This is a small python package to do rheology related calculations in passive particle tracking microrheology.
Requirements:
- python 2.7
- numpy 1.5
- scipy 0.10
- matplotlib 1.0
It may also work with some earlier versions, but these have been used for testing.
Capabilities:
- calculating mean squared displacement from positions
- higher order displacements
- maximum mean excursion (quadratic and higher as well)
- creep-compliance from MSD
- complex shear modulus from creep compliance using various methods
The last one can be done using the method proposed by Mason et al. and Dasgupta et al., and the numerical transform proposed by Evan et al. There is an improved method as well, using local fitting and then a dynamically refined data set to get the complex shear modulus.
Mason's method is limited to power functions, so be careful using it. The Evans method is very sensitive to data noise and to sampling error at high frequenxies (producing a cut off).
An example script and general tool is provided in the Examples under the ProcessRheology.py. It uses a config file to receive commands, there is a commented example in the same folder.
The full description of the configuration is in the config.txt.example file, and an example dataset and correscponding config file is also provided in the Examples folder (fov2191wDD.txt, timestamp-table.txt, config.txt). The example data is an actin network on micropillars bundled using a testbuffer containing 8mM magnesium (from 25th July 2012, Timo Maier).
The Function-test.py runs some theoretical tests and shows the results graphically. It is a useful tool to test the functions and see how the various results change when one varies the parameters (see the comments within).
Install: python setup.py build and sudo python setup.py install
should do the trick.
Usage: the common import utility will work (from Rheology import *).
I hope you find these tools useful and interesting. Any further improvements and suggestions are welcome.
2012 June, Heidelberg T.H.