FiloGen: A Model-Based Generator of Synthetic 3-D Time-Lapse
Sequences of Single Motile Cells with Growing and Branching
Filopodia

J 2018

FiloGen: A Model-Based Generator of Synthetic 3-D Time-Lapse Sequences of Single Motile Cells with Growing and Branching Filopodia

SOROKIN, Dmitry, Igor PETERLÍK, Vladimír ULMAN, David SVOBODA, Tereza NEČASOVÁ et. al.

Basic information

Original name

FiloGen: A Model-Based Generator of Synthetic 3-D Time-Lapse Sequences of Single Motile Cells with Growing and Branching Filopodia

Authors

SOROKIN, Dmitry (643 Russian Federation, 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), Tereza NEČASOVÁ (203 Czech Republic, belonging to the institution), Katsiarina MORGAENKO (112 Belarus, belonging to the institution), Lívia EISELLEOVÁ (703 Slovakia, belonging to the institution), Lenka TESAŘOVÁ (203 Czech Republic, belonging to the institution) and Martin MAŠKA (203 Czech Republic, guarantor, belonging to the institution)

Edition

IEEE Transactions on Medical Imaging, IEEE, 2018, 0278-0062

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 7.816

RIV identification code

RIV/00216224:14330/18:00101012

Organization unit

Faculty of Informatics

DOI

http://dx.doi.org/10.1109/TMI.2018.2845884

UT WoS

000451903400008

Keywords in English

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

Abstract

V originále

The existence of diverse image datasets accompanied by reference annotations is a crucial prerequisite for an objective benchmarking of bioimage analysis methods. Nevertheless, such a prerequisite is arduous to satisfy for time-lapse, multidimensional fluorescence microscopy image data, manual annotations of which are laborious and often impracticable. In this paper, we present a simulation system capable of generating 3D time-lapse sequences of single motile cells with filopodial protrusions of user-controlled structural and temporal attributes, such as the number, thickness, length, level of branching, and lifetime of filopodia, accompanied by inherently generated reference annotations. The proposed simulation system involves three globally synchronized modules, each being responsible for a separate task: the evolution of filopodia on a molecular level, linear elastic deformation of the entire cell with filopodia, and the synthesis of realistic, time-coherent cell texture. Its flexibility is demonstrated by generating multiple synthetic 3D time-lapse sequences of single lung cancer cells of two different phenotypes, qualitatively and quantitatively resembling their real counterparts 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

MUNI/A/0854/2017, interní kód MU

Name: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace VII.

Investor: Masaryk University, Category A

Citovat

SOROKIN, Dmitry, Igor PETERLÍK, Vladimír ULMAN, David SVOBODA, Tereza NEČASOVÁ, Katsiarina MORGAENKO, Lívia EISELLEOVÁ, Lenka TESAŘOVÁ and Martin MAŠKA. FiloGen: A Model-Based Generator of Synthetic 3-D Time-Lapse Sequences of Single Motile Cells with Growing and Branching Filopodia. IEEE Transactions on Medical Imaging. IEEE, 2018, vol. 37, No 12, p. 2630-2641. ISSN 0278-0062. Available from: https://dx.doi.org/10.1109/TMI.2018.2845884.

@article{1420978,
   author = {Sorokin, Dmitry and Peterlík, Igor and Ulman, Vladimír and Svoboda, David and Nečasová, Tereza and Morgaenko, Katsiarina and Eiselleová, Lívia and Tesařová, Lenka and Maška, Martin},
   article_number = {12},
   doi = {http://dx.doi.org/10.1109/TMI.2018.2845884},
   keywords = {simulation;3D time-lapse sequence;synthetic cell;cell deformation;filopodium evolution},
   language = {eng},
   issn = {0278-0062},
   journal = {IEEE Transactions on Medical Imaging},
   title = {FiloGen: A Model-Based Generator of Synthetic 3-D Time-Lapse Sequences of Single Motile Cells with Growing and Branching Filopodia},
   url = {https://doi.org/10.1109/TMI.2018.2845884},
   volume = {37},
   year = {2018}
}

TY  - JOUR
ID  - 1420978
AU  - Sorokin, Dmitry - Peterlík, Igor - Ulman, Vladimír - Svoboda, David - Nečasová, Tereza - Morgaenko, Katsiarina - Eiselleová, Lívia - Tesařová, Lenka - Maška, Martin
PY  - 2018
TI  - FiloGen: A Model-Based Generator of Synthetic 3-D Time-Lapse Sequences of Single Motile Cells with Growing and Branching Filopodia
JF  - IEEE Transactions on Medical Imaging
VL  - 37
IS  - 12
SP  - 2630-2641
EP  - 2630-2641
PB  - IEEE
SN  - 02780062
KW  - simulation;3D time-lapse sequence;synthetic cell;cell deformation;filopodium evolution
UR  - https://doi.org/10.1109/TMI.2018.2845884
N2  - The existence of diverse image datasets accompanied by reference annotations is a crucial prerequisite for an objective benchmarking of bioimage analysis methods. Nevertheless, such a prerequisite is arduous to satisfy for time-lapse, multidimensional fluorescence microscopy image data, manual annotations of which are laborious and often impracticable. In this paper, we present a simulation system capable of generating 3D time-lapse sequences of single motile cells with filopodial protrusions of user-controlled structural and temporal attributes, such as the number, thickness, length, level of branching, and lifetime of filopodia, accompanied by inherently generated reference annotations. The proposed simulation system involves three globally synchronized modules, each being responsible for a separate task: the evolution of filopodia on a molecular level, linear elastic deformation of the entire cell with filopodia, and the synthesis of realistic, time-coherent cell texture. Its flexibility is demonstrated by generating multiple synthetic 3D time-lapse sequences of single lung cancer cells of two different phenotypes, qualitatively and quantitatively resembling their real counterparts acquired using a confocal fluorescence microscope.
ER  -

SOROKIN, Dmitry, Igor PETERLÍK, Vladimír ULMAN, David SVOBODA, Tereza NEČASOVÁ, Katsiarina MORGAENKO, Lívia EISELLEOVÁ, Lenka TESAŘOVÁ and Martin MAŠKA. FiloGen: A Model-Based Generator of Synthetic 3-D Time-Lapse Sequences of Single Motile Cells with Growing and Branching Filopodia. \textit{IEEE Transactions on Medical Imaging}. IEEE, 2018, vol.~37, No~12, p.~2630-2641. ISSN~0278-0062. Available from: https://dx.doi.org/10.1109/TMI.2018.2845884.

Detailed Information on Publication Record