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Leaf segmentation and parallel phenotyping for the analysis of gene networks in plants

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Abstract
Over the last 4 years phenotyping is becoming more and more automated, decreasing a lot of manual labour. Features, which uniquely define the plant, can be extracted automatically from images. As a lot of plant data has to be processed in order to extract the features, fast processing of these features is a challenge. Therefore in this paper, a new method for automatic segmentation of individual leaves from plants with a circular arrangement of leaves (rosettes) is proposed, together with an algorithm to extract the line of symmetry of the leaf. Furthermore, in order to achieve fast processing for phenotyping plants, four feature extraction methods are parallelised in order to run on the CPU and GPU. Our evaluation results show that by parallelizing the feature extraction methods, it is possible to calculate the image moments, area, histogram and sum of intensities 5 to 45 times faster than single threaded implementations.
Keywords
Segmentation, Feature extraction, Parallelisation, Image Analysis, Phenotyping, GROWSCREEN, QUANTIFICATION, GROWTH, ARABIDOPSIS-THALIANA, IMAGE-ANALYSIS

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Please use this url to cite or link to this publication:

Chicago
Janssens, Olivier, Jonas De Vylder, Jan Aelterman, Steven Verstockt, Wilfried Philips, Dominique Van Der Straeten, Sofie Van Hoecke, and Rik Van de Walle. 2013. “Leaf Segmentation and Parallel Phenotyping for the Analysis of Gene Networks in Plants.” In 2013 Proceedings of the 21st European Signal Processing Conference (Eusipco). New York, NY, USA: IEEE.
APA
Janssens, O., De Vylder, J., Aelterman, J., Verstockt, S., Philips, W., Van Der Straeten, D., Van Hoecke, S., et al. (2013). Leaf segmentation and parallel phenotyping for the analysis of gene networks in plants. 2013 Proceedings of the 21st European signal processing conference (Eusipco). Presented at the 21st European Signal Processing conference (Eusipco 2013), New York, NY, USA: IEEE.
Vancouver
1.
Janssens O, De Vylder J, Aelterman J, Verstockt S, Philips W, Van Der Straeten D, et al. Leaf segmentation and parallel phenotyping for the analysis of gene networks in plants. 2013 Proceedings of the 21st European signal processing conference (Eusipco). New York, NY, USA: IEEE; 2013.
MLA
Janssens, Olivier, Jonas De Vylder, Jan Aelterman, et al. “Leaf Segmentation and Parallel Phenotyping for the Analysis of Gene Networks in Plants.” 2013 Proceedings of the 21st European Signal Processing Conference (Eusipco). New York, NY, USA: IEEE, 2013. Print.
@inproceedings{4144098,
  abstract     = {Over the last 4 years phenotyping is becoming more and more automated, decreasing a lot of manual labour. Features, which uniquely define the plant, can be extracted automatically from images. As a lot of plant data has to be processed in order to extract the features, fast processing of these features is a challenge. Therefore in this paper, a new method for automatic segmentation of individual leaves from plants with a circular arrangement of leaves (rosettes) is proposed, together with an algorithm to extract the line of symmetry of the leaf. Furthermore, in order to achieve fast processing for phenotyping plants, four feature extraction methods are parallelised in order to run on the CPU and GPU. Our evaluation results show that by parallelizing the feature extraction methods, it is possible to calculate the image moments, area, histogram and sum of intensities 5 to 45 times faster than single threaded implementations.},
  author       = {Janssens, Olivier and De Vylder, Jonas and Aelterman, Jan and Verstockt, Steven and Philips, Wilfried and Van Der Straeten, Dominique and Van Hoecke, Sofie and Van de Walle, Rik},
  booktitle    = {2013 Proceedings of the 21st European signal processing conference (Eusipco)},
  issn         = {2219-5491},
  keyword      = {Segmentation,Feature extraction,Parallelisation,Image Analysis,Phenotyping,GROWSCREEN,QUANTIFICATION,GROWTH,ARABIDOPSIS-THALIANA,IMAGE-ANALYSIS},
  language     = {eng},
  location     = {Marrakech, Marokko},
  pages        = {5},
  publisher    = {IEEE},
  title        = {Leaf segmentation and parallel phenotyping for the analysis of gene networks in plants},
  year         = {2013},
}

Web of Science
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