What is the package “ggf” used for?¶
It is a Python implementation of two Matlab scripts by Lars Boyde, StretcherNStress.m and GGF.m, which are used in the Guck lab to compute optical stress distributions and resulting global geometric factors for dielectric, elastic, and spheroidal objects in the optical stretcher.
What is an optical stretcher?¶
The optical stretcher consists of a dual beam laser trap, in its original configuration built from two opposing optical fibers [GAM+01]. When increasing the trapping power, compliant objects such as cells are stretched along the axis of the trap. Using video analysis, the measured shape change can be translated into physical properties of the object.
What is the global geometric factor?¶
The global geometric factor (GGF) connects (the unknown variable) compliance \(J\) (how easy it is to deform a body consisting of a certain material) and (the measured variable) strain \(\epsilon\) (how much this body is deformed). Thus, the GGF is a measure of stress (force acting on the surface of the object).
In an optical stretcher (OS) experiment, the strain \(\epsilon\)
of an object can be measured by analyzing its deformation (e.g. via a
contour in the intensity image). Using object radius and the measured
change in eccentricity, as well as several parameters of the OS
ggf can be used to compute the optical stress
\(\sigma\) from which the GGF is computed.
How should I migrate my Matlab pipeline to Python?¶
To reproduce data¶
You can access the computations performed in StretcherNStress.m via
There was a mistake in the original boundary function (see
issue #1). This affects
all cases where
poisson_ratio is non-zero. If you would like
to reproduce exactly the stress profiles of StretcherNStress.m,
please use ggf version 0.2.0.
from ggf.stress.boyde2009.core import stress theta, sigma, coeff = stress(object_index=1.366, medium_index=1.333, semi_minor=6.7241e-6, # [m] poisson_ratio=0.45, stretch_ratio=0.065, wavelength=780e-9, # [m] beam_waist=3.077, # [wavelengths] power_left=.65, # [W] power_right=.65, # [W] dist=175e-6 / 2, # [m] field_approx="davis", ret_legendre_decomp=True)
The GGF can be computed from the coefficients
from ggf import legendre2ggf legendre2ggf(coeff, poisson_ratio=.45) #> 0.8555678201976592
These methods produce the same output as the original Matlab scripts
with an accuracy that is below the standard tolerance of
For a new project¶
In general, the method
ggf.get_ggf() is recommended. The difference
to the above method is:
- It makes use of precomputed look-up tables (LUTs) which avoids long computation times. The error made by using LUTs maxes at about 1-2%.
- It does not make any assumptions about the Poisson’s ratio when computing the boundary function. This is a more intuitive approach, since the optical stress should not be dependent on the Poisson’s ratio.
- The GGF is computed from 120 Legendre coefficients by default, a number that was previously determined automatically and could have potentially been too low.
- It comes with user-convenient keyword arguments.
Please note that due to these points, the resulting GGF might vary from the GGF computed with the original Matlab script.
import ggf ggf.get_ggf(model="boyde2009", semi_major=7.1612e-6, # [m] semi_minor=6.7241e-6, # [m] object_index=1.366, medium_index=1.333, effective_fiber_distance=175e-6, # [m] mode_field_diameter=4.8e-06, # [m] power_per_fiber=.65, # [W] wavelength=780e-9, # [m] poisson_ratio=0.45) #> 0.8568420867817067