- The routines on this page are written in
Interactive Data Language.
- They are distributed under the terms of
the GNU General
Particle Tracking Routines
Holographic Optical Trapping Routines
Holographic Video Microscopy Routines
These routines are useful for analyzing holographic video microscopy
images of colloidal spheres. They fall into two broad categories.
The first uses Rayleigh-Sommerfeld back-propagation to reconstruct the
three-dimensional light field scattered by the sample.
This is a general, but approximate, approach to hologram analysis.
The second fits holographic snapshots to predictions
based on the Lorenz-Mie theory of light scattering. This approach
can extract extremely precise information from holographic snapshots,
but requires an accurate model for light scattering by the object
of interest. For colloidal spheres, fits to Lorenz-Mie theory yield
each sphere's position in three dimensions,
often with nanometer resolution, its radius with nanometer resolution,
and its complex refractive index with part-per-thousand precision. See the
tutorial to learn how to get started with SPHERETOOL, which is
a graphical interactive front end to the entire software suite.
- If you use the Rayleigh-Sommerfeld software in published research,
the appropriate citation is
S. Lee and D. G. Grier,
"Holographic microscopy of holographically trapped three-dimensional
15, 1505-1512 (2007).
- If you use the Lorenz-Mie routines
(SPHERETOOL and friends) in published research, the
appropriate citation is
S. Lee, Y. Roichman, G. Yi, S. Kim, S. Yang, A. van Blaaderen, P. van Oostrum and D. G. Grier,
"Characterizing and tracking single colloidal particles
with video holographic microscopy",
15, 18275-18282 (2007).
- If, in addition, you make use of the GPU-accelerated version of
the software, the appropriate citation is
F. C. Cheong, B. Sun, R. Dreyfus, J. Amato-Grill, K. Xiao, L. Dixon and
D. G. Grier,
"Flow visualization and flow cytometry with holographic video
17, 13071-13079 (2009).
- The GPU-accelerated routines rely on the
GPULib, which provides
IDL bindings for CUDA-accelerated array operations.
GPULib is a product of the
- FITLMSPHERE in the lmsphere subdirectory relies on Craig Markwardt's
MPFIT implementation of the Levenberg-Marquardt nonlinear
IDLvideo provides IDL with video input capabilities based
on open-source software without requiring shared-object libraries.
It is based on the MPlayer
multimedia player, which it calls through IDL's SPAWN mechanism.
This interface has been tested on GNU/Linux and Mac OS X systems,
where it can acquire frame-accurate video in real time.
It may well work under cygwin. A native Windows port may be more
- Video-reading capability is provided through
the DGGgrMPlayer object.
- The DGGffVideoRead object extends the native IDLffVideoRead
object class to provide the functionality of DGGgrMPlayer.
David G. Grier Department of Physics
Center for Soft Matter Research
(212) 998-3713 (voice) New York University
(212) 995-4016 (FAX) 4 Washington Place
firstname.lastname@example.org New York, NY 10003
Last Modified: Thu Aug 8 17:25:56 EDT 2013