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TrackMate specifications

Information


Unique identifier OMICS_26421
Name TrackMate
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Version 3.5.3
Stability Stable
Requirements
ImageJ, Fiji
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Jean-Yves Tinevez

Publication for TrackMate

TrackMate citations

 (83)
library_books

Chromosome Segregation Is Biased by Kinetochore Size

2018
Curr Biol
PMCID: 5954971
PMID: 29706521
DOI: 10.1016/j.cub.2018.03.023

[…] Live-cell imaging of IM fibroblasts stably expressing CENP-A-GFP was performed as indicated, every 60 s, and analyzed after CENP-E inhibition using TrackMate Tool in Fiji (ImageJ). Initial kinetochore and pole positions at nuclear envelope breakdown were manually tracked in four dimensions (x,y,z,t) using Manual Tracking Tool. Further analyses an […]

library_books

Dynamic tuneable G protein coupled receptor monomer dimer populations

2018
Nat Commun
PMCID: 5923235
PMID: 29703992
DOI: 10.1038/s41467-018-03727-6

[…] image sequence. Image stacks were subsequently split into donor and acceptor channel images (64 × 128 pixels) with spot detection and particle tracking conducted on each stack using the ImageJ plugin trackmate, included in the FIJI distribution of ImageJ. For spot detection an estimated spot size diameter of 3 pixels was employed, with detection following a difference of Gaussians algorithm (DoG) […]

library_books

Stable centrosomal roots disentangle to allow interphase centriole independence

2018
PLoS Biol
PMCID: 5918241
PMID: 29649211
DOI: 10.1371/journal.pbio.2003998

[…] r quantitation. The intensity of centrosomal rootletin-meGFP in cycling cells was determined by automated centrosome tracking after movie acquisition. Centrosomes were segmented and tracked using the Trackmate plugin in ImageJ/Fiji [], using LAP Tracker, and confirmed as successful by manual analysis of tracking. NEDD1-mRuby3 was tracked, a marker of the PCM that was present throughout the cell cy […]

library_books

Switching between individual and collective motility in B lymphocytes is controlled by cell matrix adhesion and inter cellular interactions

2018
Sci Rep
PMCID: 5895587
PMID: 29643414
DOI: 10.1038/s41598-018-24222-4

[…] re treated using Image J to select individual cells by their size and contrast to background and tracks over 20 min appearing after 3 h of recording were automatically registered and quantified using Trackmate. For population dynamics, individual cells, small (2 to 5 cells) and large clusters (6 or more cells) were detected and their covered surface quantified with Image J. The relative proportion […]

library_books

A homeostatic clock sets daughter centriole size in flies

2018
PMCID: 5881511
PMID: 29500190
DOI: 10.1083/jcb.201801014

[…] ji’s exponential fit algorithm, and then the backgrounds were subtracted using the subtract background function with a rolling ball radius of 10 pixels. Centrioles (Sas-6-GFP foci) were tracked using TrackMate (), a plug-in of Fiji, with the following analysis settings: track spot diameter size of 1.1 µm, initial threshold of >0.02, and quality of >0.07. Centriole growth regression curves were mad […]

library_books

Stabilizing electrochemical interfaces in viscoelastic liquid electrolytes

2018
Sci Adv
PMCID: 5866059
PMID: 29582017
DOI: 10.1126/sciadv.aao6243

[…] fixed electrode spacing of 1.5 mm was maintained during all experiments. We analyzed videos using the ImageJ-based Fiji package (National Institutes of Health) and tracked particle motions using the TrackMate plugin. Particles were identified by the Laplacian of Gaussian detector, with an estimated blob diameter of 10 μm. Trajectories of particles were generated using the simple linear assignment […]

Citations

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TrackMate institution(s)
Imagopole, Citech, Institut Pasteur, Paris, France; Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, WI, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA; Laboratory of Signaling and Pathogenesis, Centre National de la Recherche Scientifique, UMR 3691, Institut Pasteur, Paris, France; Morgridge Institute for Research, Madison, WI, USA
TrackMate funding source(s)
Supported by the European commission FP7 ICT (project ‘‘MEMI”), the Laboratory for Optical and Computational Instrumentation at the UW-Madison and National Science Foundation award #1121998 and by funds from the Stanford University.

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