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.

Základní údaje

Originální název

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

Autoři

SOROKIN, Dmitry (643 Rusko, domácí), Igor PETERLÍK (703 Slovensko, domácí), Vladimír ULMAN (203 Česká republika, domácí), David SVOBODA (203 Česká republika, domácí), Tereza NEČASOVÁ (203 Česká republika, domácí), Katsiarina MORGAENKO (112 Bělorusko, domácí), Lívia EISELLEOVÁ (703 Slovensko, domácí), Lenka TESAŘOVÁ (203 Česká republika, domácí) a Martin MAŠKA (203 Česká republika, garant, domácí)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 7.816

Kód RIV

RIV/00216224:14330/18:00101012

Organizační jednotka

Fakulta informatiky

DOI

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

UT WoS

000451903400008

Klíčová slova anglicky

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

Štítky

cbia-web

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 31. 5. 2022 17:34, RNDr. Pavel Šmerk, Ph.D.

Anotace

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.

Návaznosti

GJ16-03909Y, projekt VaV

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

Investor: Grantová agentura ČR, Vývoj spolehlivých metod pro automatizovanou kvantitativní charakterizaci buněčné motility ve fluorescenční mikroskopii

MUNI/A/0854/2017, interní kód MU

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

Investor: Masarykova univerzita, Rozsáhlé výpočetní systémy: modely, aplikace a verifikace VII., DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

Citovat

SOROKIN, Dmitry, Igor PETERLÍK, Vladimír ULMAN, David SVOBODA, Tereza NEČASOVÁ, Katsiarina MORGAENKO, Lívia EISELLEOVÁ, Lenka TESAŘOVÁ a 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, roč. 37, č. 12, s. 2630-2641. ISSN 0278-0062. Dostupné z: 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 a 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, roč.~37, č.~12, s.~2630-2641. ISSN~0278-0062. Dostupné z: https://dx.doi.org/10.1109/TMI.2018.2845884.

Podrobný výpis o publikaci