mr is a Python package providing tools for passive and active microrheology experiments.
- The widely-used particle locating algorithm originally implemented by John Crocker and Eric Weeks in IDL is reimplemented in Python. Wherever possible, I use existing tools from scipy and numpy modules. Each logical step is broken into a single-purpose function, rendering a succinct and modular code that is easy to customize and maintain. Key array-intensive steps that are not available from Python's standard scientific modules are written in C and imported.
- The trajectories of colloidal probes can be characteristized, grouped, and plotted using a suite of convenient functions.
- Various models (with more to come) relate probe statistics to rheological response, including the Generalized Stokes-Einstein implementation used in the Crocker/Grier code.
- A sql module provides convenient functions for storing and loading data from a MySQL database. (A sample database schema is included.)
- A wrapper for the powerful video handling software FFmpeg helps slice sections of video, ameliorating book-keeping headaches.
- numpy
- scipy
- MySQLdb (optional)
- pIDLy, which calls IDL from Python, only until track.pro can be reimplemented in Python
The feature-finding is stable. This packages still relies on Crocker & Weeks's track.pro to link feature positions into trajectories. Once these are obtained, the package provides tools for flitering, grouping, and analyzing them.
None of the code for active microrheology (tracking and analyzing the motions of magnetic nanowires) has yet been included in this repository.
- Particle tracking using IDL http://www.physics.emory.edu/~weeks/idl/
- A C++ implementation (also wrapped in Python) https://github.com/tacaswell/tracking
- A Matlab implementation by Daniel Blair and Eric Dufresne http://physics.georgetown.edu/matlab/
This package was developed and is maintained by Daniel Allan, as part of his PhD thesis work on microrheology in Robert L. Leheny's group at Johns Hopkins University in Baltimore, MD.
Dan can be reached at dallan@pha.jhu.edu.