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Quantitative analysis of venation patterns of Arabidopsis leaves by supervised image analysis

Stijn Dhondt UGent, Dirk Van Haerenborgh UGent, Caroline Van Cauwenbergh UGent, Roeland Merks UGent, Wilfried Philips UGent, Gerrit Beemster UGent and Dirk Inzé UGent (2012) PLANT JOURNAL. 69(3). p.553-563
abstract
The study of transgenic Arabidopsis lines with altered vascular patterns has revealed key players in the venation process, but details of the vascularization process are still unclear, partly because most lines have only been assessed qualitatively. Therefore, quantitative analyses are required to identify subtle perturbations in the pattern and to test dynamic modeling hypotheses using biological measurements. We developed an online framework, designated Leaf Image Analysis Interface (LIMANI), in which venation patterns are automatically segmented and measured on dark-field images. Image segmentation may be manually corrected through use of an interactive interface, allowing supervision and rectification steps in the automated image analysis pipeline and ensuring high-fidelity analysis. This online approach is advantageous for the user in terms of installation, software updates, computer load and data storage. The framework was used to study vascular differentiation during leaf development and to analyze the venation pattern in transgenic lines with contrasting cellular and leaf size traits. The results show the evolution of vascular traits during leaf development, suggest a self-organizing mechanism for leaf venation patterning, and reveal a tight balance between the number of end-points and branching points within the leaf vascular network that does not depend on the leaf developmental stage and cellular content, but on the leaf position on the rosette. These findings indicate that development of LIMANI improves understanding of the interaction between vascular patterning and leaf growth.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
SHORT-ROOT, LEAF VENATION, Arabidopsis, cellular content, leaf development, vascular network, imaging software, venation pattern, IN-VITRO, THALIANA, GENE, CANALIZATION, DIFFERENTIATION, MORPHOGENESIS, EXPRESSION, HYPOTHESIS
journal title
PLANT JOURNAL
Plant J.
volume
69
issue
3
pages
553 - 563
Web of Science type
Article
Web of Science id
000299553100015
JCR category
PLANT SCIENCES
JCR impact factor
6.582 (2012)
JCR rank
7/193 (2012)
JCR quartile
1 (2012)
ISSN
0960-7412
DOI
10.1111/j.1365-313X.2011.04803.x
project
Biotechnology for a sustainable economy (Bio-Economy)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
2042360
handle
http://hdl.handle.net/1854/LU-2042360
date created
2012-02-23 13:51:42
date last changed
2014-05-26 10:01:20
@article{2042360,
  abstract     = {The study of transgenic Arabidopsis lines with altered vascular patterns has revealed key players in the venation process, but details of the vascularization process are still unclear, partly because most lines have only been assessed qualitatively. Therefore, quantitative analyses are required to identify subtle perturbations in the pattern and to test dynamic modeling hypotheses using biological measurements. We developed an online framework, designated Leaf Image Analysis Interface (LIMANI), in which venation patterns are automatically segmented and measured on dark-field images. Image segmentation may be manually corrected through use of an interactive interface, allowing supervision and rectification steps in the automated image analysis pipeline and ensuring high-fidelity analysis. This online approach is advantageous for the user in terms of installation, software updates, computer load and data storage. The framework was used to study vascular differentiation during leaf development and to analyze the venation pattern in transgenic lines with contrasting cellular and leaf size traits. The results show the evolution of vascular traits during leaf development, suggest a self-organizing mechanism for leaf venation patterning, and reveal a tight balance between the number of end-points and branching points within the leaf vascular network that does not depend on the leaf developmental stage and cellular content, but on the leaf position on the rosette. These findings indicate that development of LIMANI improves understanding of the interaction between vascular patterning and leaf growth.},
  author       = {Dhondt, Stijn and Van Haerenborgh, Dirk and Van Cauwenbergh, Caroline and Merks, Roeland and Philips, Wilfried and Beemster, Gerrit and Inz{\'e}, Dirk},
  issn         = {0960-7412},
  journal      = {PLANT JOURNAL},
  keyword      = {SHORT-ROOT,LEAF VENATION,Arabidopsis,cellular content,leaf development,vascular network,imaging software,venation pattern,IN-VITRO,THALIANA,GENE,CANALIZATION,DIFFERENTIATION,MORPHOGENESIS,EXPRESSION,HYPOTHESIS},
  language     = {eng},
  number       = {3},
  pages        = {553--563},
  title        = {Quantitative analysis of venation patterns of Arabidopsis leaves by supervised image analysis},
  url          = {http://dx.doi.org/10.1111/j.1365-313X.2011.04803.x},
  volume       = {69},
  year         = {2012},
}

Chicago
Dhondt, Stijn, Dirk Van Haerenborgh, Caroline Van Cauwenbergh, Roeland Merks, Wilfried Philips, Gerrit Beemster, and Dirk Inzé. 2012. “Quantitative Analysis of Venation Patterns of Arabidopsis Leaves by Supervised Image Analysis.” Plant Journal 69 (3): 553–563.
APA
Dhondt, S., Van Haerenborgh, D., Van Cauwenbergh, C., Merks, R., Philips, W., Beemster, G., & Inzé, D. (2012). Quantitative analysis of venation patterns of Arabidopsis leaves by supervised image analysis. PLANT JOURNAL, 69(3), 553–563.
Vancouver
1.
Dhondt S, Van Haerenborgh D, Van Cauwenbergh C, Merks R, Philips W, Beemster G, et al. Quantitative analysis of venation patterns of Arabidopsis leaves by supervised image analysis. PLANT JOURNAL. 2012;69(3):553–63.
MLA
Dhondt, Stijn, Dirk Van Haerenborgh, Caroline Van Cauwenbergh, et al. “Quantitative Analysis of Venation Patterns of Arabidopsis Leaves by Supervised Image Analysis.” PLANT JOURNAL 69.3 (2012): 553–563. Print.