scholarly journals FoCuS-point: software for STED fluorescence correlation and time-gated single photon counting

2015 ◽  
Vol 32 (6) ◽  
pp. 958-960 ◽  
Author(s):  
Dominic Waithe ◽  
Mathias P. Clausen ◽  
Erdinc Sezgin ◽  
Christian Eggeling
Keyword(s):  
Single Photon ◽  
Photon Counting ◽  
Super Resolution ◽  
Correlation Spectroscopy ◽  
Single Photon Counting ◽  
Fluorescence Correlation ◽  
Point Data ◽  
User Friendly ◽  
Kinetics Of ◽  
Focus Point

Abstract Motivation: Fluorescence Correlation Spectroscopy (FCS) is a popular tool for measuring molecular mobility and how mobility relates to molecular interaction dynamics and bioactivity in living cells. The FCS technique has been significantly advanced by its combination with super-resolution STED microscopy (STED-FCS). Specifically, the use of gated detection has shown great potential for enhancing STED-FCS, but has also created a demand for software which is efficient and also implements the latest algorithms. Prior to this study, no open software has been available which would allow practical time-gating and correlation of point data derived from STED-FCS experiments. Results: The product of this study is a piece of stand-alone software called FoCuS-point. FoCuS-point utilizes advanced time-correlated single-photon counting (TCSPC) correlation algorithms along with time-gated filtering and innovative data visualization. The software has been designed to be highly user-friendly and is tailored to handle batches of data with tools designed to process files in bulk. FoCuS-point also includes advanced fitting algorithms which allow the parameters of the correlation curves and thus the kinetics of diffusion to be established quickly and efficiently. Availability and implementation: FoCuS-point is written in python and is available through the github repository: https://github.com/dwaithe/FCS_point_correlator. Furthermore, compiled versions of the code are available as executables which can be run directly in Linux, Windows and Mac OSX operating systems. Contact: [email protected]

scholarly journals Single-molecule detection on a portable 3D-printed microscope

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
James W. P. Brown ◽  
Arnaud Bauer ◽  
Mark E Polinkovsky ◽  
Akshay Bhumkar ◽  
Dominic J. B. Hunter ◽  
...  
Keyword(s):  
Single Molecule ◽  
Amyloid Fibrils ◽  
Single Photon ◽  
Photon Counting ◽  
Correlation Spectroscopy ◽  
Single Molecule Detection ◽  
Single Photon Counting ◽  
Fluorescence Correlation ◽  
3D Printed ◽  
Simple Format

AbstractSingle-molecule assays have, by definition, the ultimate sensitivity and represent the next frontier in biological analysis and diagnostics. However, many of these powerful technologies require dedicated laboratories and trained personnel and have therefore remained research tools for specialists. Here, we present a single-molecule confocal system built from a 3D-printed scaffold, resulting in a compact, plug and play device called the AttoBright. This device performs single photon counting and fluorescence correlation spectroscopy (FCS) in a simple format and is widely applicable to the detection of single fluorophores, proteins, liposomes or bacteria. The power of single-molecule detection is demonstrated by detecting single α-synuclein amyloid fibrils, that are currently evaluated as biomarkers for Parkinson’s disease, with an improved sensitivity of >100,000-fold over bulk measurements.

Super Resolution Microscopy of Offline g-STED Nanoscopy Based on Time-Correlated Single Photon Counting

2013 ◽  
Vol 40 (1) ◽  
pp. 0104001 ◽  
Author(s):  
郝翔 Hao Xiang ◽  
匡翠方 Kuang Cuifang ◽  
顾兆泰 Gu Zhaotai ◽  
李帅 Li Shuai ◽  
刘旭 Liu Xu
Keyword(s):  
Single Photon ◽  
Photon Counting ◽  
Super Resolution ◽  
Single Photon Counting ◽  
Super Resolution Microscopy

scholarly journals Fast calculation of fluorescence correlation data with asynchronous time-correlated single-photon counting

2003 ◽  
Vol 11 (26) ◽  
pp. 3583 ◽  
Author(s):  
Michael Wahl ◽  
Ingo Gregor ◽  
Mattias Patting ◽  
Jörg Enderlein
Keyword(s):  
Single Photon ◽  
Photon Counting ◽  
Fast Calculation ◽  
Single Photon Counting ◽  
Fluorescence Correlation ◽  
Correlation Data

scholarly journals Computationally-efficient spatiotemporal correlation analysis super-resolves anomalous diffusion

2020 ◽  
Author(s):  
Shawn Yoshida ◽  
William Schmid ◽  
Nam Vo ◽  
William Calabrase ◽  
Lydia Kisley
Keyword(s):  
Correlation Analysis ◽  
Anomalous Diffusion ◽  
Super Resolution ◽  
Correlation Spectroscopy ◽  
Brownian Diffusion ◽  
Computationally Efficient ◽  
Fluorescence Correlation ◽  
Diffusion Dynamics ◽  
Nanoscale Structure ◽  
User Friendly

AbstractAnomalous diffusion dynamics in confined nanoenvironments govern the macroscale properties and interactions of many biophysical and material systems. Currently, it is difficult to quantitatively link the nanoscale structure of porous media to anomalous diffusion within them. Fluorescence correlation spectroscopy super-resolution optical fluctuation imaging (fcsSOFI) has been shown to extract nanoscale structure and Brownian diffusion dynamics within gels, liquid crystals, and polymers, but has limitations which hinder its wider application to more diverse, biophysically-relevant datasets. Here, we parallelize the least-squares curve fitting step on a GPU improving computation times by up to a factor of 40, implement anomalous diffusion and two-component Brownian diffusion models, and make fcsSOFI more accessible by packaging it in a user-friendly GUI. We apply fcsSOFI to simulations of the protein fibrinogen diffusing in polyacrylamide of varying matrix densities and super-resolve locations where slower, anomalous diffusion occurs within smaller, confined pores. The improvements to fcsSOFI in speed, scope, and usability will allow for the wider adoption of super-resolution correlation analysis to diverse research topics.

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