PyDDM

This is a python package to perform Differential Dynamic Microscopy (DDM) Analysis

The functions in PyDDM.ddm_calc can be used to compute the DDM matrix and fit it to various models. The different theoretical models available to fit data are in the module PyDDM.ISF_and_DDMmatrix_theoretical_models. Details of the fitting for these models are found in PyDDM.fit_parameters_dictionaries.

Within the module PyDDM.ddm_analysis_and_fitting are a couple classes for make working with the code easy and organized.

For more on the principles of DDM, please see [1] [2] [3] .

This code, and its earlier versions, have been used in several projects of the McGorty lab at the University of San Diego. [4] [5] [6] [7] [8]

References

[1]

Cerbino, R. & Trappe, V. Differential Dynamic Microscopy: Probing Wave Vector Dependent Dynamics with a Microscope. Phys. Rev. Lett. 100, 188102 (2008)

[2]

Wilson, L. G. et al. Differential Dynamic Microscopy of Bacterial Motility. Phys. Rev. Lett. 106, 018101 (2011).

[3]

Germain, D., Leocmach, M. & Gibaud, T. Differential dynamic microscopy to characterize Brownian motion and bacteria motility. American Journal of Physics 84, 202–210 (2016).

[4]

Wulstein, D. M., Regan, K. E., Robertson-Anderson, R. M. & McGorty, R. Light-sheet microscopy with digital Fourier analysis measures transport properties over large field-of-view. Opt. Express, OE 24, 20881–20894 (2016).

[5]

Anderson, S. J. et al. Filament Rigidity Vies with Mesh Size in Determining Anomalous Diffusion in Cytoskeleton. Biomacromolecules (2019) doi:10.1021/acs.biomac.9b01057.

[6]

Wulstein, D. M., Regan, K. E., Garamella, J., McGorty, R. J. & Robertson-Anderson, R. M. Topology-dependent anomalous dynamics of ring and linear DNA are sensitive to cytoskeleton crosslinking. Science Advances 5, eaay5912 (2019).

[7]

Wang, J. & McGorty, R. Measuring capillary wave dynamics using differential dynamic microscopy. Soft Matter 15, 7412–7419 (2019).

[8]

You, R. & McGorty, R. Two-color differential dynamic microscopy for capturing fast dynamics. Review of Scientific Instruments 92, 023702 (2021).

ISF_and_DDMmatrix_theoretical_models	Mathematical models for the DDM matrix and the ISF
dcimg_mod	This module provides the DCIMGFile class for accessing Hamamatsu DCIMG files.
ddm_analysis_and_fitting	Preprocessing of data and core part of DDM analysis
ddm_calc	This module contains the code for calculating and fitting the DDM matrix.
fit_parameters_dictionaries	This module contains a dictionary for each of the different models for fitting the DDM matrix or the ISF.
utils	Created on Wed Nov 3 09:10:13 2021