Literature DB >> 26536254

Optimal Drift Correction for Superresolution Localization Microscopy with Bayesian Inference.

Ahmed Elmokadem1, Ji Yu2.   

Abstract

Single-molecule-localization-based superresolution microscopy requires accurate sample drift correction to achieve good results. Common approaches for drift compensation include using fiducial markers and direct drift estimation by image correlation. The former increases the experimental complexity and the latter estimates drift at a reduced temporal resolution. Here, we present, to our knowledge, a new approach for drift correction based on the Bayesian statistical framework. The technique has the advantage of being able to calculate the drifts for every image frame of the data set directly from the single-molecule coordinates. We present the theoretical foundation of the algorithm and an implementation that achieves significantly higher accuracy than image-correlation-based estimations.
Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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Year:  2015        PMID: 26536254      PMCID: PMC4643251          DOI: 10.1016/j.bpj.2015.09.017

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


  15 in total

1.  Drift estimation for single marker switching based imaging schemes.

Authors:  Claudia Geisler; Thomas Hotz; Andreas Schönle; Stefan W Hell; Axel Munk; Alexander Egner
Journal:  Opt Express       Date:  2012-03-26       Impact factor: 3.894

2.  Ultra-high resolution imaging by fluorescence photoactivation localization microscopy.

Authors:  Samuel T Hess; Thanu P K Girirajan; Michael D Mason
Journal:  Biophys J       Date:  2006-09-15       Impact factor: 4.033

3.  Multicolor super-resolution imaging with photo-switchable fluorescent probes.

Authors:  Mark Bates; Bo Huang; Graham T Dempsey; Xiaowei Zhuang
Journal:  Science       Date:  2007-08-16       Impact factor: 47.728

Review 4.  Superresolution localization methods.

Authors:  Alexander R Small; Raghuveer Parthasarathy
Journal:  Annu Rev Phys Chem       Date:  2013-11-21       Impact factor: 12.703

5.  Sample drift correction in 3D fluorescence photoactivation localization microscopy.

Authors:  Michael J Mlodzianoski; John M Schreiner; Steven P Callahan; Katarina Smolková; Andrea Dlasková; Jitka Santorová; Petr Ježek; Joerg Bewersdorf
Journal:  Opt Express       Date:  2011-08-01       Impact factor: 3.894

6.  Quantitative evaluation of software packages for single-molecule localization microscopy.

Authors:  Daniel Sage; Hagai Kirshner; Thomas Pengo; Nico Stuurman; Junhong Min; Suliana Manley; Michael Unser
Journal:  Nat Methods       Date:  2015-06-15       Impact factor: 28.547

7.  Localization events-based sample drift correction for localization microscopy with redundant cross-correlation algorithm.

Authors:  Yina Wang; Joerg Schnitzbauer; Zhe Hu; Xueming Li; Yifan Cheng; Zhen-Li Huang; Bo Huang
Journal:  Opt Express       Date:  2014-06-30       Impact factor: 3.894

8.  Tyrosine 221 in Crk regulates adhesion-dependent membrane localization of Crk and Rac and activation of Rac signaling.

Authors:  Yama A Abassi; Kristiina Vuori
Journal:  EMBO J       Date:  2002-09-02       Impact factor: 11.598

9.  Using fixed fiduciary markers for stage drift correction.

Authors:  Sang Hak Lee; Murat Baday; Marco Tjioe; Paul D Simonson; Ruobing Zhang; En Cai; Paul R Selvin
Journal:  Opt Express       Date:  2012-05-21       Impact factor: 3.894

10.  Investigating sub-spine actin dynamics in rat hippocampal neurons with super-resolution optical imaging.

Authors:  Vedakumar Tatavarty; Eun-Ji Kim; Vladimir Rodionov; Ji Yu
Journal:  PLoS One       Date:  2009-11-09       Impact factor: 3.240

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  12 in total

Review 1.  Super-Resolution Microscopy: Shedding Light on the Cellular Plasma Membrane.

Authors:  Matthew B Stone; Sarah A Shelby; Sarah L Veatch
Journal:  Chem Rev       Date:  2017-02-17       Impact factor: 60.622

2.  CTCF and cohesin regulate chromatin loop stability with distinct dynamics.

Authors:  Anders S Hansen; Iryna Pustova; Claudia Cattoglio; Robert Tjian; Xavier Darzacq
Journal:  Elife       Date:  2017-05-03       Impact factor: 8.140

3.  A Simple Marker-Assisted 3D Nanometer Drift Correction Method for Superresolution Microscopy.

Authors:  Hongqiang Ma; Jianquan Xu; Jingyi Jin; Yi Huang; Yang Liu
Journal:  Biophys J       Date:  2017-05-23       Impact factor: 4.033

4.  Estimating the localization spread function of static single-molecule localization microscopy images.

Authors:  Thomas R Shaw; Frank J Fazekas; Sumin Kim; Jennifer C Flanagan-Natoli; Emily R Sumrall; Sarah L Veatch
Journal:  Biophys J       Date:  2022-07-04       Impact factor: 3.699

5.  Multi-color Localization Microscopy of Single Membrane Proteins in Organelles of Live Mammalian Cells.

Authors:  Timo Appelhans; Felix R M Beinlich; Christian P Richter; Rainer Kurre; Karin B Busch
Journal:  J Vis Exp       Date:  2018-06-30       Impact factor: 1.355

6.  Single-molecule localization microscopy as nonlinear inverse problem.

Authors:  Ji Yu; Ahmed Elmokadem
Journal:  Proc Natl Acad Sci U S A       Date:  2019-09-23       Impact factor: 11.205

Review 7.  Super-resolution Microscopy with Single Molecules in Biology and Beyond-Essentials, Current Trends, and Future Challenges.

Authors:  Leonhard Möckl; W E Moerner
Journal:  J Am Chem Soc       Date:  2020-10-09       Impact factor: 15.419

Review 8.  Challenges facing quantitative large-scale optical super-resolution, and some simple solutions.

Authors:  Tal M Dankovich; Silvio O Rizzoli
Journal:  iScience       Date:  2021-02-03

9.  Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF.

Authors:  Anders S Hansen; Tsung-Han S Hsieh; Claudia Cattoglio; Iryna Pustova; Ricardo Saldaña-Meyer; Danny Reinberg; Xavier Darzacq; Robert Tjian
Journal:  Mol Cell       Date:  2019-09-12       Impact factor: 17.970

10.  Guided nuclear exploration increases CTCF target search efficiency.

Authors:  Anders S Hansen; Assaf Amitai; Claudia Cattoglio; Robert Tjian; Xavier Darzacq
Journal:  Nat Chem Biol       Date:  2019-12-02       Impact factor: 15.040

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