Software package for differential dynamic microscopy with uncertainty quantification MATLAB version 0.5.4

Description:

This package is the application of DDM-UQ method (uncertainty quantification in differential dynamic microscopy). It allows 2-D particle movement simulation; and fully automated and high-throughput estimation and analysis of image structure function, intermediate scattering function and mean squared displacement (MSD) using Gaussian process regression.

Reference:

Gu, M., Luo, Y., He, Y., Helgeson, M. E., & Valentine, M. T. (2021). Uncertainty quantification and estimation in differential dynamic microscopy. Physical Review E, just accepted, arXiv preprint arXiv:2105.01200.

Installation:

To use this package, please install (1) the Optimization Toolbox and (2) the Statistics and Machine Learning Toolbox in MATLAB.

Contents:

DDM-UQ.html - example file with description. example.m - illustrative examples. simulation.m - simulation module, allows user to simulate 2-D particle movement. processing.m - processing module, processes Fourier transformation for intensity profiles. analysis.m - analysis module, robustly estimates the image structure function, mean squared displacement and other quantities of interest. ...(other functions: kernel and log likelihood)

Authors:

Yue He, Mengyang Gu

Department of Statistics and Applied Probability University of California, Santa Barbara

Email: mengyang@pstat.ucsb.edu

This research is supported by NSF BioPACIFIC (DMR-1933487) and DMS-2053423. The authors thank the contributions by Yimin Luo, Matthew Helgeson and Megan Valentine from UCSB.