Cell tracking accuracy measurement based on comparison of
acyclic oriented graphs

J 2015

Cell tracking accuracy measurement based on comparison of acyclic oriented graphs

MATULA, Pavel, Martin MAŠKA, Dmitry SOROKIN, Petr MATULA, Carlos ORTIZ-DE-SOLÓRZANO et. al.

Základní údaje

Originální název

Cell tracking accuracy measurement based on comparison of acyclic oriented graphs

Autoři

MATULA, Pavel (203 Česká republika, garant, domácí), Martin MAŠKA (203 Česká republika, domácí), Dmitry SOROKIN (643 Rusko, domácí), Petr MATULA (203 Česká republika, domácí), Carlos ORTIZ-DE-SOLÓRZANO (724 Španělsko) a Michal KOZUBEK (203 Česká republika, domácí)

Vydání

PLoS ONE, 2015, 1932-6203

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10610 Biophysics

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.057

Kód RIV

RIV/00216224:14330/15:00080576

Organizační jednotka

Fakulta informatiky

DOI

http://dx.doi.org/10.1371/journal.pone.0144959

UT WoS

000366725800027

Klíčová slova anglicky

cell tracking; acyclic graph; measure;

Štítky

cbia-web

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 13. 4. 2018 14:53, doc. RNDr. Martin Maška, Ph.D.

Anotace

V originále

Tracking motile cells in time-lapse series is challenging and is required in many biomedical applications. Cell tracks can be mathematically represented as acyclic oriented graphs. Their vertices describe the spatio-temporal locations of individual cells, whereas the edges represent temporal relationships between them. Such a representation maintains the knowledge of all important cellular events within a captured field of view, such as migration, division, death, and transit through the field of view. The increasing number of cell tracking algorithms calls for comparison of their performance. However, the lack of a standardized cell tracking accuracy measure makes the comparison impracticable. This paper defines and evaluates an accuracy measure for objective and systematic benchmarking of cell tracking algorithms. The measure assumes the existence of a ground-truth reference, and assesses how difficult it is to transform a computed graph into the reference one. The difficulty is measured as a weighted sum of the lowest number of graph operations, such as split, delete, and add a vertex and delete, add, and alter the semantics of an edge, needed to make the graphs identical. The measure behavior is extensively analyzed based on the tracking results provided by the participants of the first Cell Tracking Challenge hosted by the 2013 IEEE International Symposium on Biomedical Imaging. We demonstrate the robustness and stability of the measure against small changes in the choice of weights for diverse cell tracking algorithms and fluorescence microscopy datasets. As the measure penalizes all possible errors in the tracking results and is easy to compute, it may especially help developers and analysts to tune their algorithms according to their needs.

Návaznosti

CZ.1.07/2.3.00/30.0030, interní kód MU

Název: Rozvoj lidských zdrojů pro oblast buněčné biologie

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Rozvoj lidských zdrojů pro oblast buněčné biologie, 2.3 Lidské zdroje ve výzkumu a vývoji

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

Přiložené soubory

Matula2015_PlosONE_PublishedVersion.pdf

Požádat o autorskou verzi souboru

Citovat

MATULA, Pavel, Martin MAŠKA, Dmitry SOROKIN, Petr MATULA, Carlos ORTIZ-DE-SOLÓRZANO a Michal KOZUBEK. Cell tracking accuracy measurement based on comparison of acyclic oriented graphs. PLoS ONE. 2015, roč. 10, č. 12, s. "e0144959", 19 s. ISSN 1932-6203. Dostupné z: https://dx.doi.org/10.1371/journal.pone.0144959.

@article{1139063,
   author = {Matula, Pavel and Maška, Martin and Sorokin, Dmitry and Matula, Petr and OrtizanddeandSolórzano, Carlos and Kozubek, Michal},
   article_number = {12},
   doi = {http://dx.doi.org/10.1371/journal.pone.0144959},
   keywords = {cell tracking; acyclic graph; measure;},
   language = {eng},
   issn = {1932-6203},
   journal = {PLoS ONE},
   title = {Cell tracking accuracy measurement based on comparison of acyclic oriented graphs},
   url = {http://dx.doi.org/10.1371/journal.pone.0144959},
   volume = {10},
   year = {2015}
}

TY  - JOUR
ID  - 1139063
AU  - Matula, Pavel - Maška, Martin - Sorokin, Dmitry - Matula, Petr - Ortiz-de-Solórzano, Carlos - Kozubek, Michal
PY  - 2015
TI  - Cell tracking accuracy measurement based on comparison of acyclic oriented graphs
JF  - PLoS ONE
VL  - 10
IS  - 12
SP  - "e0144959"
EP  - "e0144959"
SN  - 19326203
KW  - cell tracking
KW  - acyclic graph
KW  - measure;
UR  - http://dx.doi.org/10.1371/journal.pone.0144959
N2  - Tracking motile cells in time-lapse series is challenging and is required in many biomedical applications. Cell tracks can be mathematically represented as acyclic oriented graphs. Their vertices describe the spatio-temporal locations of individual cells, whereas the edges represent temporal relationships between them. Such a representation maintains the knowledge of all important cellular events within a captured field of view, such as migration, division, death, and transit through the field of view. The increasing number of cell tracking algorithms calls for comparison of their performance. However, the lack of a standardized cell tracking accuracy measure makes the comparison impracticable. This paper defines and evaluates an accuracy measure for objective and systematic benchmarking of cell tracking algorithms. The measure assumes the existence of a ground-truth reference, and assesses how difficult it is to transform a computed graph into the reference one. The difficulty is measured as a weighted sum of the lowest number of graph operations, such as split, delete, and add a vertex and delete, add, and alter the semantics of an edge, needed to make the graphs identical. The measure behavior is extensively analyzed based on the tracking results provided by the participants of the first Cell Tracking Challenge hosted by the 2013 IEEE International Symposium on Biomedical Imaging. We demonstrate the robustness and stability of the measure against small changes in the choice of weights for diverse cell tracking algorithms and fluorescence microscopy datasets. As the measure penalizes all possible errors in the tracking results and is easy to compute, it may especially help developers and analysts to tune their algorithms according to their needs.
ER  -

MATULA, Pavel, Martin MAŠKA, Dmitry SOROKIN, Petr MATULA, Carlos ORTIZ-DE-SOLÓRZANO a Michal KOZUBEK. Cell tracking accuracy measurement based on comparison of acyclic oriented graphs. \textit{PLoS ONE}. 2015, roč.~10, č.~12, s.~''e0144959'', 19 s. ISSN~1932-6203. Dostupné z: https://dx.doi.org/10.1371/journal.pone.0144959.

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