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Microrheology

Microrheology, the book

Our book on the principles and practices of microrheology (Eric M. Furst and Todd M. Squires, Microrheology, Oxford University Press, 2017) is currently available at OUP and Amazon. (The paperback is affordable!)

The book covers both passive and active microrheology and discusses the theoretical foundation through discussions of particle (elasto-)hydrodynamics, Brownian motion, and other topics.

Particle tracking with MATLAB Tutorial

This is a collection of software and sample data to help the reader get started with particle tracking microrheology. For an overview of the practice and some applications of microrheology, attached are slides from a plenary talk at the 2017 Society of Rheology annual meeting: SOR 2017 (75MB)

Particle tracking tutorial

  1. Download an updated Particle Tracking with MATLAB handout
  2. Download the MATLAB particle tracking routines
  3. To familiarize yourself with the commands in the handout, it's useful to have a sample image to work with

Planning a microrheology experiment

Like all rheometry, microrheology techniques have distinct operating ranges. Choosing the right technique, or whether to use microrheology at all, is an important step. You can use this operating diagram to plan experiments. Other questions to consider:

  • Does the experiment satisfy the conditions of the Generalized Stokes Equation?
  • Is it necessary to convert to the frequency domain? Passive microrheology is a creep experiment, and can be interpreted in the time domain.
  • When using an approximate form of the GSER, what is the effect of noise in the MSD on the numerical derivatives?

Particle tracking and image analysis resources

Follow these helpful links for useful data analysis tutorials and resources:

Microrheology data sets

Image data sets to use with particle tracking

Practice data set

Particles diffusing in water. This is a practice data set to get started with microrheology.

  • microrheology data set (204 MB). The zip file contains 400 uncompressed TIFF images, and will expand to about 800MB after uncompressing.

The data in the zip file was taken with a 63x NA 1.2 water immersion microscope objective with a 1.0x magnification tube lens. The conversion for pixels to micrometers should be about 40.6 pixels / 10 µm, but you can confirm this with the calibration image below (63x_1x.tif). The acquisition frame rate is 30 frames per second. The exposure time is set to 900 µs.

You can examine the effect of signal-to-noise ratio (SNR) on the particle tracking. This set was taken using the same objective, magnification, and frame rate, but at a lower acquisition time, 10 µs.

Microrheology of the liquid-solid transition during gelation

Data for the experiments presented in T. L. Larsen and E. M. Furst, “Microrheology of the liquid-solid transition during gelation,” Phys. Rev. Lett. 100, 146001 (2008). DOI 10.1103/PhysRevLett.100.146001.

Here are the mean-squared displacements reported in the article:

Image data sets for are archived on Zenodo for the above experiments:

List of attached files

License

Some programs included in this tutorial are based on code originally authored by David G. Grier, John C. Crocker, Eric Dufresne, and Daniel Blair. See the individual files for attribution and licensing. The program track.m is based on 'track.pro' and is copyright 1999, by John C. Crocker.

Copyright (c) 2013-2021 Eric M. Furst

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.