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TrackMate: An open and extensible platform for single-particle tracking
Open accessAbstract
We present TrackMate, an open source Fiji plugin for the automated, semi-automated, and manual tracking of single-particles. It offers a versatile and modular solution that works out of the box for end users, through a simple and intuitive user interface. It is also easily scriptable and adaptable, operating equally well on 1D over time, 2D over time, 3D over time, or other single and multi-channel image variants. TrackMate provides several visualization and analysis tools that aid in assessing the relevance of results. The utility of TrackMate is further enhanced through its ability to be readily customized to meet specific tracking problems. TrackMate is an extensible platform where developers can easily write their own detection, particle linking, visualization or analysis algorithms within the TrackMate environment. This evolving framework provides researchers with the opportunity to quickly develop and optimize new algorithms based on existing TrackMate modules without the need of having to write de novo user interfaces, including visualization, analysis and exporting tools. The current capabilities of TrackMate are presented in the context of three different biological problems. First, we perform Caenorhabditis-elegans lineage analysis to assess how light-induced damage during imaging impairs its early development. Our TrackMate-based lineage analysis indicates the lack of a cell-specific light-sensitive mechanism. Second, we investigate the recruitment of NEMO (NF-κB essential modulator) clusters in fibroblasts after stimulation by the cytokine IL-1 and show that photodamage can generate artifacts in the shape of TrackMate characterized movements that confuse motility analysis. Finally, we validate the use of TrackMate for quantitative lifetime analysis of clathrin-mediated endocytosis in plant cells.
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Fiji: an open-source platform for biological-image analysis
Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., et al. (2012) · Nature Methods · doi:10.1038/nmeth.2019 · Cited by 66,890
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Kalman, R. E. (1960) · Journal of Basic Engineering · doi:10.1115/1.3662552 · Cited by 31,751
Spiesschaert, B., Goldenbogen, B., Taferner, S., Schade, M., Mahmoud, M., Klipp, E., Osterrieder, N., & Azab, W. (2015) · Journal of Virology · doi:10.1128/jvi.01809-15 · Cited by 24
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Funk, L., Su, K.-C., Ly, J., Feldman, D., Singh, A., Moodie, B., Blainey, P. C., & Cheeseman, I. M. (2022) · Cell · doi:10.1016/j.cell.2022.10.017 · Cited by 160
Hung, C. O. Y., & Livesey, F. J. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.11.095 · Cited by 159
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Penney, J., Ralvenius, W. T., Loon, A., Cerit, O., Dileep, V., Milo, B., Pao, P., Woolf, H., & Tsai, L. (2024) · Glia · doi:10.1002/glia.24485 · Cited by 52
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Zhang, Y., Garcia-Ibanez, L., Ulbricht, C., Lok, L. S. C., Pike, J. A., Mueller-Winkler, J., Dennison, T. W., Ferdinand, J. R., Burnett, C. J. M., Yam-Puc, J. C., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29978-y · Cited by 47
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Peter, M. F., Depping, P., Schneberger, N., Severi, E., Gatterdam, K., Tindall, S., Durand, A., Heinz, V., Koenig, P.-A., Geyer, M., et al. (2021) · doi:10.1101/2021.12.03.471092 · Cited by 38
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Peter, M. F., Ruland, J. A., Depping, P., Schneberger, N., Severi, E., Moecking, J., Gatterdam, K., Tindall, S., Durand, A., Heinz, V., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31907-y · Cited by 38
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Priessner, M., Gaboriau, D. C. A., Sheridan, A., Lenn, T., Garzon-Coral, C., Dunn, A. R., Chubb, J. R., Tousley, A. M., Majzner, R. G., Manor, U., et al. (2024) · Nature Methods · doi:10.1038/s41592-023-02138-w · Cited by 35
Khaw, Y. M., Tierney, A., Cunningham, C., Soto-Díaz, K., Kang, E., Steelman, A. J., & Inoue, M. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2017213118 · Cited by 32
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McCluskey, B. M., Uji, S., Mancusi, J. L., Postlethwait, J. H., & Parichy, D. M. (2021) · PLOS Genetics · doi:10.1371/journal.pgen.1009364 · Cited by 19
Beaudet, D., Berger, C. L., & Hendricks, A. G. (2024) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2024.107323 · Cited by 15
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Munera Lopez, J., Tengganu, I. F., Liu, J., Murray, J. M., Arias Padilla, L. F., Zhang, Y., Brown, P. T., Florens, L., & Hu, K. (2022) · PLOS Pathogens · doi:10.1371/journal.ppat.1010776 · Cited by 14
Nagpal, S., Swaminathan, K., Beaudet, D., Verdier, M., Wang, S., Berger, C. L., Berger, F., & Hendricks, A. G. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114649 · Cited by 13
Brzozowska, N., Wu, L. Y. D., Khodzhaeva, V., Griffiths, W. J., Duckworth, A., Jung, H., Coorens, T. H. H., Hooks, Y., Chambers, J. E., Campbell, P. J., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02125-1 · Cited by 11
Baytshtok, V., DiMattia, M. A., & Lima, C. D. (2025) · Nature Communications · doi:10.1038/s41467-025-61694-1 · Cited by 11
Deschamps, J., Dalle Nogare, D., & Jug, F. (2023) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2023.1255159 · Cited by 11
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Wu, Y., Judge, M. T., Arnold, J., Bhandarkar, S. M., & Edison, A. S. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa631 · Cited by 8
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Grandi, C., Emmaneel, M., Nelissen, F. H. T., Roosenboom, L. W. M., Petrova, Y., Elzokla, O., & Hansen, M. M. K. (2024) · Cell Systems · doi:10.1016/j.cels.2024.05.004 · Cited by 8
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Carabalona, A., Kallo, H., Gonzalez, M., Andriichuk, L., Elomaa, E., Molinari, F., Fragkou, C., Lappalainen, P., Wessels, M. W., Saarikangas, J., et al. (2025) · eLife · doi:10.7554/elife.92748 · Cited by 4
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Puig-Tintó, M., Ortiz, S., Meek, S., Coray, R., Betancur, L. I., Hernández, A. C., Castellet, A., Kramer, E., Hoess, P., Mund, M., et al. (2026) · Cell · doi:10.1016/j.cell.2025.11.038 · Cited by 3
Nabarro, J., Leaman, R. M., Lenton, S., Mantion, L., Spears, R. J., Coles, M. C., Pushkin, D. O., Fascione, M. A., & Baumann, C. G. (2026) · The EMBO Journal · doi:10.1038/s44318-026-00711-5 · Cited by 3
Lolicato, F., Steringer, J., Saleppico, R., Beyer, D., Fernandez-Sobaberas, J., Unger, S., Klein, S., Riegerová, P., Wegehingel, S., Müller, H., et al. (2023) · doi:10.7554/elife.88579.2 · Cited by 1
Lolicato, F., Steringer, J. P., Saleppico, R., Beyer, D., Fernandez-Sobaberas, J., Unger, S., Klein, S., Riegerová, P., Wegehingel, S., Müller, H.-M., et al. (2024) · eLife · doi:10.7554/elife.88579.3
Lolicato, F., Steringer, J., Saleppico, R., Beyer, D., Fernandez-Sobaberas, J., Unger, S., Klein, S., Riegerová, P., Wegehingel, S., Müller, H., et al. (2023) · doi:10.1101/2023.04.12.536539
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Feddersen, H., Dyckmans, C., & Bramkamp, M. (2026) · eLife · doi:10.7554/elife.101517
Metadata
- Authors
- Tinevez, J.-Y., Perry, N., Schindelin, J., Hoopes, G. M., Reynolds, G. D., Laplantine, E., Bednarek, S. Y., Shorte, S. L., & Eliceiri, K. W.
- Venue
- Methods
- Publisher
- Elsevier BV
- Published
- 2017-02
- Volume
- 115
- Pages
- 80-90
- ISSN
- 1046-2023 (ISSN-L)
- OpenAlex
- W2529052661
- Cited by
- 3,380
- References
- 3
- FWCI
- 93.41
- Type
- journal article
- Language
- en
- Open access
- hybrid
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