David Grier's Home Page Department of Physics and Center for Soft Matter Research New York University

Downloadable Software

• The routines on this page are written in IDL, the Interactive Data Language.
• They are distributed under the terms of the GNU General Public License.

Particle Tracking Routines

• If you make use of this software in published research, the appropriate citation is
  J. C. Crocker and D. G. Grier, "Methods of digital video microscopy for colloidal studies", Journal of Colloid and Interface Science 179, 298-310 (1996).
• Be sure to read through the extensive resources and tutorial by John Crocker and Eric Weeks.

Holographic Optical Trapping Routines

• The original description of holographic optical trapping is
  E. R. Dufresne and D. G. Grier, "Optical tweezer arrays and optical substrates created with diffractive optical elements" Review of Scientific Instruments 69, 1974-1977 (1998)
• An appropriate overall citation for these programs is
  D. G. Grier, "A revolution in optical manipulation", Nature 424, 810-816 (2003).
• More specific citations can be found in our publication list.
• These programs and their applications are covered by patents, and should be used accordingly.

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 structures," Optics Express 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", Optics Express 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 microscopy", Optics Express 17, 13071-13079 (2009).
• The GPU-accelerated routines rely on the GPULib, which provides IDL bindings for CUDA-accelerated array operations. GPULIB must be downloaded and built separately.
• FITSPHEREDHM relies on Craig Markwardt's MPFIT implementation of the Levenberg-Marquardt nonlinear optimization algorithm.
• SPHERETOOL also uses Craig Markwardt's PLOTIMAGE routine.

Utility Routines

IDLvideo NG

IDLvideo NG is an effort to provide 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.

All video-reading capability is provided through the DGGgrMPlayer object.

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 challenging.

IDLvideo

IDLvideo is a suite of routines for transferring video data directly into IDL from video cameras or multimedia files. It is based on the OpenCV library of Open Source Computer Vision routines, which it calls through IDL's CALL_EXTERNAL mechanism.

Sources for the IDLvideo library are available here. The library has to be built and installed before the IDL routines will work.

This interface has been tested on Ubuntu linux and MacOS systems, where it can acquire frame-accurate video in real time. In principle, it can be ported to Windows. This is alpha-quality software, and the installation procedure is particularly bare-bones.

Contact Information

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
david.grier@nyu.edu        New York, NY 10003