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@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.
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