Visualizing Stable Features in Live Cell Nucleus for Evaluation
of the Cell Global Motion Compensation

J 2014

Visualizing Stable Features in Live Cell Nucleus for Evaluation of the Cell Global Motion Compensation

SOROKIN, Dmitry, Jana SUCHÁNKOVÁ, Eva BÁRTOVÁ and Pavel MATULA

Basic information

Original name

Visualizing Stable Features in Live Cell Nucleus for Evaluation of the Cell Global Motion Compensation

Authors

SOROKIN, Dmitry (643 Russian Federation, guarantor, belonging to the institution), Jana SUCHÁNKOVÁ (203 Czech Republic), Eva BÁRTOVÁ (203 Czech Republic) and Pavel MATULA (203 Czech Republic, belonging to the institution)

Edition

Folia biologica, Univerzita Karlova, 2014, 0015-5500

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

Genetics and molecular biology

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

Impact factor

Impact factor: 1.000

RIV identification code

RIV/00216224:14330/14:00073848

Organization unit

Faculty of Informatics

UT WoS

000343275800007

Keywords in English

cell global motion compensation; UV laser bleaching image registration; stable features; algorithm evaluation

Abstract

V originále

The compensation of cell motion is an important step in single-particle tracking analysis of live cells. This step is required in most of the cases, since the movement of subcellular foci is superimposed by the movement and deformation of the cell, while only the local motion of the foci is important to be analysed. The cell motion and deformation compensation is usually performed by means of image registration. There are a number of approaches with different models and properties presented in the literature that perform cell image registration. However, the evaluation of the registration approach quality on real data is a tricky problem due to the fact that some stable features in the images with a priori no local motion are needed. In this paper we propose a methodology for creating live cell nuclei image sequences with stable features imposed. The features are defined using the regions of fluorescence bleaching invoked by the UV laser. Data with different deformations are acquired and can be used for evaluation of the cell image registration methods. Along with that, we describe an image analysis technique and a metric that can characterize the quality of the method quantitatively. The proposed methodology allows building a ground truth dataset for testing and thoroughly evaluating cell image registration methods.

Links

CZ.1.07/2.3.00/30.0030, interní kód MU

Name: Rozvoj lidských zdrojů pro oblast buněčné biologie

Investor: Ministry of Education, Youth and Sports of the CR, 2.3 Human resources in research and development

GBP302/12/G157, research and development project

Name: Dynamika a organizace chromosomů během buněčného cyklu a při diferenciaci v normě a patologii

Investor: Czech Science Foundation

Citovat

SOROKIN, Dmitry, Jana SUCHÁNKOVÁ, Eva BÁRTOVÁ and Pavel MATULA. Visualizing Stable Features in Live Cell Nucleus for Evaluation of the Cell Global Motion Compensation. Folia biologica. Univerzita Karlova, 2014, vol. 60, (Suppl 1), p. 45-49. ISSN 0015-5500.

@article{1197310,
   author = {Sorokin, Dmitry and Suchánková, Jana and Bártová, Eva and Matula, Pavel},
   article_number = {(Suppl 1)},
   keywords = {cell global motion compensation; UV laser bleaching image registration; stable features; algorithm evaluation},
   language = {eng},
   issn = {0015-5500},
   journal = {Folia biologica},
   title = {Visualizing Stable Features in Live Cell Nucleus for Evaluation of the Cell Global Motion Compensation},
   volume = {60},
   year = {2014}
}

TY  - JOUR
ID  - 1197310
AU  - Sorokin, Dmitry - Suchánková, Jana - Bártová, Eva - Matula, Pavel
PY  - 2014
TI  - Visualizing Stable Features in Live Cell Nucleus for Evaluation of the Cell Global Motion Compensation
JF  - Folia biologica
VL  - 60
IS  - (Suppl 1)
SP  - 45-49
EP  - 45-49
PB  - Univerzita Karlova
SN  - 00155500
KW  - cell global motion compensation
KW  - UV laser bleaching image registration
KW  - stable features
KW  - algorithm evaluation
N2  - The compensation of cell motion is an important step in single-particle tracking analysis of live cells. This step is required in most of the cases, since the movement of subcellular foci is superimposed by the movement and deformation of the cell, while only the local motion of the foci is important to be analysed. The cell motion and deformation compensation is usually performed by means of image registration. There are a number of approaches with different models and properties presented in the literature that perform cell image registration. However, the evaluation of the registration approach quality on real data is a tricky problem due to the fact that some stable features in the images with a priori no local motion are needed. In this paper we propose a methodology for creating live cell nuclei image sequences with stable features imposed. The features are defined using the regions of fluorescence bleaching invoked by the UV laser. Data with different deformations are acquired and can be used for evaluation of the cell image registration methods. Along with that, we describe an image analysis technique and a metric that can characterize the quality of the method quantitatively. The proposed methodology allows building a ground truth dataset for testing and thoroughly evaluating cell image registration methods.
ER  -

SOROKIN, Dmitry, Jana SUCHÁNKOVÁ, Eva BÁRTOVÁ and Pavel MATULA. Visualizing Stable Features in Live Cell Nucleus for Evaluation of the Cell Global Motion Compensation. \textit{Folia biologica}. Univerzita Karlova, 2014, vol.~60, (Suppl 1), p.~45-49. ISSN~0015-5500.

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