szhetk3litpalg5o4y

A High-Throughput Phenotyping Pipeline for Image Processing and Functional Growth Curve Analysis

Ronghao Wang, Yumou Qiu, Yuzhen Zhou, Zhikai Liang, James C. Schnable
2020 Plant Phenomics  
High-throughput phenotyping system has become more and more popular in plant science research.  ...  The data analysis for such a system typically involves two steps: plant feature extraction through image processing and statistical analysis for the extracted features.  ...  Acknowledgments The authors wish to acknowledge Yuhang Xu, Jinyu Li, and Zheng Xu for their helpful suggestions and feedback.  ... 
doi:10.34133/2020/7481687 pmid:33313562 pmcid:PMC7706310 fatcat:r4v5wsv4fzgjxlpqhtz3kogdpi

A novel mesh processing based technique for 3D plant analysis

Anthony Paproki, Xavier Sirault, Scott Berry, Robert Furbank, Jurgen Fripp
2012 BMC Plant Biology  
In recent years, imaging based, automated, non-invasive, and non-destructive high-throughput plant phenotyping platforms have become popular tools for plant biology, underpinning the field of plant phenomics  ...  Result: In this paper, we present a novel 3D mesh based technique developed for temporal high-throughput plant phenomics and perform initial tests for the analysis of Gossypium hirsutum vegetative growth  ...  Acknowledgements The analysis pipeline described in this manuscript was developed as part of an infrastructure grant received under the Commonwealth Government's National Collaborative Research Infrastructure  ... 
doi:10.1186/1471-2229-12-63 pmid:22553969 pmcid:PMC3464618 fatcat:pn4lk5h6lbgcbaaysw4s5ptd64

Advanced phenotyping and phenotype data analysis for the study of plant growth and development

Md. Matiur Rahaman, Dijun Chen, Zeeshan Gillani, Christian Klukas, Ming Chen
2015 Frontiers in Plant Science  
In this review, we discuss recent developments of high-throughput plant phenotyping infrastructure including imaging techniques and corresponding principles for phenotype data analysis.  ...  High-throughput phenotyping platforms have also been developed that capture phenotype data from plants in a non-destructive manner.  ...  We are grateful to Andrew Harrison, Rafe Lyall, Björn Sommer for their critical reading of the manuscript, and also thank the reviewers for many valuable suggestions to improve this manuscript.  ... 
doi:10.3389/fpls.2015.00619 pmid:26322060 pmcid:PMC4530591 fatcat:i4wqh2jxojgrbofwkwice2nj7y

Using Plant Phenomics to Exploit the Gains of Genomics

Aditya Pratap, Sanjeev Gupta, Ramakrishnan Nair, S. Gupta, Roland Schafleitner, P. Basu, Chandra Singh, Umashanker Prajapati, Ajeet Gupta, Harsh Nayyar, Awdhesh Mishra, Kwang-Hyun Baek
2019 Agronomy  
It also discusses its evolution to modern day high throughput phenotyping (HTP), traits amenable to HTP, integration of HTP with genomics and the scope of utilizing these tools for crop improvement.  ...  The low-cost, automated and semi-automated methods for data acquisition, storage and analysis are now available which allow precise quantitative analysis of plant structure and function; and genetic dissection  ...  All recent developments in plant phenotyping are driven by the technological advancements in imaging sensors, robotics and software pipelines for analysis of images and the data.  ... 
doi:10.3390/agronomy9030126 fatcat:4vmmxxx4c5av7jcmsrzsova5oa

PI-Plat: A high-resolution image-based 3D reconstruction method to estimate growth dynamics of rice inflorescence traits [article]

Jaspreet Sandhu, Feiyu Zhu, Puneet Paul, Tian Gao, Balpreet K. Dhatt, Yufeng Ge, Paul Staswick, Hongfeng Yu, Harkamal Walia
2019 bioRxiv   pre-print
Relatively low-cost sequencing platforms have facilitated high-throughput genotyping, while phenotyping, especially for complex traits, has posed major challenges for crop improvement.  ...  AbstractBackgroundRecent advances in image-based plant phenotyping have improved our capability to study vegetative stage growth dynamics.  ...  HTPheno: An image analysis pipeline for high-throughput plant phenotyping. BMC Bioinformatics. 2011;12:148. doi:10.1186/1471-2105-12- . Chaudhury A, Barron JL.  ... 
doi:10.1101/835306 fatcat:7ml3jap34nabxfkgjt6pc2bmea

Validation of plant part measurements using a 3D reconstruction method suitable for high-throughput seedling phenotyping

Franck Golbach, Gert Kootstra, Sanja Damjanovic, Gerwoud Otten, Rick van de Zedde
2015 Machine Vision and Applications  
In plant phenotyping, there is a demand for high-throughput, non-destructive systems that can accurately analyse various plant traits by measuring features such as plant volume, leaf area, and stem length  ...  We developed image processing methods for the identification and segmentation of plant organs (stem and leaf) from the 3D plant model.  ...  Plant Phenotyping Network (EPPN), under Grant agreement no. 284443.  ... 
doi:10.1007/s00138-015-0727-5 fatcat:bnmobskudrfpji75sh3y6au6bm

High‐throughput NGS‐based genotyping and phenotyping: Role in genomics‐assisted breeding for soybean improvement

Javaid Akhter Bhat, Deyue Yu
2021 Legume Science  
Hence, high-throughput genotyping (HTG) providing higher genome-wide marker density, as well as accurate and precise phenotyping using high-throughput digital phenotyping (HTP) platforms, can significantly  ...  Soybean is an important food crop that provides edible protein and oil for human and animal nutrition.  ...  for high-throughput MAS of soybean plants showing enhanced SCN resistance.  ... 
doi:10.1002/leg3.81 fatcat:hq43tetixresxodls4xvagfube

Optimizing experimental procedures for quantitative evaluation of crop plant performance in high throughput phenotyping systems

Astrid Junker, Moses M. Muraya, Kathleen Weigelt-Fischer, Fernando Arana-Ceballos, Christian Klukas, Albrecht E. Melchinger, Rhonda C. Meyer, David Riewe, Thomas Altmann
2015 Frontiers in Plant Science  
, and the image analysis and statistical methods for data evaluation.  ...  Non-invasive and high throughput (HT) phenotyping technologies offer the opportunity to monitor and quantify performance dynamics of several hundreds of plants at a time.  ...  The IAP (Integrated Analysis Platform) open-source software for high-throughput plant image analyses (Klukas et al., 2014) was used for image-based plant feature extraction.  ... 
doi:10.3389/fpls.2014.00770 pmid:25653655 pmcid:PMC4299434 fatcat:4k5wi5ib6rblxj7ied4vl34x24

Holistic and component plant phenotyping using temporal image sequence

Sruti Das Choudhury, Srinidhi Bashyam, Yumou Qiu, Ashok Samal, Tala Awada
2018 Plant Methods  
Tala, "Holistic and component plant phenotyping using temporal image sequence" (2018). CSE Journal Articles. 164.  ...  Abstract Background: Image-based plant phenotyping facilitates the extraction of traits noninvasively by analyzing large number of plants in a relatively short period of time.  ...  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
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