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Phenotyping on microscopic scale using DIC microscopy

Jonas De Vylder, Stijn Dhondt UGent, Hiep Luong UGent, Dirk Inzé UGent and Wilfried Philips UGent (2014) Phenodays, Abstracts. p.43-43
abstract
Image analysis of Arabidopsis (Arabidopsis thaliana) plants is an important method for studying plant growth. Most work on automated analysis focuses on full rosette analysis, often in a high-throughput monitoring system. In this talk we propose a new workflow that analysis plant growth on a microscopic scale. This approach results in more detail than the common growth measurements, i.e. analysis of the number of cells, the average cell size, etc. The proposed workflow uses differential interference contrast (DIC) microscopy to visualise cells. DIC microscopy is preferred over fluorescence techniques because it provides a very fast methodology (i.e. image analysis is already possible after 1 day) and it also results in clear contrast in the samples. Although these images are easy to interpret by a human operator, they pose several challenges for automated computer vision methods. In our proposed talk we circumvent most of these challenges by combining multiple images, acquired with different microscopy settings. This approach allows us to automatically segment and analyse cells in the images. The proposed workflow enables a new form of automated phenotyping on microscopic scale.
Please use this url to cite or link to this publication:
author
organization
year
type
conference
publication status
published
subject
keyword
DIC microscopy, image segmentation, image analysis, image fusion
in
Phenodays, Abstracts
pages
43 - 43
conference name
Phenodays
conference location
beaune, france
conference start
2014-10-29
conference end
2014-10-31
project
iMinds icon MMIQQA
language
English
UGent publication?
yes
classification
C3
copyright statement
I have transferred the copyright for this publication to the publisher
id
5753075
handle
http://hdl.handle.net/1854/LU-5753075
date created
2014-11-11 10:05:51
date last changed
2016-12-19 15:37:23
@inproceedings{5753075,
  abstract     = {Image analysis of Arabidopsis (Arabidopsis thaliana) plants is an important method for studying plant growth. Most work on automated analysis focuses on full rosette analysis, often in a high-throughput monitoring system. In this talk we propose a new workflow that analysis plant growth on a microscopic scale. This approach results in more detail than the common growth measurements, i.e. analysis of the number of cells, the average cell size, etc. The proposed workflow uses differential interference contrast (DIC) microscopy to visualise cells. DIC microscopy is preferred over fluorescence techniques because it provides a very fast methodology (i.e. image analysis is already possible after 1 day) and it also results in clear contrast in the samples. Although these images are easy to interpret by a human operator, they pose several challenges for automated computer vision methods. In our proposed talk we circumvent most of these challenges by combining multiple images, acquired with different microscopy settings. This approach allows us to automatically segment and analyse cells in the images. The proposed workflow enables a new form of automated phenotyping on microscopic scale.},
  author       = {De Vylder, Jonas and Dhondt, Stijn and Luong, Hiep and Inz{\'e}, Dirk and Philips, Wilfried},
  booktitle    = {Phenodays, Abstracts},
  keyword      = {DIC microscopy,image segmentation,image analysis,image fusion},
  language     = {eng},
  location     = {beaune, france},
  pages        = {43--43},
  title        = {Phenotyping on microscopic scale using DIC microscopy},
  year         = {2014},
}

Chicago
De Vylder, Jonas, Stijn Dhondt, Hiep Luong, Dirk Inzé, and Wilfried Philips. 2014. “Phenotyping on Microscopic Scale Using DIC Microscopy.” In Phenodays, Abstracts, 43–43.
APA
De Vylder, Jonas, Dhondt, S., Luong, H., Inzé, D., & Philips, W. (2014). Phenotyping on microscopic scale using DIC microscopy. Phenodays, Abstracts (pp. 43–43). Presented at the Phenodays.
Vancouver
1.
De Vylder J, Dhondt S, Luong H, Inzé D, Philips W. Phenotyping on microscopic scale using DIC microscopy. Phenodays, Abstracts. 2014. p. 43–43.
MLA
De Vylder, Jonas, Stijn Dhondt, Hiep Luong, et al. “Phenotyping on Microscopic Scale Using DIC Microscopy.” Phenodays, Abstracts. 2014. 43–43. Print.