Detailed Information on Publication Record
2017
MitoGen: A Framework for Generating 3D Synthetic Time-Lapse Sequences of Cell Populations in Fluorescence Microscopy
SVOBODA, David and Vladimír ULMANBasic information
Original name
MitoGen: A Framework for Generating 3D Synthetic Time-Lapse Sequences of Cell Populations in Fluorescence Microscopy
Authors
SVOBODA, David (203 Czech Republic, guarantor, belonging to the institution) and Vladimír ULMAN (203 Czech Republic, belonging to the institution)
Edition
IEEE Transactions on Medical Imaging, IEEE Engineering in Medicine and Biology Society, 2017, 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:
Impact factor
Impact factor: 6.131
RIV identification code
RIV/00216224:14330/17:00094555
Organization unit
Faculty of Informatics
UT WoS
000392418000027
Keywords in English
Simulation; Molecular and cellular imaging; Microscopy; Cell; Image synthesis
Tags
International impact, Reviewed
Změněno: 14/6/2022 11:50, RNDr. Pavel Šmerk, Ph.D.
Abstract
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.
Links
| GA14-22461S, research and development project |
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