Maier and Haraszti Chemistry Central Journal 2012, 6:144

http://journal.chemistrycentral.com/content/6/1/144

SOFTWAR E

Open Access

Python algorithms in particle tracking

microrheology
Timo Maier1,2 and Tamas Haraszti1,2*
Abstract
Background: Particle tracking passive microrheology relates recorded trajectories of microbeads, embedded in soft
samples, to the local mechanical properties of the sample. The method requires intensive numerical data processing
and tools allowing control of the calculation errors.
Results: We report the development of a software package collecting functions and scripts written in Python for
automated and manual data processing, to extract viscoelastic information about the sample using recorded particle
trajectories. The resulting program package analyzes the fundamental diusion characteristics of particle trajectories
and calculates the frequency dependent complex shear modulus using methods published in the literature. In order
to increase conversion accuracy, segmentwise, double step, range-adaptive tting and dynamic sampling algorithms
are introduced to interpolate the data in a splinelike manner.
Conclusions: The presented set of algorithms allows for exible data processing for particle tracking microrheology.
The package presents improved algorithms for mean square displacement estimation, controlling eects of frame loss
during recording, and a novel numerical conversion method using segmentwise interpolation, decreasing the
conversion error from about 100% to the order of 1%.
Keywords: Particle tracking microrheology, Numerical conversion method, Software library, Dynamic interpolation

Background
Particle tracking microrheology is a modern tool to investigate the viscoelastic properties of soft matter, for example, biopolymers and the interior, or the membrane of
living cells [1,2] on the microscopic scale. Though embedding tracer particles into such a sample alters the local
structure, this method is still considered non-invasive and
provides important information not available by other
methods [1-4].
The physical background of the method lies in the thermal motion of the tracer particle, which can be connected
to the viscoelastic properties of the local environment
through the generalized Langevin equation [5,6]. Neglecting the inertia term, which contributes to frequencies
in the megahertz range, and assuming that the memory
function is linearly related to the frequency dependent
*Correspondence: [email protected]
1 Max-Planck Institute for Intelligent Systems, Advanced Materials and
Biosystems, Heisenberg str. 3, 70569 Stuttgart, Germany
2 Biophysical Chemistry, Institute of Physical Chemistry, University of
Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany

viscosity of the medium (through a generalized StokesEinstein relation)[3,5-8], the mean square displacement
(MSD) of the particle can be directly related to the creep
compliance as:
J( ) =

3 a
< r2 ( ) >,
ND kB T

(1)

where denotes the time step in which the particle moves

r distance, < r2 ( ) > the mean square displacement,
ND the dimensionality of the motion (usually ND = 2 for
particle tracking digital microscopy), kB the Boltzmann
constant, T is the absolute temperature and a the particle
radius, respectively.
Active microrheology (using optical or magnetic tweezers) and macroscopic rheometry commonly characterize
the sample elasticity with the frequency-dependent complex shear modulus, G (), which is a complex quantity
[4,9,10]. Its real part is known as the storage modulus
G () and the imaginary part is the loss modulus, G ().
While J(t) is a description in the time domain, G () is
an equivalent characterization in the frequency domain.

2012 Maier and Haraszti; licensee Chemistry Central Ltd. This is an Open Access article distributed under the terms of the
Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use,
distribution, and reproduction in any medium, provided the original work is properly cited.

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The two types of description are equivalent and interconnected with the relation:
G () =

1
,

iJ ()

(2)

where J () is the Fourier transform of J(t). Assuming that

the particle tracks are previously obtained, the frequency
dependent complex shear modulus G () can be derived
using equations (1) and (2) after calculating the mean
square displacement.
There are two major algorithm libraries available on the
Interned addressing data handling for microrheology: the
algorithm collection of J. Crocker et al. written in the
interactive data language (IDL) [11], which was translated
to Matlab and expanded by the Kilfoil lab [12]. A separate stand alone algorithm is provided by M. Tassieri for
calculating the complex shear modulus from the creep
compliance, written in LabView [13]. However, an extensible integrated framework relying on freely accessible
software and source code integrating multiple conversion
methods is not yet available.
In this paper we present a software package written in
the interpreted programing language Python (http://www.
python.org) collecting functions to support particle tracking microrheology related calculations, with emphasis on
those parts providing enhanced functionality. This library
is meant to be an open source, platform independent,
freely extendable set of algorithms allowing to extract
rheology information from particle tracks obtained
previously.
The Rheology software library contains two example
scripts. One called ProcessRheology.py, a conguration
driven program performing all processing steps from particle trajectory inputs, thus presenting the various capabilities of the library (Figure 1). This program can be
employed as a self-standing calculator or its code can
be used as a template for the user testing the Rheology
library. The other is the Function-test.py, containing test
calculations, and which was also employed to produce the
gures in this article (see the content of the Additional
le 1).

Implementation
Dependencies

The software depends on the following Python packages

for calculations and displaying results:
Numpy: a library for array manipulation and
calculations [14];
Scipy: the Python scientic library, from which we
used the gamma function and the nonlinear least
squares tting function [14];
Matplotlib: a Matlab-like plotting library to generate
information graphs of the results [15].

Figure 1 Process ow chart of microrheology data. The

fundamental processing steps in particle tracking microrheology as
followed by the ProcessRheology.py script. There are several
parameters that may aect the details of the process, including the
sampling in the MSD calculation and which way the complex shear
modulus is calculated (see the main text for details). In this article we
focus mainly on the later tree steps in the process: the MSD
calculation and conversion methods.

After installation, its functions are available using following import command within the interpreter or a
Python script:
from Rheology import *
Data presentation, data format

Instead of dening individual classes for each data type

(MSD, creep compliance and complex shear modulus), an
alternative technique in Python is to employ generalized
lists, the so called dictionaries or dicts. A dict is a container class holding data which are indexed with arbitrary
keys (marked by quotes in this paper). This is a very general and exible data structure, which we used for all data
in the Rheology package. For example, MSD dicts contain
keys tau and MSD referring to arrays holding the time
lag and the mean square displacement data, respectively.
Particle trajectories

Particle tracking microrheology starts with the imaging experiments and the image treatment in a strict

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sense, however, obtaining particle trajectories from video

microscopy is well described in the literature [16-20]
including the statistical diculties of the process [21-23].
There are various implementations of particle tracking
algorithms available in IDL (see the same website as
for the rheology code) [11,24], Matlab [12,25], LabView
[20,26] or C++ languages [27]. An implementation of the
Grier method [16] is also translated to Python [28].
Thus, we start our discussion by extracting rheological information from the particle trajectories, leaving the
implementation of data input/output to the user. As a
good starting template, we recommend the ReadTable()
and SaveTable() functions in the ProcessRheology.py example script.
Drift correction

Several experimental systems show a drift: a slow oriented

motion of the sample versus the imaging frame, which is
caused by various factors of the experimenting apparatus.
To remove this drift, which is independent of the sample, there are multiple possibilities one may consider. If a
reference bead bound to the sample is available, its trajectory provides the drift itself. If multiple particles are
tracked in the same time interval, an average trajectory
may be calculated and used as a reference. If these possibilities are not available, one has to consider whether
the long time motion is due to drift or it is a characteristic of the investigated sample, because subtracting it
changes the resulted long time lag (low frequency) part of
the viscoelastic characteristics.
The simplest way of data treatment in such cases is
to calculate a smoothened trajectory: e. g. using a running average, and either subtract this smoothened data
or, in one further step, t a low order polynomial to the
smoothened data and subtract the tted values from the
trajectory.
A very simple implementation is available for two
dimensional data sets as:
GetData(timestamps, poslist, indx=0,
order=3,resolution=0.1434, Nd= 1000)
This algorithm takes a position list (parameter poslist),
which is a list of dicts, each describing the positions of a
particle. The indx parameter is used to select one of them.
A position dict contains X, and Y, which are arrays of
the x and y positions. The dict also contains an index
array denoted with key indx, identifying the image index
(serial number) of the given positions. Using this index
allows the tracking algorithm to miss individual frames (e.
g. when the particle drifted out of focus). This index is also
used to dene the time point of a position, either by identifying the corresponding time stamps, provided in seconds
in the timestamps array, or if this variable is set to None,

Page 3 of 9

multiplying the index by the optional tscale parameter.

The Nd parameter gives the number of points used in the
running average and the order parameter identies the
order of the polynomial to be tted for drift correction. If
Nd is set to 1, the running averaging is o, and if order is
-1, the drift correction is turned o. The resolution is used
to scale the coordinates to micrometers (the same value
for both coordinates).
Mean square displacement (MSD)

Characterizing a soft sample using particle tracking

microrheology strongly relies on the determination of
the mean square displacement. Calculating the MSD has
two possible sets of assumptions: 1.) ensemble averages
are based on recording many tracer particles and assuming homogeneity across the sample. This is the averaging
method considered in theories, and has the advantage
allowing estimation of the time-dependent aging of the
system. Technically this can be achieved by using video
recording-based particle tracking, where the number of
tracers can be increased to the order of tens. 2.) Assuming ergodicity, one can switch from ensemble averaging to
time averaging. This is very important for systems which
are not homogeneous and for cases where only few particles (1 5) can be observed at a time. For samples of
biological origin, time averaging is more suitable because
these samples are seldom homogeneous.
Calculating the time average is done by splitting up the
trajectory into non-overlapping parts and averaging their
displacement. Because the number of intervals decreases
with an increasing lag time, this method has very high
error for large lag time values. Alternatively, it is also possible to split the trajectory into overlapping regions and
then do the averaging. The resulting statistical errors follow a non-normal distribution, but it has been shown that
using overlapping segments the resulted MSD may show
improved accuracy [29,30] when using lag time values up
to about the quarter of the measurement length (N/4 for
N data points). The results of a test calculation using positions randomly calculated from a normal distribution with
standard deviation of X = Y = 0.15 m in both X and
Y directions are presented in Figure 2. The MSD oscillates around the theoretical value of < r( )2 >= 2(X2 +
Y2 ) = 0.09 m2 as expected, but the data calculated using
overlapping intervals show visibly better accuracy.
msd = MSD(positionlist, tau= 0)
MSD() is the function to calculate the mean square displacement from a single trajectory. The data points are
presented as a two dimensional array positionlist, containing coordinates ((x, y) or (x, y, z)) in each row.
The second parameter (tau) is used to generate the lag
time values (steps) for which the MSD is calculated. This

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MSD, m2

0.1

0.01

0.001
0.01

0.1

10

100

, seconds

Figure 2 mean square displacement data calculated from

simulated data. The distribution of X and Y positions were generated
based on a normal distribution with = 0.15 m. The theoretical
MSD is constant at 0.09 m2 (black line). Data with non-overlapping
intervals (red + symbols) show higher scattering, the ones calculated
with overlapping intervals (green ) show a much lower error.

parameter can take various values: If an array or list of

integer values are given, then those are used as index step
values. If a single integer is given between 0 and the number of positions, then so many index steps (lag time values)
are generated in an equidistant manner. If nothing, or 0 is
given, then values 1 . . . N/4 are used.
Each tau value results in M = M(tau) pairs, where
the step r[ i + tau] r[ i] is calculated. M also depends on
whether the set was generated using overlapping intervals
(if overlap = True is set).
If an array of time values (in seconds) are provided for
the position data using the optional tvector parameter, the
algorithm will check the time step between each data pair
used. Calculating the mean value of these time steps and
using a relative error, every value outside the mean (1
tolerance) will be ignored (by default tolerance = 0.1).
This process eliminates jumps in the data caused by computer latency during recording.
The function returns a dictionary containing tau,
dtau, MSD, DMSD keys. If the time values were not
provided, then tau holds the index steps between the
positions and dtau is not used.
Creep compliance

Assuming that the generalized Stokes-Einstein relation

holds, the creep compliance is linearly proportional to the
MSD [6]. The MSD to J() function calculates the creep
compliance using equation (1).
J = MSD to J(msd, t0= 0.1, tend= 150,
T= 25.0, a= 1.0)
The calculation requires a dict structure (msd) having
the time values under the tau key, and the MSD values

under the MSD key (error values are optional). Further

parameters are the temperature T of the experiment in
Celsius degrees, the radius a of the applied tracer particle
in micrometers, and optionally the dimensionality of the
motion D (denoted as ND in equation (1)), which is set to
D = 2 by default.
Calculating the frequency dependent shear modulus
from J(t) with the numerical method proposed by Evans
et al. requires extrapolated values to the zero time point
and to innite time values. These values are estimated
here, allowing the user to override them before being used
to calculate the complex shear modulus G (). The zero
time value J0 = J(t = 0) is extrapolated from a linear t
in the t < t0 region, and the end extrapolation is obtained
from a linear t to the tend < t part. The slope of the
extrapolated end part is 1/, where is the steady state
viscosity [31].
The function returns a new dict containing: J (in
1/Pa), tau, eta, J0, const, dJ, and the t parameters
as a0, b0 for the rst part and a1, b1 for the end part,
where the linear equation J = ai t + bi (i = 0, 1) holds.
Calculating the frequency dependent complex shear modulus

While the connection presented by equation (2) is simple,

there is a major problem with determining J() numerically. It is well known in numerical analysis that applying
a numerical Fourier transform increases the experimental noise enormously [32]. In microrheology, there are
four commonly applied methods to solve this problem.
The rst two address the noise of the Fourier transform
directly by averaging or by tting, the second two were
suggested in the last decade to improve the transform
itself [6,9,31-33].
In a homogeneous system, where multiple particles can
be tracked, converting their MSD to creep compliance and
then G () using a discrete Fourier transform, allows one
to average the converted values and decrease the noise
this way [32,33]. For cases when the creep compliance can
be modeled using an analytical form, the Fourier transform of the tted analytical function may be calculated
and used to estimate of G () [9].
As we have discussed above, samples of biological origin
are often not homogeneous and their MSD does not follow a well-described analytical function. However, model
calculations suggest, in agreement with experiments, that
biopolymers and many polymer gels show power law
behavior at various time ranges [34-36]. The third and
fourth conversion approaches have been suggested for
such systems in the microrheology literature. One uses
a power law approximation of the MSD or the creepcompliance [6] (we shall call the Mason method), and the
other calculates a linear interpolation between the data
points and applying a discrete Fourier transform on it [31]
(we shall cite as the Evans method).

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Because these methods have their strength and weakness, we summarize them and their implementation
below. Recently we have shown that the accuracy of the
Evans method can be greatly improved by using local
interpolation of the data in a splinelike manner without
forcing a single function to be tted to the whole data
set. This improvement is also included in the Rheology
framework and will be discussed below.
The Mason method

This is a fast conversion method based on the Fourier

transformation of a power function, which has been used
in various works in the last decade [6-8,37-39]. Briey,
let us consider a generalized diusion process, where the
MSD is following a power law: < r(t)2 >= 2ND Dt
[40], where D is the generalized diusion coecient, and
0 < 2. In the case of = 1 we can talk about regular Brownian diusion, < 1 describes subdiusion and
> 1 superdiusion, indicating active forces participating in the process. Using the generalized Stokes-Einstein
equation (1) we consider Brownian and subdiusion processes, thus 1 [5,40]. In this case the creep compliance
will also be described with a power function as:
J(t) = J0 t

(3)

The complex shear modulus can be directly calculated

using a gamma function (Figure 3), in the form of:
i

G () = e

i
2

e 2

=
. (4)
J0 (1 + )
J(t = 1/) (1 + )

Usually this equation is presented containing the MSD

[41], but the key feature, the symmetry between the
time dependent creep-compliance and the frequency

1000

G, G, Pa

100

10

dependent complex shear modulus, is more apparent in

this form. The method generalizes this symmetry between
t : = 1/t, and assumes it holds for the whole
measured time range [6], even when the exponent of the
power law varies with time.
However, this is a highly specic case, and the symmetry
does not hold for most of the functions [41]. To improve
the t quality, a slightly more complicated version of this
formula has been proposed by Dasgupta et al. in [38],
based on empirical corrections.
The J to G Mason() function implements both methods based on references [6,38] and the leastsq() function
of scipy, which is a modied Levenberg-Marquardt minimization algorithm.
G = J to G Mason(J,N=30, advanced=True,
logstep=True)
The algorithm takes a creep-compliance dict (J), and
ts a power function locally in the form of equation (3)
to estimate and calculates the complex shear modulus at = 1/t using equation (4). The algorithm uses
a Gaussian function to weight the neighbors in the local
t as it is described by Mason et al. [6]. N denes the
desired number of resulted data points, which are created
by equidistant sampling in the linear or logarithmic space
between 1/tmax . . . 1/tmin . The logarithmic sampling is
activated by the logstep parameter, which is set by default.
The resulted dict contains omega and f for the circular frequency and frequency respectively, and a G array
storing the corresponding complex shear moduli.
There are several further parameters to control the process, from which setting the advanced parameter forces
the use of the method proposed by Dasgupta et al. instead
of the original Mason method, and the verbose switch provides graphical feedback on how the local tting proceeds.
A test example is presented in Figure 3 using a creep
compliance in the form of equation (3) and converted
both numerically and analytically. Because this method is
accurate for power law creep compliances, the conversion
matches within machine precision.
The Evans method

The fourth method we again discuss in detail. It is based

on the work published by Evans et al. [31]. This method
considers a linear interpolation between the N data points
and provides a conversion in the form of equation (5)[41].

0.1

0.01
0.001

0.01

0.1

10

100

, 1/s

Figure 3 Testing the Mason method. Complex shear modulus

(storage modulus (red +) and loss modulus (green )) calculated
from a power law creep compliance in the form of J( ) = 0.1 0.75
and converted using the J to G Mason() function and theoretically
(solid line) using equation (4).

G () =

iJ0 +

N

k=0 (Ak+1

Ak )eitk

(5)

where Ai s are dened by:

Ak =

Jk Jk1
1
, where 0 < k N, A0 = 0, AN+1 = .
tk tk1

(6)

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J0 and are already estimated using the linear ts in

the MSD to J() function. Using equation (5) is straightforward, and allow for the calculation of G () at any
values. The natural selection of a suitable frequency range
would be from 0 to N T (the unit is 1/s) in N/2 steps as
it is common for the discrete Fourier transform of equally
sampled data [32]. The corresponding function is:
G = J to G(J)
The algorithm generates a linear array of frequencies,
but the number of points is limited to be maximum 1000,
usually more than sucient (MSD and creep compliance
data arrays may hold several thousand points). The result
is a similar dictionary as it was for the Mason method,
and can be tested using a Maxwell-uid, which has a linear creep compliance in the form of J(t) = 1/E + t/
(Figure 4).
There are various details worth mentioning about this
method, which may aect the accuracy of the result in
general cases. It is clear in equation (5), that the method is
sensitive to the Ak+1 Ak terms, which, in extreme cases,
may be either very small for a nearly linear part of J(t) or
very high for sudden jumps in the experimental data. In
order to reduce round-o errors, one may eliminate the
close to zero values, (when |Ak+1 Ak | < ) by activating
the lter parameter.
This numerical conversion method has two basic problems. First, from equation (5) it is apparent that the
complex shear modulus is directly related to the numerical Fourier transform of the Ak+1 Ak set, and thus very
sensitive to the noise of these data. Second, the limited

bandwidth causes the Ak values to be a poor representation of the local derivative of the creep compliance,
resulting in a strong deviation (usually an unphysical cuto ) of the calculated shear modulus. This latter problem is
well represented on a test example of a Kelvin-Voigt solid
characterized by a Youngs modulus of E = 10 Pa and
viscosity = 0.2 Pas (Figure 5).
The conversion can be improved by increasing the
bandwidth of the data, or decreasing the frequency range
where G () is calculated (using the omax parameter). A
third alternative is using model interpolations to increase
the bandwidth numerically. Because most experimental
data cannot be tted with a single analytical function for
all values, we have developed a method to t the MSD at
consecutive intervals in a splinelike manner [41].
Adaptive splinelike tting

Biopolymer samples commonly show monotonic MSD,

frequently described by power laws at various time segments. This makes the choice of the power function a
good candidate for the local tting. To count for deviations from power laws at short time values, the tting
system also allows the use of a Kelvin-Voigt solid as an
alternative model for short time scales, in the case of more
elastic samples. Including a Maxwell uid as an option was
not necessary, since the Evans method provides perfect
ts for linear MSDs (see Figure 4).
Because this algorithm has not been published previously, we describe it here in detail. The procedure is
designed to run automatically being controlled only by
selecting the start interval of the data and a scaler, which
denes how fast the tting range should increase with
time. The key steps are:

10
100

0.1

10
G, G, Pa

G, G, Pa

0.01

0.001
0.1

0.0001
0.1

10
, 1/s

100

1000

Figure 4 Maxwell uid, testing the Evans method. The complex

shear modulus of a Maxwell uid with Young modulus of E = 10 Pa
and viscosity = 0.2 Pas, calculated using J to G() (symbols) and
analytically (solid line). The storage modulus (red +) and loss modulus
(green ) data calculated numerically ts well to the theoretical
values presented by the solid black lines.

0.01
0.1

10
, 1/s

100

1000

Figure 5 Kelvin-Voigt solid. Storage modulus (red +) and loss

modulus (green ) calculated for a simulated Kelvin-Voigt solid using
the J to G() function. The numerical results deviate signicantly from
the theoretical values represented by the solid lines.

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1. dene the data range using indices i0 = 0 and

i1 = i(t0 ), containing at least 4 data points;
2. t function from i0 . . . i1 , calculate the squared error
of each point and estimate the average error;
2
3. nd the last point around i1 where 2 (i2 ) < mean
and redene i1 as this point i1 = i2 (stretching or
shrinking the tting range to a reasonable maximum)
4. recalculate the t and errors, store as the current
segment
5. if we reached the end (or close to the end), nish the
cycle, return with the results
6. otherwise, dene the new tting range, using the
scaler parameter (by default use i0 . . . scaler i0 )
7. return to 2 (see Additional le 1)
The exact procedure calculating the new range in each
step may vary depending on the mode an optional keyword parameter, allowing for some control for functions
which show fast changes or slow changes with noise. The
default method (mode=scaler) described above works
well for most MSDs with some noise but monotonic
trends. (More details are available in the help of the library
and the cong.example text le in the Examples folder of
the package).
The corresponding function call is:
fits = MSD power fit(msd, t0=0.2,
scaler=10.0).
Completing the above algorithm, in the next step the
program checks where the ts would cross each-other in
the neighboring ranges, and readjusts them to the crossing
point, if it lies within the union of the two ranges. This step
helps to maintain a smoother approximation of the experimental data. Turning verbosity on using verbose=True,
one may see details about how the algorithm operates.
Dynamic and static interpolation

The return value (ts) is a list of dicts, each containing

the tting parameters of one segment. This list can be
directly used to calculate the interpolation of the original
data using:
msd2 = MSD interpolate(msd, fits, smoothing
= True, Nsmoothing=10, insert=10,
factor=3)

The interpolation and insertion of new points before the

rst data point will increase the bandwidth of the original data. The factor parameter controls the oversampling
of the original data (here it is set to 3 oversampling).
Inserting new data points between 0 and the rst time 0
is specied by insert = 10.
Estimating how many new points are required during
this resampling procedure is a dicult question in general.

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The above example uses a static approach, simply inserting factor points between every two original data points,
which results in a very large equidistant data set. Alternatively we provide a dynamic method, which is controlled
by an error parameter.
Investigating the form of equations (2) and (6), one can
see that the accuracy of the Evans method is strongly
related to how accurately equation (6) approximates the
local derivative of J(t). Knowing the analytical form of
the interpolating functions, this error can be approximated using the function (f ) and its second derivative
(f ) [32,41]. Based on this approximation and specifying a
local error , the minimal step size at any time point h(t)
can be estimated as:

fk (tk )
.
(7)
h=
fk  (tk )
Using h as a minimal step size for each tted segment, the program can dynamically interpolate the data
and increase the number of points only where the creep
compliance changes faster. This results in a non-equally
sampled data set, which (after calculating the creep compliance) can be well handled by both the MSD to J() function and subsequently the numerical conversion method
J to G(), resulting in an improved complex shear modulus. To eliminate further bandwidth problems, the maximal desired circular frequency max can be forced to N
T
using the omax parameter.
The consequence of this tting and interpolation procedure is an increased bandwidth and decreased noise
in the interpolated data set. The resulting accuracy is
some orders of magnitude larger than the specied but
strongly related to it. Therefore the user has to estimate
the suitable for the given problem. For example, inserting 10 new points between 0 t0 and requesting an
accuracy of = 5 104 , the algorithm has corrected
the errors of Figure 5 to about 1% relative error on average (Figure 6). The Mason method produces about 100%
relative error for the loss modulus of the same conversion,
originating from the failure of its power law assumption,
and can not be improved by interpolation [41].
The advantage of employing non-equally sampled data
as the result of the dynamic interpolation is clear if we
compare the required smallest time step produced by this
method. The results indicate hmin 2 106 s, which
would increase the number of data points about 5000
in the case of equidistant sampling. In comparison, the
increment of the number of data points is only about 20%.
For data sets following various trends in the dierent
time segments (thus the tting procedure identies multiple tted regions), the transition between the regions can
be smoothened using a linear interpolation between the
two smoothing functions. The range of this smoothing is

Maier and Haraszti Chemistry Central Journal 2012, 6:144

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Page 8 of 9

Additional le

100

Additional le 1: rheology.zip - compressed ZIP archive containing

the Rheology Python package. The archive contains several les. The
source code in the Rheology subfolder, a setup.py for installation,
README.txt and License.txt les and the Example subfolder. Installation (as
usual in python):

G, G, Pa

10

python setup.py build; python setup.py install

0.1

0.01
0.1

10
, 1/s

100

1000

Figure 6 Dynamic resampling. Dynamic resampling can correct the

errors of the Evans method resulting in an improved t. The storage
modulus (red +) and loss modulus (green ) data calculated
numerically shows a good t to the theoretically predicted values
(black lines).

The Example subfolder contains two Python scripts. The Function-test.py

can be used to run test calculations and see the example plots presenting
that all functions work properly. The gures presented in this paper were
also generated by this script.
The ProcessRheology.py is a batch processing script, controlled by
commands and parameters provided in a cong.txt plain text le. An
example of this le is also included here, containing detailed description of
every parameter. This scripts is a fully functioning microrheology data
evaluation toolkit, utilizing the functions of the Rheology package.

Abbreviations
MSD, Mean square displacement.
Competing interests
The Authors declare that they have not competing interests.

dened by the NSmooth parameter. The range is identied in the original data, but then applied to the rened
data set. The result is an MSD, where sudden jumps are
reduced, minimizing the presence of oscillatory artifacts
in the resulted complex shear modulus G ().

Conclusions
In this paper we have presented a free software solution
for analyzing particle tracking data for microrheology.
Our software library implements the time average calculation of mean square displacement with control over the
time shift in the data, and conversion methods to calculate the creep compliance and the complex shear modulus.
Beyond the two most common methods mentioned in the
literature, we have developed a dynamic local tting procedure, which allows spline-like tting of the MSD and
improved conversion accuracy to about 1% from about
100% for a Kelvin-Voigt model test.

Availability and requirements

Lists the following:
Project name: Rheology for Python
Project home page: http://launchpad.net/
microrheologypy/
Operating systems: Platform independent (Linux,
Windows and Max OSX tested)
Programing language: Python 2.7
Other requirements: Numpy 1.5, Scipy 0.1,
Matplotlib 1.0
License: LGPL v3
Any restrictions to use by non-academics: see
license

Authors contributions
TM and TH have developed the Python software together discussing and
testing the various features, and both contributed to writing this manuscript.
Both authors read and approved the nal manuscript.
Acknowledgements
This work was supported by the Ministry of Science, Research, and the Arts of

Baden-Wurttemberg
(AZ:720.830-5-10a). The authors would like to thank to
Professor Dr. Joachim P. Spatz, Dr. Heike Boehm and the Max-Planck Society
for the generous nancial support and Dr. Claire Cobley for assistance.
Received: 13 September 2012 Accepted: 14 November 2012
Published: 27 November 2012
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Cite this article as: Maier and Haraszti: Python algorithms in particle tracking microrheology. Chemistry Central Journal 2012 6:144.

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