TRAgen: A Tool for Generation of Synthetic Time-Lapse Image
Sequences of Living Cells

D 2015

TRAgen: A Tool for Generation of Synthetic Time-Lapse Image Sequences of Living Cells

ULMAN, Vladimír, Zoltán ORÉMUŠ and David SVOBODA

Basic information

Original name

TRAgen: A Tool for Generation of Synthetic Time-Lapse Image Sequences of Living Cells

Name in Czech

TRAgen: nástroj pro generování syntetických časosběrných obrazových sekvencí živých buněk

Authors

ULMAN, Vladimír (203 Czech Republic, guarantor, belonging to the institution), Zoltán ORÉMUŠ (703 Slovakia, belonging to the institution) and David SVOBODA (203 Czech Republic, belonging to the institution)

Edition

Heidelberg, Německo, Proceedings of 18th International Conference on Image Analysis and Processing, p. 623-634, 12 pp. 2015

Publisher

Springer International Publishing

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Germany

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

storage medium (CD, DVD, flash disk)

Impact factor

Impact factor: 0.402 in 2005

RIV identification code

RIV/00216224:14330/15:00080843

Organization unit

Faculty of Informatics

ISBN

978-3-319-23230-0

ISSN

DOI

http://dx.doi.org/10.1007/978-3-319-23231-7_56

UT WoS

000364991200056

Keywords (in Czech)

Biomedical Imaging; Simulation; Evaluation; Cell Tracking

Keywords in English

Biomedical images; Simulations; Evaluation; Cell Tracking

Abstract

V originále

In biomedical image processing, correct tracking of individual cells is important task for the study of dynamic cellular processes. It is, however, often difficult to decide whether obtained tracking results are correct or not. This is mainly due to complexity of the data that can show hundreds of cells, due to improper data sampling either in time or in space, or when the time-lapse sequence consists of blurred noisy images. This prohibits manual extraction of reliable ground truth (GT) data as well. Nonetheless, if reliable testing data with GT were available, one could compare the results of the examined tracking algorithm with the GT and assess its performance quantitatively. In this paper, we introduce a novel versatile tool capable of generating 2D image sequences showing simulated living cell populations with GT for evaluation of biomedical tracking. The simulated events include namely cell motion, cell division, and cell clustering up to tissue-level density. The method is primarily designed to operate at inter-cellular scope.

Links

GA14-22461S, research and development project

Name: Vývoj a studium metod pro kvantifikaci živých buněk (Acronym: Live Cell Quantification)

Investor: Czech Science Foundation

Files attached

ICIAP15.pdf

Request the author's version of the file

Citovat

ULMAN, Vladimír, Zoltán ORÉMUŠ and David SVOBODA. TRAgen: A Tool for Generation of Synthetic Time-Lapse Image Sequences of Living Cells. In Vittorio Murino, Enrico Puppo, Gianni Vernazza. Proceedings of 18th International Conference on Image Analysis and Processing. Heidelberg, Německo: Springer International Publishing, 2015, p. 623-634. ISBN 978-3-319-23230-0. Available from: https://dx.doi.org/10.1007/978-3-319-23231-7_56.

@inproceedings{1300779,
   author = {Ulman, Vladimír and Orémuš, Zoltán and Svoboda, David},
   address = {Heidelberg, Německo},
   booktitle = {Proceedings of 18th International Conference on Image Analysis and Processing},
   doi = {http://dx.doi.org/10.1007/978-3-319-23231-7_56},
   editor = {Vittorio Murino, Enrico Puppo, Gianni Vernazza},
   keywords = {Biomedical images; Simulations; Evaluation; Cell Tracking},
   howpublished = {paměťový nosič},
   language = {eng},
   location = {Heidelberg, Německo},
   isbn = {978-3-319-23230-0},
   pages = {623-634},
   publisher = {Springer International Publishing},
   title = {TRAgen: A Tool for Generation of Synthetic Time-Lapse Image Sequences of Living Cells},
   year = {2015}
}

TY  - JOUR
ID  - 1300779
AU  - Ulman, Vladimír - Orémuš, Zoltán - Svoboda, David
PY  - 2015
TI  - TRAgen: A Tool for Generation of Synthetic Time-Lapse Image Sequences of Living Cells
PB  - Springer International Publishing
CY  - Heidelberg, Německo
SN  - 9783319232300
KW  - Biomedical images
KW  - Simulations
KW  - Evaluation
KW  - Cell Tracking
N2  - In biomedical image processing, correct tracking of individual cells is important task for the study of dynamic cellular processes. It is, however, often difficult to decide whether obtained tracking results are correct or not. This is mainly due to complexity of the data that can show hundreds of cells, due to improper data sampling either in time or in space, or when the time-lapse sequence consists of blurred noisy images. This prohibits manual extraction of reliable ground truth (GT) data as well. Nonetheless, if reliable testing data with GT were available, one could compare the results of the examined tracking algorithm with the GT and assess its performance quantitatively. In this paper, we introduce a novel versatile tool capable of generating 2D image sequences showing simulated living cell populations with GT for evaluation of biomedical tracking. The simulated events include namely cell motion, cell division, and cell clustering up to tissue-level density. The method is primarily designed to operate at inter-cellular scope.
ER  -

ULMAN, Vladimír, Zoltán ORÉMUŠ and David SVOBODA. TRAgen: A Tool for Generation of Synthetic Time-Lapse Image Sequences of Living Cells. In Vittorio Murino, Enrico Puppo, Gianni Vernazza. \textit{Proceedings of 18th International Conference on Image Analysis and Processing}. Heidelberg, Německo: Springer International Publishing, 2015, p.~623-634. ISBN~978-3-319-23230-0. Available from: https://dx.doi.org/10.1007/978-3-319-23231-7\_{}56.

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