Literature DB >> 22677390

Non-bias-limited tracking of spherical particles, enabling nanometer resolution at low magnification.

Marijn T J van Loenhout1, Jacob W J Kerssemakers, Iwijn De Vlaminck, Cees Dekker.   

Abstract

We present a three-dimensional tracking routine for nondiffraction-limited particles, which significantly reduces pixel bias. Our technique allows for increased resolution compared to that of previous methods, especially at low magnification or at high signal/noise ratio. This enables tracking with nanometer accuracy in a wide field of view and tracking of many particles. To reduce bias induced by pixelation, the tracking algorithm uses interpolation of the image on a circular grid to determine the x-, y-, and z-positions. We evaluate the proposed algorithm by tracking simulated images and compare it to well-known center-of-mass and cross-correlation methods. The final resolution of the described method improves up to an order of magnitude in three dimensions compared to conventional tracking methods. We show that errors in x,y-tracking can seriously affect z-tracking if interpolation is not used. We validate our results with experimental data obtained for conditions matching those used in the simulations. Finally, we show that the increased performance of the proposed algorithm uniquely enables it to extract accurate data for the persistence length and end-to-end distance of 107 DNA tethers in a single experiment.
Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Mesh:

Year:  2012        PMID: 22677390      PMCID: PMC3353059          DOI: 10.1016/j.bpj.2012.03.073

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  23 in total

1.  Quantitative comparison of algorithms for tracking single fluorescent particles.

Authors:  M K Cheezum; W F Walker; W H Guilford
Journal:  Biophys J       Date:  2001-10       Impact factor: 4.033

2.  Highly parallel magnetic tweezers by targeted DNA tethering.

Authors:  Iwijn De Vlaminck; Thomas Henighan; Marijn T J van Loenhout; Indriati Pfeiffer; Julius Huijts; Jacob W J Kerssemakers; Allard J Katan; Anja van Langen-Suurling; Emile van der Drift; Claire Wyman; Cees Dekker
Journal:  Nano Lett       Date:  2011-10-27       Impact factor: 11.189

3.  Subnanometre single-molecule localization, registration and distance measurements.

Authors:  Alexandros Pertsinidis; Yunxiang Zhang; Steven Chu
Journal:  Nature       Date:  2010-07-07       Impact factor: 49.962

4.  Real-time particle tracking at 10,000 fps using optical fiber illumination.

Authors:  Oliver Otto; Fabian Czerwinski; Joanne L Gornall; Gunter Stober; Lene B Oddershede; Ralf Seidel; Ulrich F Keyser
Journal:  Opt Express       Date:  2010-10-25       Impact factor: 3.894

5.  Braiding DNA: experiments, simulations, and models.

Authors:  G Charvin; A Vologodskii; D Bensimon; V Croquette
Journal:  Biophys J       Date:  2005-03-18       Impact factor: 4.033

6.  Subpiconewton dynamic force spectroscopy using magnetic tweezers.

Authors:  M Kruithof; F Chien; M de Jager; J van Noort
Journal:  Biophys J       Date:  2007-12-07       Impact factor: 4.033

7.  Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure.

Authors:  Gleb Shtengel; James A Galbraith; Catherine G Galbraith; Jennifer Lippincott-Schwartz; Jennifer M Gillette; Suliana Manley; Rachid Sougrat; Clare M Waterman; Pakorn Kanchanawong; Michael W Davidson; Richard D Fetter; Harald F Hess
Journal:  Proc Natl Acad Sci U S A       Date:  2009-02-06       Impact factor: 11.205

8.  Fast, bias-free algorithm for tracking single particles with variable size and shape.

Authors:  Andrew J Berglund; Matthew D McMahon; Jabez J McClelland; J Alexander Liddle
Journal:  Opt Express       Date:  2008-09-01       Impact factor: 3.894

9.  Quantitative measurements of force and displacement using an optical trap.

Authors:  R M Simmons; J T Finer; S Chu; J A Spudich
Journal:  Biophys J       Date:  1996-04       Impact factor: 4.033

10.  Tracking kinesin-driven movements with nanometre-scale precision.

Authors:  J Gelles; B J Schnapp; M P Sheetz
Journal:  Nature       Date:  1988-02-04       Impact factor: 49.962

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  35 in total

1.  High Spatiotemporal-Resolution Magnetic Tweezers: Calibration and Applications for DNA Dynamics.

Authors:  David Dulin; Tao Ju Cui; Jelmer Cnossen; Margreet W Docter; Jan Lipfert; Nynke H Dekker
Journal:  Biophys J       Date:  2015-11-17       Impact factor: 4.033

2.  Mechano-regulation of Peptide-MHC Class I Conformations Determines TCR Antigen Recognition.

Authors:  Peng Wu; Tongtong Zhang; Baoyu Liu; Panyu Fei; Lei Cui; Rui Qin; Huaying Zhu; Danmei Yao; Ryan J Martinez; Wei Hu; Chenyi An; Yong Zhang; Junwei Liu; Jiawei Shi; Juan Fan; Weiwei Yin; Jie Sun; Chun Zhou; Xun Zeng; Chenqi Xu; Jianan Wang; Brian D Evavold; Cheng Zhu; Wei Chen; Jizhong Lou
Journal:  Mol Cell       Date:  2019-01-30       Impact factor: 17.970

3.  Single-pixel interior filling function approach for detecting and correcting errors in particle tracking.

Authors:  Stanislav Burov; Patrick Figliozzi; Binhua Lin; Stuart A Rice; Norbert F Scherer; Aaron R Dinner
Journal:  Proc Natl Acad Sci U S A       Date:  2016-12-27       Impact factor: 11.205

4.  Model-free 3D localization with precision estimates for brightfield-imaged particles.

Authors:  Daniel T Kovari; David Dunlap; Eric R Weeks; Laura Finzi
Journal:  Opt Express       Date:  2019-10-14       Impact factor: 3.894

5.  High-Performance Image-Based Measurements of Biological Forces and Interactions in a Dual Optical Trap.

Authors:  Jessica L Killian; James T Inman; Michelle D Wang
Journal:  ACS Nano       Date:  2018-11-20       Impact factor: 15.881

6.  Extending the range for force calibration in magnetic tweezers.

Authors:  Peter Daldrop; Hergen Brutzer; Alexander Huhle; Dominik J Kauert; Ralf Seidel
Journal:  Biophys J       Date:  2015-05-19       Impact factor: 4.033

7.  3D active stabilization for single-molecule imaging.

Authors:  Simao Coelho; Jongho Baek; James Walsh; J Justin Gooding; Katharina Gaus
Journal:  Nat Protoc       Date:  2020-12-02       Impact factor: 13.491

8.  H2A mono-ubiquitination differentiates FACT's functions in nucleosome assembly and disassembly.

Authors:  Yi-Zhou Wang; Cuifang Liu; Jicheng Zhao; Juan Yu; Anfeng Luo; Xue Xiao; Shuo-Xing Dou; Lu Ma; Peng-Ye Wang; Ming Li; Guohong Li; Jianbin Yan; Ping Chen; Wei Li
Journal:  Nucleic Acids Res       Date:  2022-01-25       Impact factor: 16.971

9.  Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events.

Authors:  Je-Kyung Ryu; Sang-Hyun Rah; Richard Janissen; Jacob W J Kerssemakers; Andrea Bonato; Davide Michieletto; Cees Dekker
Journal:  Nucleic Acids Res       Date:  2022-01-25       Impact factor: 16.971

10.  Magnetic forces and DNA mechanics in multiplexed magnetic tweezers.

Authors:  Iwijn De Vlaminck; Thomas Henighan; Marijn T J van Loenhout; Daniel R Burnham; Cees Dekker
Journal:  PLoS One       Date:  2012-08-03       Impact factor: 3.240

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