Literature DB >> 28414216

Unraveling the Thousand Word Picture: An Introduction to Super-Resolution Data Analysis.

Antony Lee, Konstantinos Tsekouras, Christopher Calderon1, Carlos Bustamante, Steve Pressé2.   

Abstract

Super-resolution microscopy provides direct insight into fundamental biological processes occurring at length scales smaller than light's diffraction limit. The analysis of data at such scales has brought statistical and machine learning methods into the mainstream. Here we provide a survey of data analysis methods starting from an overview of basic statistical techniques underlying the analysis of super-resolution and, more broadly, imaging data. We subsequently break down the analysis of super-resolution data into four problems: the localization problem, the counting problem, the linking problem, and what we've termed the interpretation problem.

Entities:  

Year:  2017        PMID: 28414216      PMCID: PMC5487374          DOI: 10.1021/acs.chemrev.6b00729

Source DB:  PubMed          Journal:  Chem Rev        ISSN: 0009-2665            Impact factor:   60.622


  254 in total

1.  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

Review 2.  Model selection and psychological theory: a discussion of the differences between the Akaike information criterion (AIC) and the Bayesian information criterion (BIC).

Authors:  Scott I Vrieze
Journal:  Psychol Methods       Date:  2012-02-06

3.  Quantification and correction of systematic errors due to detector time-averaging in single-molecule tracking experiments.

Authors:  Nicolas Destainville; Laurence Salomé
Journal:  Biophys J       Date:  2005-11-18       Impact factor: 4.033

Review 4.  Quantum dots as cellular probes.

Authors:  A Paul Alivisatos; Weiwei Gu; Carolyn Larabell
Journal:  Annu Rev Biomed Eng       Date:  2005       Impact factor: 9.590

5.  High-density mapping of single-molecule trajectories with photoactivated localization microscopy.

Authors:  Suliana Manley; Jennifer M Gillette; George H Patterson; Hari Shroff; Harald F Hess; Eric Betzig; Jennifer Lippincott-Schwartz
Journal:  Nat Methods       Date:  2008-01-13       Impact factor: 28.547

6.  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

7.  Anomalous diffusion models and their properties: non-stationarity, non-ergodicity, and ageing at the centenary of single particle tracking.

Authors:  Ralf Metzler; Jae-Hyung Jeon; Andrey G Cherstvy; Eli Barkai
Journal:  Phys Chem Chem Phys       Date:  2014-11-28       Impact factor: 3.676

8.  Characterization and development of photoactivatable fluorescent proteins for single-molecule-based superresolution imaging.

Authors:  Siyuan Wang; Jeffrey R Moffitt; Graham T Dempsey; X Sunney Xie; Xiaowei Zhuang
Journal:  Proc Natl Acad Sci U S A       Date:  2014-05-27       Impact factor: 11.205

9.  Simultaneous multiple-emitter fitting for single molecule super-resolution imaging.

Authors:  Fang Huang; Samantha L Schwartz; Jason M Byars; Keith A Lidke
Journal:  Biomed Opt Express       Date:  2011-04-29       Impact factor: 3.732

10.  FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data.

Authors:  Junhong Min; Cédric Vonesch; Hagai Kirshner; Lina Carlini; Nicolas Olivier; Seamus Holden; Suliana Manley; Jong Chul Ye; Michael Unser
Journal:  Sci Rep       Date:  2014-04-03       Impact factor: 4.379

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  25 in total

1.  A Bayesian Nonparametric Approach to Single Molecule Förster Resonance Energy Transfer.

Authors:  Ioannis Sgouralis; Shreya Madaan; Franky Djutanta; Rachael Kha; Rizal F Hariadi; Steve Pressé
Journal:  J Phys Chem B       Date:  2019-01-10       Impact factor: 2.991

2.  SMALL-LABS: Measuring Single-Molecule Intensity and Position in Obscuring Backgrounds.

Authors:  Benjamin P Isaacoff; Yilai Li; Stephen A Lee; Julie S Biteen
Journal:  Biophys J       Date:  2019-02-16       Impact factor: 4.033

3.  Resolving Cytosolic Diffusive States in Bacteria by Single-Molecule Tracking.

Authors:  Julian Rocha; Jacqueline Corbitt; Ting Yan; Charles Richardson; Andreas Gahlmann
Journal:  Biophys J       Date:  2019-04-09       Impact factor: 4.033

4.  Quantifying Protein Copy Number in Super Resolution Using an Imaging-Invariant Calibration.

Authors:  Francesca Cella Zanacchi; Carlo Manzo; Raffaella Magrassi; Nathan D Derr; Melike Lakadamyali
Journal:  Biophys J       Date:  2019-05-03       Impact factor: 4.033

5.  Errors in Energy Landscapes Measured with Particle Tracking.

Authors:  Michał J Bogdan; Thierry Savin
Journal:  Biophys J       Date:  2018-07-03       Impact factor: 4.033

6.  Robust model-based analysis of single-particle tracking experiments with Spot-On.

Authors:  Anders S Hansen; Maxime Woringer; Jonathan B Grimm; Luke D Lavis; Robert Tjian; Xavier Darzacq
Journal:  Elife       Date:  2018-01-04       Impact factor: 8.140

Review 7.  Advances in Chromatin and Chromosome Research: Perspectives from Multiple Fields.

Authors:  Andrews Akwasi Agbleke; Assaf Amitai; Jason D Buenrostro; Aditi Chakrabarti; Lingluo Chu; Anders S Hansen; Kristen M Koenig; Ajay S Labade; Sirui Liu; Tadasu Nozaki; Sergey Ovchinnikov; Andrew Seeber; Haitham A Shaban; Jan-Hendrik Spille; Andrew D Stephens; Jun-Han Su; Dushan Wadduwage
Journal:  Mol Cell       Date:  2020-08-07       Impact factor: 17.970

8.  A Programmable DNA-Silicification-Based Nanocavity for Single-Molecule Plasmonic Sensing.

Authors:  Le Liang; Peng Zheng; Chi Zhang; Ishan Barman
Journal:  Adv Mater       Date:  2021-01-18       Impact factor: 30.849

9.  A Protocol for Studying Transcription Factor Dynamics Using Fast Single-Particle Tracking and Spot-On Model-Based Analysis.

Authors:  Asmita Jha; Anders S Hansen
Journal:  Methods Mol Biol       Date:  2022

10.  Viewpoint: Single Molecules at 31: What's Next?

Authors:  W E Moerner
Journal:  Nano Lett       Date:  2020-11-10       Impact factor: 11.189

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