TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines

被引：445

作者：

Ershov, Dmitry ^{[1
,2
]}

Phan, Minh-Son ^{[1
]}

Pylvanainen, Joanna W. ^{[3
,4
,5
,6
]}

Rigaud, Stephane U. ^{[1
]}

Le Blanc, Laure ^{[7
]}

Charles-Orszag, Arthur ^{[7
]}

Conway, James R. W. ^{[3
,4
]}

Laine, Romain F. ^{[8
,9
,11
]}

Roy, Nathan H. ^{[10
]}

Bonazzi, Daria

Dumenil, Guillaume

Jacquemet, Guillaume ^{[3
,4
,5
,6
]}

Tinevez, Jean-Yves ^{[1
]}

机构：

[1] Univ Paris Cite, Inst Pasteur, Image Anal Hub, Paris, France

[2] Univ Paris Cite, Inst Pasteur, Biostat & Bioinformat Hub, Paris, France

[3] Univ Turku, Turku Biosci Ctr, Turku, Finland

[4] Abo Akad Univ, Turku, Finland

[5] Abo Akad Univ, Fac Sci & Engn, Biosci, Turku, Finland

[6] Univ Turku, Turku Bioimaging, Turku, Finland

[7] Univ Paris Cite, Inst Pasteur, Pathogenesis Vasc Infect Unit, INSERM UMR1225, Paris, France

[8] UCL, MRC Lab Mol Cell Biol, London, England

[9] Francis Crick Inst, London, England

[10] SUNY Upstate Med Univ, Dept Microbiol & Immunol, Syracuse, NY USA

[11] Micrographia Bio Translat & Innovat Hub, London, England

来源：

NATURE METHODS | 2022年 / 19卷 / 07期

基金：

芬兰科学院; 欧盟地平线“2020”;

关键词：

NEISSERIA-MENINGITIDIS; LARGE-SCALE; PLATFORM;

D O I：

10.1038/s41592-022-01507-1

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

TrackMate is an automated tracking software used to analyze bioimages and is distributed as a Fiji plugin. Here, we introduce a new version of TrackMate. TrackMate 7 is built to address the broad spectrum of modern challenges researchers face by integrating state-of-the-art segmentation algorithms into tracking pipelines. We illustrate qualitatively and quantitatively that these new capabilities function effectively across a wide range of bio-imaging experiments. TrackMate 7 combines the benefits of machine and deep learning-based image segmentation with accurate object tracking to enable improved 2D and 3D tracking of diverse objects in biological research.

引用

页码：829 / +

页数：12

共 38 条

[1] Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification [J].

Arganda-Carreras, Ignacio ;

Kaynig, Verena ;

Rueden, Curtis ;

Eliceiri, Kevin W. ;

Schindelin, Johannes ;

Cardona, Albert ;

Seung, H. Sebastian .

BIOINFORMATICS, 2017, 33 (15) :2424-2426

[2] ilastik: interactive machine learning for (bio) image analysis [J].

Berg, Stuart ;

Kutra, Dominik ;

Kroeger, Thorben ;

Straehle, Christoph N. ;

Kausler, Bernhard X. ;

Haubold, Carsten ;

Schiegg, Martin ;

Ales, Janez ;

Beier, Thorsten ;

Rudy, Markus ;

Eren, Kemal ;

Cervantes, Jaime I. ;

Xu, Buote ;

Beuttenmueller, Fynn ;

Wolny, Adrian ;

Zhang, Chong ;

Koethe, Ullrich ;

Hamprecht, Fred A. ;

Kreshuk, Anna .

NATURE METHODS, 2019, 16 (12) :1226-1232

[3] Pathogen-derived extracellular vesicles mediate virulence in the fatal human pathogen Cryptococcus gattii [J].

Bielska, Ewa ;

Sisquella, Marta Arch ;

Aldeieg, Maha ;

Birch, Charlotte ;

O'Donoghue, Eloise J. ;

May, Robin C. .

NATURE COMMUNICATIONS, 2018, 9

[4] Biomedical image augmentation using Augmentor [J].

Bloice, Marcus D. ;

Roth, Peter M. ;

Holzinger, Andreas .

BIOINFORMATICS, 2019, 35 (21) :4522-4524

[5] Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl [J].

Caicedo, Juan C. ;

Goodman, Allen ;

Karhohs, Kyle W. ;

Cimini, Beth A. ;

Ackerman, Jeanelle ;

Haghighi, Marzieh ;

Heng, CherKeng ;

Becker, Tim ;

Minh Doan ;

McQuin, Claire ;

Rohban, Mohammad ;

Singh, Shantanu ;

Carpenter, Anne E. .

NATURE METHODS, 2019, 16 (12) :1247-+

[6] Objective comparison of particle tracking methods [J].

Chenouard, Nicolas ;

Smal, Ihor ;

de Chaumont, Fabrice ;

Maska, Martin ;

Sbalzarini, Ivo F. ;

Gong, Yuanhao ;

Cardinale, Janick ;

Carthel, Craig ;

Coraluppi, Stefano ;

Winter, Mark ;

Cohen, Andrew R. ;

Godinez, William J. ;

Rohr, Karl ;

Kalaidzidis, Yannis ;

Liang, Liang ;

Duncan, James ;

Shen, Hongying ;

Xu, Yingke ;

Magnusson, Klas E. G. ;

Jalden, Joakim ;

Blau, Helen M. ;

Paul-Gilloteaux, Perrine ;

Roudot, Philippe ;

Kervrann, Charles ;

Waharte, Francois ;

Tinevez, Jean-Yves ;

Shorte, Spencer L. ;

Willemse, Joost ;

Celler, Katherine ;

van Wezel, Gilles P. ;

Dan, Han-Wei ;

Tsai, Yuh-Show ;

Ortiz de Solorzano, Carlos ;

Olivo-Marin, Jean-Christophe ;

Meijering, Erik .

NATURE METHODS, 2014, 11 (03) :281-U247

[7] Multiple Hypothesis Tracking for Cluttered Biological Image Sequences [J].

Chenouard, Nicolas ;

Bloch, Isabelle ;

Olivo-Marin, Jean-Christophe .

IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE, 2013, 35 (11) :2736-2750

[8] A new online tool for visualization of volumetric data [J].

Fantham, Marcus ;

Kaminski, Clemens F. .

NATURE PHOTONICS, 2017, 11 (02) :69-69

[9] Large-scale analysis of the meningococcus genome by gene disruption:: Resistance to complement-mediated lysis [J].

Geoffroy, MC ;

Floquet, S ;

Métais, A ;

Nassif, X ;

Pelicic, V .

GENOME RESEARCH, 2003, 13 (03) :391-398

[10] Large-scale study of the interactions between proteins involved in type IV pilus biology in Neisseria meningitidis: characterization of a subcomplex involved in pilus assembly [J].

Georgiadou, Michaella ;

Castagnini, Marta ;

Karimova, Gouzel ;

Ladant, Daniel ;

Pelicic, Vladimir .

MOLECULAR MICROBIOLOGY, 2012, 84 (05) :857-873

← 1 2 3 4 →