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

Dmitry Ershov^#^{1

2}, Minh-Son Phan^#¹, Joanna W Pylvänäinen^#^{3

4

5}, Stéphane U Rigaud^#¹, Laure Le Blanc⁶, Arthur Charles-Orszag⁶, James R W Conway³, Romain F Laine^{7

8

9}, Nathan H Roy¹⁰, Daria Bonazzi⁶, Guillaume Duménil⁶, Guillaume Jacquemet^{11

12

13}, Jean-Yves Tinevez¹⁴

Affiliations

¹ Institut Pasteur, Université de Paris Cité, Image Analysis Hub, Paris, France.
² Institut Pasteur, Université de Paris Cité, Biostatistics and Bioinformatic Hub, Paris, France.
³ Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
⁴ Åbo Akademi University, Faculty of Science and Engineering, Biosciences, Turku, Finland.
⁵ Turku Bioimaging, University of Turku and Åbo Akademi University, Turku, Finland.
⁶ Institut Pasteur, Université Paris Cité, INSERM UMR1225, Pathogenesis of Vascular Infections unit, Paris, France.
⁷ MRC Laboratory for Molecular Cell Biology, University College London, London, UK.
⁸ The Francis Crick Institute, London, UK.
⁹ Micrographia Bio, Translation and Innovation Hub, London, UK.
¹⁰ Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY, USA.
¹¹ Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland. guillaume.jacquemet@abo.fi.
¹² Åbo Akademi University, Faculty of Science and Engineering, Biosciences, Turku, Finland. guillaume.jacquemet@abo.fi.
¹³ Turku Bioimaging, University of Turku and Åbo Akademi University, Turku, Finland. guillaume.jacquemet@abo.fi.
¹⁴ Institut Pasteur, Université de Paris Cité, Image Analysis Hub, Paris, France. jean-yves.tinevez@pasteur.fr.

^# Contributed equally.

PMID: 35654950
DOI: 10.1038/s41592-022-01507-1

Free article

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

Dmitry Ershov et al. Nat Methods. 2022 Jul.

Free article

. 2022 Jul;19(7):829-832.

doi: 10.1038/s41592-022-01507-1. Epub 2022 Jun 2.

Authors

Affiliations

¹ Institut Pasteur, Université de Paris Cité, Image Analysis Hub, Paris, France.
² Institut Pasteur, Université de Paris Cité, Biostatistics and Bioinformatic Hub, Paris, France.
³ Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
⁴ Åbo Akademi University, Faculty of Science and Engineering, Biosciences, Turku, Finland.
⁵ Turku Bioimaging, University of Turku and Åbo Akademi University, Turku, Finland.
⁶ Institut Pasteur, Université Paris Cité, INSERM UMR1225, Pathogenesis of Vascular Infections unit, Paris, France.
⁷ MRC Laboratory for Molecular Cell Biology, University College London, London, UK.
⁸ The Francis Crick Institute, London, UK.
⁹ Micrographia Bio, Translation and Innovation Hub, London, UK.
¹⁰ Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY, USA.
¹¹ Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland. guillaume.jacquemet@abo.fi.
¹² Åbo Akademi University, Faculty of Science and Engineering, Biosciences, Turku, Finland. guillaume.jacquemet@abo.fi.
¹³ Turku Bioimaging, University of Turku and Åbo Akademi University, Turku, Finland. guillaume.jacquemet@abo.fi.
¹⁴ Institut Pasteur, Université de Paris Cité, Image Analysis Hub, Paris, France. jean-yves.tinevez@pasteur.fr.

^# Contributed equally.

PMID: 35654950
DOI: 10.1038/s41592-022-01507-1

Abstract

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.

PubMed Disclaimer

References

1. Sbalzarini, I. F. & Koumoutsakos, P. Feature point tracking and trajectory analysis for video imaging in cell biology. J. Struct. Biol. 151, 182–195 (2005). - DOI
1. Chenouard, N., Bloch, I. & Olivo-Marin, J.-C. Multiple hypothesis tracking for cluttered biological image sequences. IEEE Trans. Pattern Anal. Mach. Intell. 35, 2736–3750 (2013). - DOI
1. Piccinini, F., Kiss, A. & Horvath, P. CellTracker (not only) for dummies. Bioinformatics 32, 955–957 (2016). - DOI
1. Tinevez, J.-Y. et al. TrackMate: an open and extensible platform for single-particle tracking. Methods 115, 80–90 (2017). - DOI
1. McQuin, C. et al. CellProfiler 3.0: Next-generation image processing for biology. PLoS Biol. 16, e2005970 (2018). - DOI

Publication types

Actions

MeSH terms

Actions
Actions
Actions

Grants and funding

MR/T027924/1/MRC_/Medical Research Council/United Kingdom

LinkOut - more resources

Full Text Sources
- HAL archives ouvertes - Access Free Full Text
- Nature Publishing Group
Research Materials
- Addgene Non-profit plasmid repository

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

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

Affiliations

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

Authors

Affiliations

Abstract

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Research Materials