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3-D Histogram-Based Segmentation and Leaf Detection for Rosette Plants
[chapter]
2015
Lecture Notes in Computer Science
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Here we present a 3-D histogram-based segmentation and recognition approach for top view images of rosette plants such as Arabidopsis thaliana and tobacco. ...
Furthermore a Euclidean-distance-map-based method for the detection of leaves and the corresponding plant leaf segmentation was developed. ...
In the last step the region growing algorithm labels each leaf region. Pipeline Parameters Besides the trained 3-D histogram cubes several parameters influence the segmentation and leaf detection. ...
doi:10.1007/978-3-319-16220-1_5
fatcat:avwdemrnlbbntodmfmqba33wzq
Rosette Tracker: An Open Source Image Analysis Tool for Automatic Quantification of Genotype Effects
2012
Plant Physiology
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In contrast with previously described monitoring tools, Rosette Tracker allows us to simultaneously quantify plant growth, photosynthesis, and leaf temperature-related parameters through the analysis of ...
We introduce Rosette Tracker, a new open source image analysis tool for evaluation of plant-shoot phenotypes. ...
ACKNOWLEDGMENTS The authors wish to thank Pieter Callebert, Laury Chaerle, and Xavier Vanrobaeys for setup and image acquisition of the time-lapse sequence in Example 2. ...
doi:10.1104/pp.112.202762
pmid:22942389
pmcid:PMC3490612
fatcat:n7sskorbljae7cdrljut5kdxoe
Developmental normalization of phenomics data generated by high throughput plant phenotyping systems
2020
Plant Methods
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The normalization is determined by cross-correlation at multiple time points of the time-series measurements, which may include rosette area, leaf size, and number. ...
DAPD is an effective method to control for temporal differences in development within plant phenotyping datasets. ...
Acknowledgements We thank Andrew Robinson for helping set up the infrastructure for data storage and transfer. We thank Dr. Ricarda Jost and Dr. Meiyan Ren for assisting with experiments. ...
doi:10.1186/s13007-020-00653-x
pmid:32817754
pmcid:PMC7424680
fatcat:coxifch5kbhpdkfzz27yyq7yfy
Developmental Normalization of Phenomics Data Generated by High Throughput Plant Phenotyping Systems
[article]
2020
bioRxiv
pre-print
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The normalization is determined by cross-correlation at multiple time points of the time-series measurements, which may include rosette area, leaf size, and number. ...
Sowing time is commonly used as the temporal reference for Arabidopsis thaliana (Arabidopsis) experiments in high throughput plant phenotyping (HTPP) systems. ...
These stages were identified by the leaf number based on the adjusted BBCH scale [3].
number trend may vary from plant to plant within the same line/mutant population at a time point. ...
doi:10.1101/2020.05.17.100917
fatcat:b2txl47nkrebxiwrk53d4bjsoi
Plant high-throughput phenotyping using photogrammetry and imaging techniques to measure leaf length and rosette area
2016
Computers and Electronics in Agriculture
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16 Plant phenotyping is central to understand causal effects of genotypes and environments 17 on trait expression and is a critical factor in expediting plant breeding. ...
In recent years, photogrammetry and image processing techniques have been introduced to 21 plant phenotyping, but cost efficiency issues remain when combining these two techniques 22 ...
Figure A) to 778 D) stands for Day 1 to Day 4, respectively. The green histograms are the distributions for 779 parameter a and the blue histograms are for parameter b. ...
doi:10.1016/j.compag.2016.04.002
fatcat:2vmv3qo4czdrvf5ex2mzugbyay
Antiviral ARGONAUTEs Against Turnip Crinkle Virus Revealed by Image-based Trait Analysis
2019
Plant Physiology
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This process captured and analyzed growth and leaf color of Arabidopsis (Arabidopsis thaliana) plants in response to virus infection over time. ...
A quantitative phenotyping protocol using an image-based color trait analysis pipeline on the PlantCV platform, with temporal red, green, and blue imaging and a computational segmentation algorithm, was ...
Kira Veley for support and critique of the study. We also thank Robyn Allscheid for constructive editorial advices on this manuscript. ...
doi:10.1104/pp.19.00121
pmid:31043494
pmcid:PMC6752898
fatcat:tadll5r4zbfqpeighdtu27es2a
Leveraging multiple datasets for deep leaf counting
[article]
2017
arXiv
pre-print
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Here, we propose an automated, deep learning based approach for counting leaves in model rosette plants. ...
While state-of-the-art results on leaf counting with deep learning methods have recently been reported, they obtain the count as a result of leaf segmentation and thus require per-leaf (instance) segmentation ...
We acknowledge and thank NVIDIA for providing hardware essential for our work. Finally we would like to thank all the organisers of the CVPPP workshop for making it happen. ...
arXiv:1709.01472v1
fatcat:3a23hdso5bfvlppkblf3n3mnra
Counting Dense Leaves under Natural Environments via anImproved Deep-Learning-Based Object Detection Algorithm
2021
Agriculture
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The leaf is the organ that is crucial for photosynthesis and the production of nutrients in plants; as such, the number of leaves is one of the key indicators with which to describe the development and ...
To address the challenge in counting dense and overlapped plant leaves under natural environments, we proposed an improved deep-learning-based object detection algorithm by merging a space-to-depth module ...
Aich and Stavness [24] used deep convolutional and deconvolutional network (DCDN) to segment the rosette plant region and to count the rosette plant leaves. Giuffrida et al. ...
doi:10.3390/agriculture11101003
fatcat:ubny6uzznvhclpywascmumhwoq
Leveraging multiple datasets for deep leaf counting
[article]
2017
bioRxiv
pre-print
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Here, we propose an automated, deep learning based approach for counting leaves in model rosette plants. ...
While state-of-the-art results on leaf counting with deep learning methods have recently been reported, they obtain the count as a result of leaf segmentation and thus require per-leaf (instance) segmentation ...
We acknowledge and thank NVIDIA for providing hardware essential for our work. Finally we would like to thank all the organisers of the CVPPP workshop for making it happen. ...
doi:10.1101/185173
fatcat:modrbsebzbh2xanomyaauvarsq
Leveraging Multiple Datasets for Deep Leaf Counting
2017
2017 IEEE International Conference on Computer Vision Workshops (ICCVW)
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Here, we propose an automated, deep learning based approach for counting leaves in model rosette plants. ...
While stateof-the-art results on leaf counting with deep learning methods have recently been reported, they obtain the count as a result of leaf segmentation and thus require per-leaf (instance) segmentation ...
We acknowledge and thank NVIDIA for providing hardware essential for our work. Finally we would like to thank all the organisers of the CVPPP workshop for making it happen. ...
doi:10.1109/iccvw.2017.243
dblp:conf/iccvw/DobrescuGT17
fatcat:b6j4r6itvvfzrnqoqyogjb2rv4
Antiviral Functions of ARGONAUTE Proteins During Turnip Crinkle Virus Infection Revealed by Image-based Trait Analysis in Arabidopsis
[article]
2018
bioRxiv
pre-print
Preserved Fulltext
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The file type is application/pdf.
This process captured and analyzed growth and leaf color of Arabidopsis plants in response to virus infection over time. ...
A quantitative phenotyping protocol using an image-based color trait analysis pipeline on the PlantCV platform, with temporal red, green and blue (RGB) imaging and a computational segmentation algorithm ...
(B) One example of original raw plant 905 image, segmented pseudo-color image, and overlaid image of Col-0 plant inoculated with TCV CPB
Fig 3 . 3 TCV infection-caused temporal changes in rosette size ...
doi:10.1101/487322
fatcat:ff7lhf7zt5cmfpdtlk65nhdmxi
Contour-Based Plant Leaf Image Segmentation Using Visual Saliency
[chapter]
2015
Lecture Notes in Computer Science
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In this paper, we presented a new method that is based on active contours combined with saliency map for plant leaf segmentation. ...
Segmentation based on active contour has been received widespread concerns recently for its good flexible performance. ...
Fig. 1 . 1 Saliency detect algorithm
Fig. 2 . 2 Spatial distance compute (Colorfigure online)
Fig. 3 .Fig. 4 . 34 Image-based plant phenotyping detect (Color figure online) Diseased plant leaf detect ...
doi:10.1007/978-3-319-21963-9_5
fatcat:p546jly3arf6fdfm5eawjzp3be
Leaf segmentation in plant phenotyping: a collation study
2015
Machine Vision and Applications
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Here we focus on the most common rosette model plants, Arabidopsis and young tobacco. ...
Image-based plant phenotyping is a growing application area of computer vision in agriculture. A key task is the segmentation of all individual leaves in images. ...
Acknowledgments We would like to thank participants of the 2014 CVPPP workshop for comments and annotators that have contributed to this work. ...
doi:10.1007/s00138-015-0737-3
fatcat:c4dmf4exezgi3kiaxdipw3h7ai
Arabidopsis CYCD3 D-type cyclins link cell proliferation and endocycles and are rate-limiting for cytokinin responses
2007
Proceedings of the National Academy of Sciences of the United States of America
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overall organ growth, as well as mediating cytokinin effects in apical growth and development. cell division ͉ cyclin D ͉ flowering time ͉ plant development Author contributions: W.D., S.S., M.M., and ...
Current understanding of the integration of cell division and expansion in the development of plant lateral organs such as leaves is limited. ...
We thank Susan Howroyd for technical help, the Swiss Centre for Functional Genomics (Zürich, Switzerland) for microarray analysis, and T. Jack ...
doi:10.1073/pnas.0704166104
pmid:17726100
pmcid:PMC1964848
fatcat:7pdhct4vybdhzjhatheftsvyl4
Novel Low Cost 3D Surface Model Reconstruction System for Plant Phenotyping
2017
Journal of Imaging
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In order to improve the quality of the 3D models, we segmented the plant objects based on the PlantCV platform. ...
We present an image-based 3D plant reconstruction system that can be achieved by using a single camera and a rotation stand. ...
Figure 3 . 3 Pseudo code for the object segmentation based on the PlantCV (Plant Computer Vision) suite. are the input images and R(x,y) are the segmented result images. , and , are the values from HSV ...
doi:10.3390/jimaging3030039
fatcat:pg3lwiomdvfkbizdpboit2codu
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