On Proper Simulation of Chromatin Structure in Static Images As
Well As in Time-Lapse Sequences in Fluorescence Microscopy

D 2015

On Proper Simulation of Chromatin Structure in Static Images As Well As in Time-Lapse Sequences in Fluorescence Microscopy

SVOBODA, David, Vladimír ULMAN and Igor PETERLÍK

Basic information

Original name

On Proper Simulation of Chromatin Structure in Static Images As Well As in Time-Lapse Sequences in Fluorescence Microscopy

Authors

SVOBODA, David (203 Czech Republic, guarantor, belonging to the institution), Vladimír ULMAN (203 Czech Republic, belonging to the institution) and Igor PETERLÍK (703 Slovakia, belonging to the institution)

Edition

Stoughton (WI, USA), Proceedings of 2015 IEEE International Symposium on Biomedical Imaging, p. 712-716, 5 pp. 2015

Publisher

Engineering in Medicine and Biology Society

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

storage medium (CD, DVD, flash disk)

RIV identification code

RIV/00216224:14330/15:00080650

Organization unit

Faculty of Informatics

ISBN

978-1-4799-2374-8

ISSN

DOI

http://dx.doi.org/10.1109/ISBI.2015.7163972

UT WoS

000380546000171

Keywords in English

Simulation; Synthetic cell; Chromatin structure; Nucleus deformation; Linear elasticity; FEM

Abstract

V originále

In fluorescence microscopy, where the benchmark datasets for validating the various image analysis methods are difficult to obtain, a great demand is either for manually annotated real image data or for computer generated ones. In the last two decades, the latter case has become more and more accessible due to an increasing computer capabilities. However, the development of elaborate models, especially in the field of fluorescence microscopy imaging, is less progressive. In this paper, we propose a novel approach, based on well established concepts, to properly imitate the structure of chromatin inside the cell nucleus as well as its dynamics. The performance of the approach was quantitatively evaluated against the real data. The results show that the produced images are sufficiently plausible and visually resemble their real counter parts, both for fixed and living cells.

Links

GA14-22461S, research and development project

Name: Vývoj a studium metod pro kvantifikaci živých buněk (Acronym: Live Cell Quantification)

Investor: Czech Science Foundation

Citovat

SVOBODA, David, Vladimír ULMAN and Igor PETERLÍK. On Proper Simulation of Chromatin Structure in Static Images As Well As in Time-Lapse Sequences in Fluorescence Microscopy. In Proceedings of 2015 IEEE International Symposium on Biomedical Imaging. Stoughton (WI, USA): Engineering in Medicine and Biology Society, 2015, p. 712-716. ISBN 978-1-4799-2374-8. Available from: https://dx.doi.org/10.1109/ISBI.2015.7163972.

@inproceedings{1218636,
   author = {Svoboda, David and Ulman, Vladimír and Peterlík, Igor},
   address = {Stoughton (WI, USA)},
   booktitle = {Proceedings of 2015 IEEE International Symposium on Biomedical Imaging},
   doi = {http://dx.doi.org/10.1109/ISBI.2015.7163972},
   keywords = {Simulation; Synthetic cell; Chromatin structure; Nucleus deformation; Linear elasticity; FEM},
   howpublished = {paměťový nosič},
   language = {eng},
   location = {Stoughton (WI, USA)},
   isbn = {978-1-4799-2374-8},
   pages = {712-716},
   publisher = {Engineering in Medicine and Biology Society},
   title = {On Proper Simulation of Chromatin Structure in Static Images As Well As in Time-Lapse Sequences in Fluorescence Microscopy},
   year = {2015}
}

TY  - JOUR
ID  - 1218636
AU  - Svoboda, David - Ulman, Vladimír - Peterlík, Igor
PY  - 2015
TI  - On Proper Simulation of Chromatin Structure in Static Images As Well As in Time-Lapse Sequences in Fluorescence Microscopy
PB  - Engineering in Medicine and Biology Society
CY  - Stoughton (WI, USA)
SN  - 9781479923748
KW  - Simulation
KW  - Synthetic cell
KW  - Chromatin structure
KW  - Nucleus deformation
KW  - Linear elasticity
KW  - FEM
N2  - In fluorescence microscopy, where the benchmark datasets for validating the various image analysis methods are difficult to obtain, a great demand is either for manually annotated real image data or for computer generated ones. In the last two decades, the latter case has become more and more accessible due to an increasing computer capabilities. However, the development of elaborate models, especially in the field of fluorescence microscopy imaging, is less progressive. In this paper, we propose a novel approach, based on well established concepts, to properly imitate the structure of chromatin inside the cell nucleus as well as its dynamics. The performance of the approach was quantitatively evaluated against the real data. The results show that the produced images are sufficiently plausible and visually resemble their real counter parts, both for fixed and living cells.
ER  -

SVOBODA, David, Vladimír ULMAN and Igor PETERLÍK. On Proper Simulation of Chromatin Structure in Static Images As Well As in Time-Lapse Sequences in Fluorescence Microscopy. In \textit{Proceedings of 2015 IEEE International Symposium on Biomedical Imaging}. Stoughton (WI, USA): Engineering in Medicine and Biology Society, 2015, p.~712-716. ISBN~978-1-4799-2374-8. Available from: https://dx.doi.org/10.1109/ISBI.2015.7163972.

Detailed Information on Publication Record