MitoGen: A Framework for Generating 3D Synthetic Time-Lapse
Sequences of Cell Populations in Fluorescence Microscopy

J 2017

MitoGen: A Framework for Generating 3D Synthetic Time-Lapse Sequences of Cell Populations in Fluorescence Microscopy

SVOBODA, David a Vladimír ULMAN

Základní údaje

Originální název

MitoGen: A Framework for Generating 3D Synthetic Time-Lapse Sequences of Cell Populations in Fluorescence Microscopy

Autoři

SVOBODA, David (203 Česká republika, garant, domácí) a Vladimír ULMAN (203 Česká republika, domácí)

Vydání

IEEE Transactions on Medical Imaging, IEEE Engineering in Medicine and Biology Society, 2017, 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: 6.131

Kód RIV

RIV/00216224:14330/17:00094555

Organizační jednotka

Fakulta informatiky

DOI

http://dx.doi.org/10.1109/TMI.2016.2606545

UT WoS

000392418000027

Klíčová slova anglicky

Simulation; Molecular and cellular imaging; Microscopy; Cell; Image synthesis

Štítky

CBIA, cbia-web

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 14. 6. 2022 11:50, RNDr. Pavel Šmerk, Ph.D.

Anotace

V originále

The proper analysis of biological microscopy images is an important and complex task. Therefore, it requires verification of all steps involved in the process, including image segmentation and tracking algorithms. It is generally better to verify algorithms with computer-generated ground truth datasets, which, compared to manually annotated data, nowadays have reached high quality and can be produced in large quantities even for 3D time-lapse image sequences. Here, we propose a novel framework, called MitoGen, which is capable of generating ground truth datasets with fully 3D time-lapse sequences of synthetic fluorescence-stained cell populations. MitoGen shows biologically justified cell motility, shape and texture changes as well as cell divisions. Standard fluorescence microscopy phenomena such as photobleaching, blur with real point spread function (PSF), and several types of noise, are simulated to obtain realistic images. The MitoGen framework is scalable in both space and time. MitoGen generates visually plausible data that shows good agreement with real data in terms of image descriptors and mean square displacement (MSD) trajectory analysis. Additionally, it is also shown in this paper that four publicly available segmentation and tracking algorithms exhibit similar performance on both real and MitoGen-generated data. The implementation of MitoGen is freely available.

Návaznosti

GA14-22461S, projekt VaV

Název: Vývoj a studium metod pro kvantifikaci živých buněk (Akronym: Live Cell Quantification)

Investor: Grantová agentura ČR, Development and Study of Methods for Live Cell Quantification

Citovat

SVOBODA, David a Vladimír ULMAN. MitoGen: A Framework for Generating 3D Synthetic Time-Lapse Sequences of Cell Populations in Fluorescence Microscopy. IEEE Transactions on Medical Imaging. IEEE Engineering in Medicine and Biology Society, 2017, roč. 36, č. 1, s. 310-321. ISSN 0278-0062. Dostupné z: https://dx.doi.org/10.1109/TMI.2016.2606545.

@article{1354015,
   author = {Svoboda, David and Ulman, Vladimír},
   article_number = {1},
   doi = {http://dx.doi.org/10.1109/TMI.2016.2606545},
   keywords = {Simulation; Molecular and cellular imaging; Microscopy; Cell; Image synthesis},
   language = {eng},
   issn = {0278-0062},
   journal = {IEEE Transactions on Medical Imaging},
   title = {MitoGen: A Framework for Generating 3D Synthetic Time-Lapse Sequences of Cell Populations in Fluorescence Microscopy},
   url = {http://dx.doi.org/10.1109/TMI.2016.2606545},
   volume = {36},
   year = {2017}
}

TY  - JOUR
ID  - 1354015
AU  - Svoboda, David - Ulman, Vladimír
PY  - 2017
TI  - MitoGen: A Framework for Generating 3D Synthetic Time-Lapse Sequences of Cell Populations in Fluorescence Microscopy
JF  - IEEE Transactions on Medical Imaging
VL  - 36
IS  - 1
SP  - 310-321
EP  - 310-321
PB  - IEEE Engineering in Medicine and Biology Society
SN  - 02780062
KW  - Simulation
KW  - Molecular and cellular imaging
KW  - Microscopy
KW  - Cell
KW  - Image synthesis
UR  - http://dx.doi.org/10.1109/TMI.2016.2606545
N2  - The proper analysis of biological microscopy images is an important and complex task. Therefore, it requires verification of all steps involved in the process, including image segmentation and tracking algorithms. It is generally better to verify algorithms with computer-generated ground truth datasets, which, compared to manually annotated data, nowadays have reached high quality and can be produced in large quantities even for 3D time-lapse image sequences. Here, we propose a novel framework, called MitoGen, which is capable of generating ground truth datasets with fully 3D time-lapse sequences of synthetic fluorescence-stained cell populations. MitoGen shows biologically justified cell motility, shape and texture changes as well as cell divisions. Standard fluorescence microscopy phenomena such as photobleaching, blur with real point spread function (PSF), and several types of noise, are simulated to obtain realistic images. The MitoGen framework is scalable in both space and time. MitoGen generates visually plausible data that shows good agreement with real data in terms of image descriptors and mean square displacement (MSD) trajectory analysis. Additionally, it is also shown in this paper that four publicly available segmentation and tracking algorithms exhibit similar performance on both real and MitoGen-generated data. The implementation of MitoGen is freely available.
ER  -

SVOBODA, David a Vladimír ULMAN. MitoGen: A Framework for Generating 3D Synthetic Time-Lapse Sequences of Cell Populations in Fluorescence Microscopy. \textit{IEEE Transactions on Medical Imaging}. IEEE Engineering in Medicine and Biology Society, 2017, roč.~36, č.~1, s.~310-321. ISSN~0278-0062. Dostupné z: https://dx.doi.org/10.1109/TMI.2016.2606545.

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