title: TrackMate: An open and extensible platform for single-particle tracking.
abstract: 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.
authors.affiliation: Imagopole, Citech, Institut Pasteur, 75724 Paris, France. Electronic address: tinevez@pasteur.fr.
authors.forename: Jean-Yves
authors.initials: JY
authors.lastname: Tinevez
authors.affiliation: Imagopole, Citech, Institut Pasteur, 75724 Paris, France.
authors.forename: Nick
authors.initials: N
authors.lastname: Perry
authors.affiliation: Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Johannes
authors.initials: J
authors.lastname: Schindelin
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Genevieve M
authors.initials: GM
authors.lastname: Hoopes
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Gregory D
authors.initials: GD
authors.lastname: Reynolds
authors.affiliation: Laboratory of Signaling and Pathogenesis, Centre National de la Recherche Scientifique, UMR 3691, Institut Pasteur, 75724 Paris, France.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Laplantine
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Sebastian Y
authors.initials: SY
authors.lastname: Bednarek
authors.affiliation: Imagopole, Citech, Institut Pasteur, 75724 Paris, France.
authors.forename: Spencer L
authors.initials: SL
authors.lastname: Shorte
authors.affiliation: Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, WI 53706, USA; Morgridge Institute for Research, Madison, WI 53719, USA.
authors.forename: Kevin W
authors.initials: KW
authors.lastname: Eliceiri
mesh_terms: D033942:Adaptor Proteins, Vesicular Transport / Q000235:genetics / Q000378:metabolism; D000465:Algorithms; D000818:Animals; D017360:Arabidopsis / Q000378:metabolism / Q000648:ultrastructure; D017173:Caenorhabditis elegans; D058948:Cell Tracking / Q000379:methods* / Q000706:statistics & numerical data; D002966:Clathrin / Q000235:genetics / Q000378:metabolism; D004625:Embryo, Nonmammalian / Q000378:metabolism / Q000648:ultrastructure*; D004705:Endocytosis; D005347:Fibroblasts / Q000378:metabolism / Q000648:ultrastructure; D018506:Gene Expression Regulation, Plant; D007091:Image Processing, Computer-Assisted / Q000706:statistics & numerical data*; D055537:Light Signal Transduction; D059828:Plant Cells / Q000378:metabolism / Q000648:ultrastructure; D059010:Single-Cell Analysis / Q000379:methods* / Q000706:statistics & numerical data; D012984:Software
chemical_list: D033942:Adaptor Proteins, Vesicular Transport; D002966:Clathrin
keywords: Clathin-mediated endocytosis; Image analysis; Microscopy; Open-source software; Phototoxicity; Single-particle tracking