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

Olivier Janssens UGent, Jonas De Vylder, Jan Aelterman UGent, Steven Verstockt UGent, Wilfried Philips UGent, Dominique Van Der Straeten UGent, Sofie Van Hoecke UGent and Rik Van de Walle UGent (2013) 2013 Proceedings of the 21st European signal processing conference (Eusipco).
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.
Please use this url to cite or link to this publication:
author
organization
year
type
conference (proceedingsPaper)
publication status
published
subject
keyword
Segmentation, Feature extraction, Parallelisation, Image Analysis, Phenotyping, GROWSCREEN, QUANTIFICATION, GROWTH, ARABIDOPSIS-THALIANA, IMAGE-ANALYSIS
in
2013 Proceedings of the 21st European signal processing conference (Eusipco)
pages
5 pages
publisher
IEEE
place of publication
New York, NY, USA
conference name
21st European Signal Processing conference (Eusipco 2013)
conference location
Marrakech, Marokko
conference start
2013-09-09
conference end
2013-09-13
Web of Science type
Proceedings Paper
Web of Science id
000341754500275
ISSN
2219-5491
language
English
UGent publication?
yes
classification
P1
copyright statement
I have transferred the copyright for this publication to the publisher
id
4144098
handle
http://hdl.handle.net/1854/LU-4144098
date created
2013-09-24 15:13:01
date last changed
2017-01-02 09:53:30
@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},
}

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.