An objective comparison of cell-tracking algorithms

J 2017

An objective comparison of cell-tracking algorithms

ULMAN, Vladimír, Martin MAŠKA, Klas E G MAGNUSSON, Olaf RONNEBERGER, Carsten HAUBOLD et. al.

Basic information

Original name

An objective comparison of cell-tracking algorithms

Name in Czech

Objektivní porovnání algoritmů pro sledování buněk

Authors

ULMAN, Vladimír (203 Czech Republic, guarantor, belonging to the institution), Martin MAŠKA (203 Czech Republic, belonging to the institution), Klas E G MAGNUSSON (752 Sweden), Olaf RONNEBERGER (276 Germany), Carsten HAUBOLD (276 Germany), Nathalie HARDER (276 Germany), Pavel MATULA (203 Czech Republic, belonging to the institution), Petr MATULA (203 Czech Republic, belonging to the institution), David SVOBODA (203 Czech Republic, belonging to the institution), Miroslav RADOJEVIC (528 Netherlands), Ihor SMAL (528 Netherlands), Karl ROHR (276 Germany), Joakim JALDÉN (752 Sweden), Helen M BLAU (752 Sweden), Oleh DZYUBACHYK (528 Netherlands), Boudewijn LELIEVELDT (528 Netherlands), Pengdong XIAO (156 China), Yuexiang LI (156 China), Siu-Yeung CHO (156 China), Alexandre C DUFOUR (250 France), Jean-Christophe OLIVO-MARIN (250 France), Constantino C REYES-ALDASORO (724 Spain), Jose A SOLIS-LEMUS (724 Spain), Robert BENSCH (276 Germany), Thomas BROX (276 Germany), Johannes STEGMAIER (276 Germany), Ralf MIKUT (276 Germany), Steffen WOLF (276 Germany), Fred A HAMPRECHT (276 Germany), Tiago ESTEVES (620 Portugal), Pedro QUELHAS (620 Portugal), Ömer DEMIREL (756 Switzerland), Lars MALMSTRÖM (752 Sweden), Florian JUG (276 Germany), Pavel TOMANCAK (276 Germany), Erik MEIJERING (528 Netherlands), Arrate MUÑOZ-BARRUTIA (724 Spain), Michal KOZUBEK (203 Czech Republic, belonging to the institution) and Carlos ORTIZ-DE-SOLORZANO (724 Spain)

Edition

Nature Methods, Macmillan Publishers Limited, part of Springer Nature, 2017, 1548-7091

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:

URL

Impact factor

Impact factor: 26.919

RIV identification code

RIV/00216224:14330/17:00095272

Organization unit

Faculty of Informatics

DOI

http://dx.doi.org/10.1038/nmeth.4473

UT WoS

000416604800015

Keywords (in Czech)

Pohyb buněk; Zpracování obrazu

Keywords in English

Cell migration; Image processing

Abstract

ORIG CZ

V originále

We present a combined report on the results of three editions of the Cell Tracking Challenge, an ongoing initiative aimed at promoting the development and objective evaluation of cell tracking algorithms. We analyze the results using performance measures for segmentation and tracking that rank all participating methods. We also analyze the performance of all algorithms in terms of biological measures and their practical usability.

In Czech

Článek prezentuje zprávu zahrnující výsledky tří vydání Cell Tracking Challenge, pokračující iniciativě zaměřené na rozvoj a objektivní porovnávání algoritmů sledování buněk. Článek analyzuje výsledky detekování a sledování buněk pomocí několika výkonnostních metrik a na základě toho vypočítává pořadí hodnocených metod. Článek dále analyzuje výkonnosti těchto algoritmů na základě tzv. biologicky inspirovaných metric a také na základě jejich praktické užitnosti.

Links

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

LTC17016, research and development project

Name: Benchmarking algoritmů segmentace a sledování buněk

Investor: Ministry of Education, Youth and Sports of the CR, Benchmarking of algorithms for cell segmentation and tracking, INTER-COST

Citovat

ULMAN, Vladimír, Martin MAŠKA, Klas E G MAGNUSSON, Olaf RONNEBERGER, Carsten HAUBOLD, Nathalie HARDER, Pavel MATULA, Petr MATULA, David SVOBODA, Miroslav RADOJEVIC, Ihor SMAL, Karl ROHR, Joakim JALDÉN, Helen M BLAU, Oleh DZYUBACHYK, Boudewijn LELIEVELDT, Pengdong XIAO, Yuexiang LI, Siu-Yeung CHO, Alexandre C DUFOUR, Jean-Christophe OLIVO-MARIN, Constantino C REYES-ALDASORO, Jose A SOLIS-LEMUS, Robert BENSCH, Thomas BROX, Johannes STEGMAIER, Ralf MIKUT, Steffen WOLF, Fred A HAMPRECHT, Tiago ESTEVES, Pedro QUELHAS, Ömer DEMIREL, Lars MALMSTRÖM, Florian JUG, Pavel TOMANCAK, Erik MEIJERING, Arrate MUÑOZ-BARRUTIA, Michal KOZUBEK and Carlos ORTIZ-DE-SOLORZANO. An objective comparison of cell-tracking algorithms. Nature Methods. Macmillan Publishers Limited, part of Springer Nature, 2017, vol. 14, No 12, p. 1141-1152. ISSN 1548-7091. Available from: https://dx.doi.org/10.1038/nmeth.4473.

@article{1399989,
   author = {Ulman, Vladimír and Maška, Martin and Magnusson, Klas E G and Ronneberger, Olaf and Haubold, Carsten and Harder, Nathalie and Matula, Pavel and Matula, Petr and Svoboda, David and Radojevic, Miroslav and Smal, Ihor and Rohr, Karl and Jaldén, Joakim and Blau, Helen M and Dzyubachyk, Oleh and Lelieveldt, Boudewijn and Xiao, Pengdong and Li, Yuexiang and Cho, SiuandYeung and Dufour, Alexandre C and OlivoandMarin, JeanandChristophe and ReyesandAldasoro, Constantino C and SolisandLemus, Jose A and Bensch, Robert and Brox, Thomas and Stegmaier, Johannes and Mikut, Ralf and Wolf, Steffen and Hamprecht, Fred A and Esteves, Tiago and Quelhas, Pedro and Demirel, Ömer and Malmström, Lars and Jug, Florian and Tomancak, Pavel and Meijering, Erik and MuñozandBarrutia, Arrate and Kozubek, Michal and OrtizanddeandSolorzano, Carlos},
   article_number = {12},
   doi = {http://dx.doi.org/10.1038/nmeth.4473},
   keywords = {Cell migration; Image processing},
   language = {eng},
   issn = {1548-7091},
   journal = {Nature Methods},
   title = {An objective comparison of cell-tracking algorithms},
   url = {https://www.nature.com/articles/nmeth.4473},
   volume = {14},
   year = {2017}
}

TY  - JOUR
ID  - 1399989
AU  - Ulman, Vladimír - Maška, Martin - Magnusson, Klas E G - Ronneberger, Olaf - Haubold, Carsten - Harder, Nathalie - Matula, Pavel - Matula, Petr - Svoboda, David - Radojevic, Miroslav - Smal, Ihor - Rohr, Karl - Jaldén, Joakim - Blau, Helen M - Dzyubachyk, Oleh - Lelieveldt, Boudewijn - Xiao, Pengdong - Li, Yuexiang - Cho, Siu-Yeung - Dufour, Alexandre C - Olivo-Marin, Jean-Christophe - Reyes-Aldasoro, Constantino C - Solis-Lemus, Jose A - Bensch, Robert - Brox, Thomas - Stegmaier, Johannes - Mikut, Ralf - Wolf, Steffen - Hamprecht, Fred A - Esteves, Tiago - Quelhas, Pedro - Demirel, Ömer - Malmström, Lars - Jug, Florian - Tomancak, Pavel - Meijering, Erik - Muñoz-Barrutia, Arrate - Kozubek, Michal - Ortiz-de-Solorzano, Carlos
PY  - 2017
TI  - An objective comparison of cell-tracking algorithms
JF  - Nature Methods
VL  - 14
IS  - 12
SP  - 1141-1152
EP  - 1141-1152
PB  - Macmillan Publishers Limited, part of Springer Nature
SN  - 15487091
KW  - Cell migration
KW  - Image processing
UR  - https://www.nature.com/articles/nmeth.4473
L2  - https://www.nature.com/articles/nmeth.4473
N2  - We present a combined report on the results of three editions of the Cell Tracking Challenge, an ongoing initiative aimed at promoting the development and objective evaluation of cell tracking algorithms. We analyze the results using performance measures for segmentation and tracking that rank all participating methods. We also analyze the performance of all algorithms in terms of biological measures and their practical usability.
ER  -

ULMAN, Vladimír, Martin MAŠKA, Klas E G MAGNUSSON, Olaf RONNEBERGER, Carsten HAUBOLD, Nathalie HARDER, Pavel MATULA, Petr MATULA, David SVOBODA, Miroslav RADOJEVIC, Ihor SMAL, Karl ROHR, Joakim JALDÉN, Helen M BLAU, Oleh DZYUBACHYK, Boudewijn LELIEVELDT, Pengdong XIAO, Yuexiang LI, Siu-Yeung CHO, Alexandre C DUFOUR, Jean-Christophe OLIVO-MARIN, Constantino C REYES-ALDASORO, Jose A SOLIS-LEMUS, Robert BENSCH, Thomas BROX, Johannes STEGMAIER, Ralf MIKUT, Steffen WOLF, Fred A HAMPRECHT, Tiago ESTEVES, Pedro QUELHAS, Ömer DEMIREL, Lars MALMSTRÖM, Florian JUG, Pavel TOMANCAK, Erik MEIJERING, Arrate MUÑOZ-BARRUTIA, Michal KOZUBEK and Carlos ORTIZ-DE-SOLORZANO. An objective comparison of cell-tracking algorithms. \textit{Nature Methods}. Macmillan Publishers Limited, part of Springer Nature, 2017, vol.~14, No~12, p.~1141-1152. ISSN~1548-7091. Available from: https://dx.doi.org/10.1038/nmeth.4473.

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