Model-Based Generation of Synthetic 3D Time-Lapse Sequences of
Motile Cells with Growing Filopodia

D 2017

Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Motile Cells with Growing Filopodia

SOROKIN, Dmitry, Igor PETERLÍK, Vladimír ULMAN, David SVOBODA, Martin MAŠKA et. al.

Basic information

Original name

Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Motile Cells with Growing Filopodia

Authors

SOROKIN, Dmitry (643 Russian Federation, guarantor, belonging to the institution), Igor PETERLÍK (703 Slovakia, belonging to the institution), Vladimír ULMAN (203 Czech Republic, belonging to the institution), David SVOBODA (203 Czech Republic, belonging to the institution) and Martin MAŠKA (203 Czech Republic, belonging to the institution)

Edition

Melbourne, 14th IEEE International Symposium on Biomedical Imaging, p. 822-826, 5 pp. 2017

Publisher

IEEE

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

electronic version available online

References:

URL

RIV identification code

RIV/00216224:14330/17:00094698

Organization unit

Faculty of Informatics

ISBN

978-1-5090-1172-8

ISSN

DOI

http://dx.doi.org/10.1109/ISBI.2017.7950644

UT WoS

000414283200191

Keywords in English

Simulation; 3D time-lapse sequence; synthetic cell; cell deformation; filopodium evolution

Abstract

V originále

The existence of benchmark datasets is essential to objectively evaluate various image analysis methods. Nevertheless, manual annotations of fluorescence microscopy image data are very laborious and not often practicable, especially in the case of 3D+t experiments. In this work, we propose a simulation system capable of generating 3D time-lapse sequences of single motile cells with filopodial protrusions, accompanied by inherently generated ground truth. The system consists of three globally synchronized modules, each responsible for a separate task: the evolution of filopodia on a molecular level, linear elastic deformation of the entire cell with filopodia, and generation of realistic, time-coherent cell texture. The capability of our system is demonstrated by generating a synthetic 3D time-lapse sequence of a single lung cancer cell with two growing filopodia, visually resembling its real counterpart acquired using a confocal fluorescence microscope.

Links

GJ16-03909Y, research and development project

Name: Vývoj spolehlivých metod pro automatizovanou kvantitativní charakterizaci buněčné motility ve fluorescenční mikroskopii

Investor: Czech Science Foundation

Citovat

SOROKIN, Dmitry, Igor PETERLÍK, Vladimír ULMAN, David SVOBODA and Martin MAŠKA. Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Motile Cells with Growing Filopodia. Online. In 14th IEEE International Symposium on Biomedical Imaging. Melbourne: IEEE, 2017, p. 822-826. ISBN 978-1-5090-1172-8. Available from: https://dx.doi.org/10.1109/ISBI.2017.7950644.

@inproceedings{1376851,
   author = {Sorokin, Dmitry and Peterlík, Igor and Ulman, Vladimír and Svoboda, David and Maška, Martin},
   address = {Melbourne},
   booktitle = {14th IEEE International Symposium on Biomedical Imaging},
   doi = {http://dx.doi.org/10.1109/ISBI.2017.7950644},
   keywords = {Simulation; 3D time-lapse sequence; synthetic cell; cell deformation; filopodium evolution},
   howpublished = {elektronická verze "online"},
   language = {eng},
   location = {Melbourne},
   isbn = {978-1-5090-1172-8},
   pages = {822-826},
   publisher = {IEEE},
   title = {Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Motile Cells with Growing Filopodia},
   url = {http://dx.doi.org/10.1109/ISBI.2017.7950644},
   year = {2017}
}

TY  - JOUR
ID  - 1376851
AU  - Sorokin, Dmitry - Peterlík, Igor - Ulman, Vladimír - Svoboda, David - Maška, Martin
PY  - 2017
TI  - Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Motile Cells with Growing Filopodia
PB  - IEEE
CY  - Melbourne
SN  - 9781509011728
KW  - Simulation
KW  - 3D time-lapse sequence
KW  - synthetic cell
KW  - cell deformation
KW  - filopodium evolution
UR  - http://dx.doi.org/10.1109/ISBI.2017.7950644
N2  - The existence of benchmark datasets is essential to objectively evaluate various image analysis methods. Nevertheless, manual annotations of fluorescence microscopy image data are very laborious and not often practicable, especially in the case of 3D+t experiments. In this work, we propose a simulation system capable of generating 3D time-lapse sequences of single motile cells with filopodial protrusions, accompanied by inherently generated ground truth. The system consists of three globally synchronized modules, each responsible for a separate task: the evolution of filopodia on a molecular level, linear elastic deformation of the entire cell with filopodia, and generation of realistic, time-coherent cell texture. The capability of our system is demonstrated by generating a synthetic 3D time-lapse sequence of a single lung cancer cell with two growing filopodia, visually resembling its real counterpart acquired using a confocal fluorescence microscope.
ER  -

SOROKIN, Dmitry, Igor PETERLÍK, Vladimír ULMAN, David SVOBODA and Martin MAŠKA. Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Motile Cells with Growing Filopodia. Online. In \textit{14th IEEE International Symposium on Biomedical Imaging}. Melbourne: IEEE, 2017, p.~822-826. ISBN~978-1-5090-1172-8. Available from: https://dx.doi.org/10.1109/ISBI.2017.7950644.

Detailed Information on Publication Record