The Cell Tracking Challenge: 10 years of objective benchmarking

J 2023

The Cell Tracking Challenge: 10 years of objective benchmarking

MAŠKA, Martin; Vladimír ULMAN; Pablo DELGADO-RODRIGUEZ; Estibaliz GÓMEZ-DE-MARISCAL; Tereza NEČASOVÁ et al.

Základní údaje

Originální název

The Cell Tracking Challenge: 10 years of objective benchmarking

Autoři

MAŠKA, Martin ; Vladimír ULMAN ; Pablo DELGADO-RODRIGUEZ; Estibaliz GÓMEZ-DE-MARISCAL; Tereza NEČASOVÁ; Fidel A Guerrero PEÑA; Tsang Ing REN; Elliot M MEYEROWITZ; Tim SCHERR; Katharina LÖFFLER; Ralf MIKUT; Tianqi GUO; Yin WANG; Jan P ALLEBACH; Rina BAO; Noor M AL-SHAKARJI; Gani RAHMON; Imad Eddine TOUBAL; Kannappan PALANIAPPAN; Filip LUX; Petr MATULA; Ko SUGAWARA; Klas E G MAGNUSSON; Layton AHO; Andrew R COHEN; Assaf ARBELLE; Tal BEN-HAIM; Tammy Riklin RAVIV; Fabian ISENSEE; Paul F JÄGER; Klaus H MAIER-HEIN; Yanming ZHU; Cristina EDERRA; Ainhoa URBIOLA; Erik MEIJERING; Alexandre CUNHA; Arrate MUÑOZ-BARRUTIA; Michal KOZUBEK a Carlos ORTIZ-DE-SOLÓRZANO

Vydání

Nature Methods, 2023, 1548-7091

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 36.100

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14330/23:00130820

Organizační jednotka

Fakulta informatiky

Klíčová slova anglicky

cell segmentation;cell tracking;benchmarking

Štítky

cbia-web

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 8. 4. 2024 15:39, RNDr. Pavel Šmerk, Ph.D.

Anotace

V originále

The Cell Tracking Challenge is an ongoing benchmarking initiative that has become a reference in cell segmentation and tracking algorithm development. Here, we present a significant number of improvements introduced in the challenge since our 2017 report. These include the creation of a new segmentation-only benchmark, the enrichment of the dataset repository with new datasets that increase its diversity and complexity, and the creation of a silver standard reference corpus based on the most competitive results, which will be of particular interest for data-hungry deep learning-based strategies. Furthermore, we present the up-to-date cell segmentation and tracking leaderboards, an in-depth analysis of the relationship between the performance of the state-of-the-art methods and the properties of the datasets and annotations, and two novel, insightful studies about the generalizability and the reusability of top-performing methods. These studies provide critical practical conclusions for both developers and users of traditional and machine learning-based cell segmentation and tracking algorithms.

Návaznosti

EF18_046/0016045, projekt VaV

Název: Modernizace národní infrastruktury pro biologické a medicínské zobrazování Czech-BioImaging

GA21-20374S, projekt VaV

Název: Segmentace a sledování buněk se složitým tvarem

Investor: Grantová agentura ČR, Segmentace a sledování buněk se složitým tvarem

LM2023050, projekt VaV

Název: Národní infrastruktura pro biologické a medicínské zobrazování

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Czech BioImaging: Národní výzkumná infrastruktura pro biologické a medicínské zobrazování

MUNI/A/1081/2022, interní kód MU

Název: Modelování, analýza a verifikace (2023)

Investor: Masarykova univerzita, Modelování, analýza a verifikace (2023)

Citovat

MAŠKA, Martin; Vladimír ULMAN; Pablo DELGADO-RODRIGUEZ; Estibaliz GÓMEZ-DE-MARISCAL; Tereza NEČASOVÁ; Fidel A Guerrero PEÑA; Tsang Ing REN; Elliot M MEYEROWITZ; Tim SCHERR; Katharina LÖFFLER; Ralf MIKUT; Tianqi GUO; Yin WANG; Jan P ALLEBACH; Rina BAO; Noor M AL-SHAKARJI; Gani RAHMON; Imad Eddine TOUBAL; Kannappan PALANIAPPAN; Filip LUX; Petr MATULA; Ko SUGAWARA; Klas E G MAGNUSSON; Layton AHO; Andrew R COHEN; Assaf ARBELLE; Tal BEN-HAIM; Tammy Riklin RAVIV; Fabian ISENSEE; Paul F JÄGER; Klaus H MAIER-HEIN; Yanming ZHU; Cristina EDERRA; Ainhoa URBIOLA; Erik MEIJERING; Alexandre CUNHA; Arrate MUÑOZ-BARRUTIA; Michal KOZUBEK a Carlos ORTIZ-DE-SOLÓRZANO. The Cell Tracking Challenge: 10 years of objective benchmarking. Nature Methods. 2023, roč. 20, č. 7, s. 1010-1020. ISSN 1548-7091. Dostupné z: https://doi.org/10.1038/s41592-023-01879-y.

@article{2285029,
   author = {Maška, Martin and Ulman, Vladimír and DelgadoandRodriguez, Pablo and GómezanddeandMariscal, Estibaliz and Nečasová, Tereza and Peña, Fidel A Guerrero and Ren, Tsang Ing and Meyerowitz, Elliot M and Scherr, Tim and Löffler, Katharina and Mikut, Ralf and Guo, Tianqi and Wang, Yin and Allebach, Jan P and Bao, Rina and AlandShakarji, Noor M and Rahmon, Gani and Toubal, Imad Eddine and Palaniappan, Kannappan and Lux, Filip and Matula, Petr and Sugawara, Ko and Magnusson, Klas E G and Aho, Layton and Cohen, Andrew R and Arbelle, Assaf and BenandHaim, Tal and Raviv, Tammy Riklin and Isensee, Fabian and Jäger, Paul F and MaierandHein, Klaus H and Zhu, Yanming and Ederra, Cristina and Urbiola, Ainhoa and Meijering, Erik and Cunha, Alexandre and MuñozandBarrutia, Arrate and Kozubek, Michal and OrtizanddeandSolórzano, Carlos},
   article_number = {7},
   doi = {https://doi.org/10.1038/s41592-023-01879-y},
   keywords = {cell segmentation;cell tracking;benchmarking},
   language = {eng},
   issn = {1548-7091},
   journal = {Nature Methods},
   title = {The Cell Tracking Challenge: 10 years of objective benchmarking},
   url = {https://doi.org/10.1038/s41592-023-01879-y},
   volume = {20},
   year = {2023}
}

TY  - JOUR
ID  - 2285029
AU  - Maška, Martin - Ulman, Vladimír - Delgado-Rodriguez, Pablo - Gómez-de-Mariscal, Estibaliz - Nečasová, Tereza - Peña, Fidel A Guerrero - Ren, Tsang Ing - Meyerowitz, Elliot M - Scherr, Tim - Löffler, Katharina - Mikut, Ralf - Guo, Tianqi - Wang, Yin - Allebach, Jan P - Bao, Rina - Al-Shakarji, Noor M - Rahmon, Gani - Toubal, Imad Eddine - Palaniappan, Kannappan - Lux, Filip - Matula, Petr - Sugawara, Ko - Magnusson, Klas E G - Aho, Layton - Cohen, Andrew R - Arbelle, Assaf - Ben-Haim, Tal - Raviv, Tammy Riklin - Isensee, Fabian - Jäger, Paul F - Maier-Hein, Klaus H - Zhu, Yanming - Ederra, Cristina - Urbiola, Ainhoa - Meijering, Erik - Cunha, Alexandre - Muñoz-Barrutia, Arrate - Kozubek, Michal - Ortiz-de-Solórzano, Carlos
PY  - 2023
TI  - The Cell Tracking Challenge: 10 years of objective benchmarking
JF  - Nature Methods
VL  - 20
IS  - 7
SP  - 1010-1020
EP  - 1010-1020
SN  - 15487091
KW  - cell segmentation;cell tracking;benchmarking
UR  - https://doi.org/10.1038/s41592-023-01879-y
N2  - The Cell Tracking Challenge is an ongoing benchmarking initiative that has become a reference in cell segmentation and tracking algorithm development. Here, we present a significant number of improvements introduced in the challenge since our 2017 report. These include the creation of a new segmentation-only benchmark, the enrichment of the dataset repository with new datasets that increase its diversity and complexity, and the creation of a silver standard reference corpus based on the most competitive results, which will be of particular interest for data-hungry deep learning-based strategies. Furthermore, we present the up-to-date cell segmentation and tracking leaderboards, an in-depth analysis of the relationship between the performance of the state-of-the-art methods and the properties of the datasets and annotations, and two novel, insightful studies about the generalizability and the reusability of top-performing methods. These studies provide critical practical conclusions for both developers and users of traditional and machine learning-based cell segmentation and tracking algorithms.
ER  -

MAŠKA, Martin; Vladimír ULMAN; Pablo DELGADO-RODRIGUEZ; Estibaliz GÓMEZ-DE-MARISCAL; Tereza NEČASOVÁ; Fidel A Guerrero PEÑA; Tsang Ing REN; Elliot M MEYEROWITZ; Tim SCHERR; Katharina LÖFFLER; Ralf MIKUT; Tianqi GUO; Yin WANG; Jan P ALLEBACH; Rina BAO; Noor M AL-SHAKARJI; Gani RAHMON; Imad Eddine TOUBAL; Kannappan PALANIAPPAN; Filip LUX; Petr MATULA; Ko SUGAWARA; Klas E G MAGNUSSON; Layton AHO; Andrew R COHEN; Assaf ARBELLE; Tal BEN-HAIM; Tammy Riklin RAVIV; Fabian ISENSEE; Paul F JÄGER; Klaus H MAIER-HEIN; Yanming ZHU; Cristina EDERRA; Ainhoa URBIOLA; Erik MEIJERING; Alexandre CUNHA; Arrate MUÑOZ-BARRUTIA; Michal KOZUBEK a Carlos ORTIZ-DE-SOLÓRZANO. The Cell Tracking Challenge: 10 years of objective benchmarking. \textit{Nature Methods}. 2023, roč.~20, č.~7, s.~1010-1020. ISSN~1548-7091. Dostupné z: https://doi.org/10.1038/s41592-023-01879-y.

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