Browse
Submit Data
Databases
API
Help

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Direct Photon-by-Photon Analysis of Time-Resolved Pulsed Excitation Data using Bayesian Nonparametrics.

ABSTRACT: Lifetimes of chemical species are typically estimated by either fitting time-correlated single-photon counting (TCSPC) histograms or phasor analysis from time-resolved photon arrivals. While both methods yield lifetimes in a computationally efficient manner, their performance is limited by choices made on the number of distinct chemical species contributing photons. However, the number of species is encoded in the photon arrival times collected for each illuminated spot and need not be set by hand a priori. Here, we propose a direct photon-by-photon analysis of data drawn from pulsed excitation experiments to infer, simultaneously and self-consistently, the number of species and their associated lifetimes from a few thousand photons. We do so by leveraging new mathematical tools within the Bayesian nonparametric. We benchmark our method for both simulated and experimental data for 1-4 species.

SUBMITTER: Tavakoli M

PROVIDER: S-EPMC8373049 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Pitching single-focus confocal data analysis one photon at a time with Bayesian nonparametrics.

Project description:Fluorescence time traces are used to report on dynamical properties of molecules. The basic unit of information in these traces is the arrival time of individual photons, which carry instantaneous information from the molecule, from which they are emitted, to the detector on timescales as fast as microseconds. Thus, it is theoretically possible to monitor molecular dynamics at such timescales from traces containing only a sufficient number of photon arrivals. In practice, however, traces are stochastic and in order to deduce dynamical information through traditional means-such as fluorescence correlation spectroscopy (FCS) and related techniques-they are collected and temporally autocorrelated over several minutes. So far, it has been impossible to analyze dynamical properties of molecules on timescales approaching data acquisition without collecting long traces under the strong assumption of stationarity of the process under observation or assumptions required for the analytic derivation of a correlation function. To avoid these assumptions, we would otherwise need to estimate the instantaneous number of molecules emitting photons and their positions within the confocal volume. As the number of molecules in a typical experiment is unknown, this problem demands that we abandon the conventional analysis paradigm. Here, we exploit Bayesian nonparametrics that allow us to obtain, in a principled fashion, estimates of the same quantities as FCS but from the direct analysis of traces of photon arrivals that are significantly smaller in size, or total duration, than those required by FCS.

| S-EPMC8445401 | biostudies-literature

16-Ch Time-resolved Single-Molecule Spectroscopy Using Line Excitation.

Project description:Single-molecule spectroscopy on freely-diffusing molecules allows detecting conformational changes of biomolecules without perturbation from surface immobilization. Resolving fluorescence lifetimes increases the sensitivity in detecting conformational changes and overcomes artifacts common in intensity-based measurements. Common to all freely-diffusing techniques, however, are the long acquisition times. We report a time-resolved multispot system employing a 16-channel SPAD array and TCSPC electronics, which overcomes the throughput issue. Excitation is obtained by shaping a 532 nm pulsed laser into a line, matching the linear SPAD array geometry. We show that the line-excitation is a robust and cost-effective approach to implement multispot systems based on linear detector arrays.

| S-EPMC5463578 | biostudies-literature

Live-cell superresolution imaging by pulsed STED two-photon excitation microscopy.

Project description:Two-photon laser scanning microscopy (2PLSM) allows fluorescence imaging in thick biological samples where absorption and scattering typically degrade resolution and signal collection of one-photon imaging approaches. The spatial resolution of conventional 2PLSM is limited by diffraction, and the near-infrared wavelengths used for excitation in 2PLSM preclude the accurate imaging of many small subcellular compartments of neurons. Stimulated emission depletion (STED) microscopy is a superresolution imaging modality that overcomes the resolution limit imposed by diffraction and allows fluorescence imaging of nanoscale features. Here, we describe the design and operation of a superresolution two-photon microscope using pulsed excitation and STED lasers. We examine the depth dependence of STED imaging in acute tissue slices and find enhancement of 2P resolution ranging from approximately fivefold at 20 μm to approximately twofold at 90-μm deep. The depth dependence of resolution is found to be consistent with the depth dependence of depletion efficiency, suggesting resolution is limited by STED laser propagation through turbid tissue. Finally, we achieve live imaging of dendritic spines with 60-nm resolution and demonstrate that our technique allows accurate quantification of neuronal morphology up to 30-μm deep in living brain tissue.

| S-EPMC3576532 | biostudies-literature

3D-resolved fluorescence and phosphorescence lifetime imaging using temporal focusing wide-field two-photon excitation.

Project description:Fluorescence and phosphorescence lifetime imaging are powerful techniques for studying intracellular protein interactions and for diagnosing tissue pathophysiology. While lifetime-resolved microscopy has long been in the repertoire of the biophotonics community, current implementations fall short in terms of simultaneously providing 3D resolution, high throughput, and good tissue penetration. This report describes a new highly efficient lifetime-resolved imaging method that combines temporal focusing wide-field multiphoton excitation and simultaneous acquisition of lifetime information in frequency domain using a nanosecond gated imager from a 3D-resolved plane. This approach is scalable allowing fast volumetric imaging limited only by the available laser peak power. The accuracy and performance of the proposed method is demonstrated in several imaging studies important for understanding peripheral nerve regeneration processes. Most importantly, the parallelism of this approach may enhance the imaging speed of long lifetime processes such as phosphorescence by several orders of magnitude.

| S-EPMC3601594 | biostudies-other

Two-Photon Excitation STED Microscopy with Time-Gated Detection.

Project description:We report on a novel two-photon excitation stimulated emission depletion (2PE-STED) microscope based on time-gated detection. The time-gated detection allows for the effective silencing of the fluorophores using moderate stimulated emission beam intensity. This opens the possibility of implementing an efficient 2PE-STED microscope with a stimulated emission beam running in a continuous-wave. The continuous-wave stimulated emission beam tempers the laser architecture's complexity and cost, but the time-gated detection degrades the signal-to-noise ratio (SNR) and signal-to-background ratio (SBR) of the image. We recover the SNR and the SBR through a multi-image deconvolution algorithm. Indeed, the algorithm simultaneously reassigns early-photons (normally discarded by the time-gated detection) to their original positions and removes the background induced by the stimulated emission beam. We exemplify the benefits of this implementation by imaging sub-cellular structures. Finally, we discuss of the extension of this algorithm to future all-pulsed 2PE-STED implementationd based on time-gated detection and a nanosecond laser source.

| S-EPMC4725939 | biostudies-literature

Time-Resolved Macromolecular Crystallography at Pulsed X-ray Sources.

Project description:The focus of structural biology is shifting from the determination of static structures to the investigation of dynamical aspects of macromolecular function. With time-resolved macromolecular crystallography (TRX), intermediates that form and decay during the macromolecular reaction can be investigated, as well as their reaction dynamics. Time-resolved crystallographic methods were initially developed at synchrotrons. However, about a decade ago, extremely brilliant, femtosecond-pulsed X-ray sources, the free electron lasers for hard X-rays, became available to a wider community. TRX is now possible with femtosecond temporal resolution. This review provides an overview of methodological aspects of TRX, and at the same time, aims to outline the frontiers of this method at modern pulsed X-ray sources.

| S-EPMC6470897 | biostudies-literature

Photoluminescence of InAs/GaAs quantum dots under direct two-photon excitation.

Project description:Self-assembled quantum dots grown by molecular beam epitaxy have been a hotbed for various fundamental research and device applications over the past decades. Among them, InAs/GaAs quantum dots have shown great potential for applications in quantum information, quantum computing, infrared photodetection, etc. Though intensively studied, some of the optical nonlinear properties of InAs/GaAs quantum dots, specifically the associated two-photon absorption of the wetting and barrier layers, have not been investigated yet. Here we report a study of the photoluminescence of these dots by using direct two-photon excitation. The quadratic power law dependence of the photoluminescence intensity, together with the ground-state resonant peak of quantum dots appearing in the photoluminescence excitation spectrum, unambiguously confirms the occurrence of the direct two-photon absorption in the dots. A three-level rate equation model is proposed to describe the photogenerated carrier dynamics in the quantum dot-wetting layer-GaAs system. Moreover, higher-order power law dependence of photoluminescence intensity is observed on both the GaAs substrate and the wetting layer by two-photon excitation, which is accounted for by a model involving the third-harmonic generation at the sample interface. Our results open a door for understanding the optical nonlinear effects associated with this fundamentally and technologically important platform.

| S-EPMC7331710 | biostudies-literature

Density Estimation for Protein Conformation Angles Using a Bivariate von Mises Distribution and Bayesian Nonparametrics.

Project description:Interest in predicting protein backbone conformational angles has prompted the development of modeling and inference procedures for bivariate angular distributions. We present a Bayesian approach to density estimation for bivariate angular data that uses a Dirichlet process mixture model and a bivariate von Mises distribution. We derive the necessary full conditional distributions to fit the model, as well as the details for sampling from the posterior predictive distribution. We show how our density estimation method makes it possible to improve current approaches for protein structure prediction by comparing the performance of the so-called "whole" and "half" position distributions. Current methods in the field are based on whole position distributions, as density estimation for the half positions requires techniques, such as ours, that can provide good estimates for small datasets. With our method we are able to demonstrate that half position data provides a better approximation for the distribution of conformational angles at a given sequence position, therefore providing increased efficiency and accuracy in structure prediction.

| S-EPMC2835366 | biostudies-literature

Interferometric temporal focusing microscopy using three-photon excitation fluorescence.

Project description:Super-resolution microscopy has become a powerful tool for biological research. However, its spatial resolution and imaging depth are limited, largely due to background light. Interferometric temporal focusing (ITF) microscopy, which combines structured illumination microscopy and three-photon excitation fluorescence microscopy, can overcome these limitations. Here, we demonstrate ITF microscopy using three-photon excitation fluorescence, which has a spatial resolution of 106 nm at an imaging depth of 100 µm with an excitation wavelength of 1060 nm.

| S-EPMC5905902 | biostudies-literature

Direct observation of photocarrier electron dynamics in C<sub>60</sub> films on graphite by time-resolved two-photon photoemission.

Project description:Time-resolved two-photon photoemission (TR-2PPE) spectroscopy is employed to probe the electronic states of a C60 fullerene film formed on highly oriented pyrolytic graphite (HOPG), acting as a model two-dimensional (2D) material for multi-layered graphene. Owing to the in-plane sp2-hybridized nature of the HOPG, the TR-2PPE spectra reveal the energetics and dynamics of photocarriers in the C60 film: after hot excitons are nascently formed in C60 via intramolecular excitation by a pump photon, they dissociate into photocarriers of free electrons and the corresponding holes, and the electrons are subsequently detected by a probe photon as photoelectrons. The decay rate of photocarriers from the C60 film into the HOPG is evaluated to be 1.31 × 1012 s-1, suggesting a weak van der Waals interaction at the interface, where the photocarriers tentatively occupy the lowest unoccupied molecular orbital (LUMO) of C60. The photocarrier electron dynamics following the hot exciton dissociation in the organic thin films has not been realized for any metallic substrates exhibiting strong interactions with the overlayer. Furthermore, the thickness dependence of the electron lifetime in the LUMO reveals that the electron hopping rate in C60 layers is 3.3 ± 1.2 × 1013 s-1.

| S-EPMC5075791 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data