DLSuR 0.0.17

Dynamic light scattering microrheology data analysis package

DLSuR: Dynamic light scattering microrheology in Python

DLSuR is a data analysis package for analyzing the scattering intensity from a dynamic light scattering instrument and deriving the microrheology spectrum in the Python programming language.

To use DLSuR, you need to:

• have data from a dynamic light scattering instrument,
• save the data in the specific format that is listed in this paper[cite], and
• be sure to collect data following the methods listed in this paper[cite]

The DLSuR environment

Easy Implementation

The DLSuR method is simple to implement, utilizing just the scattering autocorrelation of embedded particles in a given soft material sample. The methods are split into different ways to analyze and visualize one's data.

By using only the scattering autocorrelation, the methodology of analyzing the mean-squared displacement of embedded particles to derive the frequency-dependent complex modulus becomes much simpler than other microrheology techniques such as video particle tracking.

Large Range of Rheological Behavior

DLSuR has the capability of measuring up to six decades in rheological behavior without using time-temperature superposition. This is a major advantage over state-of-the-art rheological techniques such as oscillatory rheometers.

How to cite

If you use this package, please cite the following paper:

Cai P. C., Krajina B. A., Kratochvil M. J., Zou L., Zhu A., Burgener E. B., Bollyky P. L., Milla C. E., Webber M. J., Spakowitz A. J., Heilshorn S. C. (2020). Dynamic Light Scattering Microrheology for Soft and Living Materials.

Installation

Dependencies

DLSuR requires:

• Python (>= 3.7)
• SciPy
• NumPy
• Matplotlib
• Pandas
• Seaborn
• Sphinx (>=1.4)

Standard installation (on CPU hardware)

We strongly recommend running DLSuR in an Anaconda environment, because this simplifies the installation of other dependencies. You may install the latest version of DLSuR using the package manager pip, which will automatically download DLSuR from the Python Package Index (PyPI):

pip install DLSuR

Linux and macOS are the two officially supported operating systems.

Installation from source

Assuming the DLSuR source has been downloaded, you may install it by running

pip install -r requirements.txt
python setup.py install

Developers can also install Kymatio via:

pip install -r requirements.txt
python setup.py develop

Documentation

The documentation of Kymatio is officially hosted on the DLSuR website.

Online resources

• GitHub repository
• GitHub issue tracker
• BSD-3-Clause license

Building the documentation from source

The documentation can also be found in the doc/ subfolder of the GitHub repository. To build the documentation locally, please clone this repository and run

pip install -r requirements_optional.txt
cd doc; make clean; make html

Support

We wish to thank Stanford University, National Science Foundation, Stanford Bio-X Initiative for their financial support.