Robust single-particle tracking in live-cell time-lapse sequences.
Khuloud Jaqaman,Dinah Loerke,Marcel Mettlen,Hirotaka Kuwata,Sergio Grinstein,Sandra L. Schmid,Gaudenz Danuser +6 more
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TLDR
This approach shows that the GTPase dynamin differentially affects the kinetics of long- and short-lived endocytic structures and that the motion of CD36 receptors along cytoskeleton-mediated linear tracks increases their aggregation probability.Abstract:
Single-particle tracking (SPT) is often the rate-limiting step in live-cell imaging studies of subcellular dynamics. Here we present a tracking algorithm that addresses the principal challenges of SPT, namely high particle density, particle motion heterogeneity, temporary particle disappearance, and particle merging and splitting. The algorithm first links particles between consecutive frames and then links the resulting track segments into complete trajectories. Both steps are formulated as global combinatorial optimization problems whose solution identifies the overall most likely set of particle trajectories throughout a movie. Using this approach, we show that the GTPase dynamin differentially affects the kinetics of long- and short-lived endocytic structures and that the motion of CD36 receptors along cytoskeleton-mediated linear tracks increases their aggregation probability. Both applications indicate the requirement for robust and complete tracking of dense particle fields to dissect the mechanisms of receptor organization at the level of the plasma membrane.read more
Citations
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Journal ArticleDOI
TrackMate: An open and extensible platform for single-particle tracking.
Jean-Yves Tinevez,Nick Perry,Johannes Schindelin,Genevieve M. Hoopes,Gregory D. Reynolds,Emmanuel Laplantine,Sebastian Y. Bednarek,Spencer L. Shorte,Kevin W. Eliceiri +8 more
TL;DR: TrackMate is an extensible platform where developers can easily write their own detection, particle linking, visualization or analysis algorithms within the TrackMate environment and is validated for quantitative lifetime analysis of clathrin-mediated endocytosis in plant cells.
Book ChapterDOI
Methods for cell and particle tracking.
TL;DR: The latest developments in computerized image analysis are surveyed and the various computational approaches, software tools, and quantitative measures for tracking and motion analysis of cells and particles in time-lapse microscopy images are discussed.
Journal ArticleDOI
Improved structure, function and compatibility for CellProfiler
Lee Kamentsky,Thouis R. Jones,Adam Fraser,Mark-Anthony Bray,David J. Logan,Katherine L. Madden,Vebjorn Ljosa,Curtis Rueden,Kevin W. Eliceiri,Anne Carpenter +9 more
TL;DR: CellProfiler 2.0 is described, which has been engineered to meet the needs of its growing user base, with new algorithms and features to facilitate high-throughput work.
Journal ArticleDOI
In vitro cell migration and invasion assays.
Nina Kramer,Angelika Walzl,Christine Unger,Margit Rosner,Georg Krupitza,Markus Hengstschläger,Helmut Dolznig +6 more
TL;DR: A concise summary of established migration/invasion assays described in the literature is provided, list advantages, limitations and drawbacks, give a tabular overview for convenience and depict the basic principles of the assays graphically.
Journal ArticleDOI
Objective comparison of particle tracking methods
Nicolas Chenouard,Ihor Smal,Fabrice de Chaumont,Martin Maška,Martin Maška,Ivo F. Sbalzarini,Yuanhao Gong,Janick Cardinale,Craig Carthel,Stefano Coraluppi,Mark R. Winter,Andrew R. Cohen,William J. Godinez,Karl Rohr,Yannis Kalaidzidis,Liang Liang,James S. Duncan,Hongying Shen,Yingke Xu,Klas E. G. Magnusson,Joakim Jalden,Helen M. Blau,Perrine Paul-Gilloteaux,Philippe Roudot,Charles Kervrann,François Waharte,Jean-Yves Tinevez,Spencer L. Shorte,Joost Willemse,Katherine Celler,Gilles P. van Wezel,Han-Wei Dan,Yuh-Show Tsai,Carlos Ortiz de Solórzano,Jean-Christophe Olivo-Marin,Erik Meijering +35 more
TL;DR: Although no single method performed best across all scenarios, the results revealed clear differences between the various approaches, leading to notable practical conclusions for users and developers.
References
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Journal ArticleDOI
Regulated portals of entry into the cell
Sean D. Conner,Sandra L. Schmid +1 more
TL;DR: ‘Endocytosis’ encompasses several diverse mechanisms by which cells internalize macromolecules and particles into transport vesicles derived from the plasma membrane and must be viewed in a broader context than simple vesicular trafficking.
Journal ArticleDOI
Methods of Digital Video Microscopy for Colloidal Studies
John C. Crocker,David G. Grier +1 more
TL;DR: In this article, a set of image processing algorithms for extracting quantitative data from digitized video microscope images of colloidal suspensions is described, which can locate submicrometer spheres to within 10 nm in the focal plane and 150 nm in depth.
Book
Design and Analysis of Modern Tracking Systems
Samuel S. Blackman,Robert Populi +1 more
TL;DR: The Basics of Target Tracking and Multi Target Tracking with an Agile Beam Radar, and Multiple Hypothesis Tracking System Design and Application.
Journal ArticleDOI
An algorithm for tracking multiple targets
TL;DR: An algorithm for tracking multiple targets in a cluttered environment is developed, capable of initiating tracks, accounting for false or missing reports, and processing sets of dependent reports.
Journal ArticleDOI
Dynasore, a Cell-Permeable Inhibitor of Dynamin
Eric Macia,Marcelo Ehrlich,Ramiro Massol,Emmanuel Boucrot,Christian Brunner,Tomas Kirchhausen +5 more
TL;DR: Dynamin acts at two steps during clathrin coat formation; GTP hydrolysis is probably needed at both steps; Dynasore acts as a potent inhibitor of endocytic pathways known to depend on dynamin by rapidly blocking coated vesicle formation within seconds of dynasore addition.