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David Grier's Home Page

Department of Physics and Center for Soft Matter Research
New York University

Downloadable Software

Tracking

Particle Tracking Routines

ProgramPurpose
bpass.pro Implements a real-space bandpass filter which suppress pixel noise and long-wavelength image variations while retaining information of a characteristic size.
fastfeature.pro Find the centroids of disk-like features in an image quickly.
feature.pro Finds and measures roughly circular 'features' within an image.
featuretool.pro Graphical interface for setting parameters for FEATURE.
tracking.tgzGzipped tar archive

HOT

Holographic Optical Trapping Routines

ProgramPurpose
holo_init.pro Set up the HOLO_COMMON common block for HOT applications.
fastphase.pro Calculates the phase hologram encoding a desired trapping pattern by superposing fields as fast as possible.
dsphase.pro Calculates the phase hologram encoding a desired optical intensity pattern using superposition followed by direct search refinement.
vortex.pro Returns a phase hologram encoding a helical mode.
maketheta.pro Creates an array whose values are the angles in radians relative to the x-axis of each pixel in the array.
makerho.pro Creates an array whose values are the distances from the center of each pixel in the array.
hot.tgzGzipped tar archive

HVM

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.

ProgramPurpose
rayleighsommerfeld.pro Computes Rayleigh-Sommerfeld back-propagation of a normalized hologram of the type measured by digital video microscopy
gpu_rayleighsommerfeld.pro Computes Rayleigh-Sommerfeld back-propagation of a normalized hologram of the type measured by digital video microscopy. Uses GPUlib for hardware acceleration.
fitspheredhm.pro Measure the radius, refractive index, and three-dimensional position of a colloidal sphere immersed in a dielectric medium by fitting its digital holographic microscopy (DHM) image to Mie scattering theory.
spheredhm.pro Computes holographic microscopy image of a sphere immersed in a transparent medium.
spherefield.pro Calculates the complex electric field scattered by a sphere illuminated by a plane wave linearly polarized in the x direction.
sphericalfield.pro Calculates the complex electric field defined by an array of scattering coefficients.
gpu_sphericalfield.pro Calculates the electric field in a light scattering pattern defined by a set of Lorenz-Mie scattering coefficients. Uses gpulib for hardware acceleration.
sphere_coefficients.pro Calculates the Mie scattering coefficients for a homogeneous isotropic sphere illuminated by a coherent plane wave linearly polarized in the x direction.
spheredhmprofile.pro Calculates the radial profile of the in-line hologram of a sphere, as obtained with digital holographic microscopy.
coatedspheretoo1.pro Interactively find reasonable fitting parameters for digital holographic microscopy images of core shell colloidal spheres.
spheretool_cleanup.pro Perform housekeeping tasks when SPHERETOOL exits.
spheretool_event.pro Event handler for spheretool.
spheretool_gpu_detect.pro Determine whether or not spheretool can run with GPU acceleration.
spheretool.pro Interactively find reasonable fitting parameters for digital holographic microscopy images of colloidal spheres.
spheretool_saveroutine.pro Metaprogramming: Saves an IDL routine that implements holographic video microscopy fits according to the current settings of SPHERETOOL.
spheretool_widgets.pro Creates the widget hierarchy for SPHERETOOL
hvm.tgzGzipped tar archive

Tracking

Utility Routines

ProgramPurpose
read_gdf.pro Read in data files created by WRITE_GDF.
write_gdf.pro Writes IDL-style data to disk in a format which can be easily read back in.
deinterlace.pro Deinterlaces an (interlaced) image.
aziavg.pro Average a two dimensional data set over angles about its center.
azistd.pro Calcuate the standard deviation from the mean of a two dimensional data set, averaged over angles, as a function of radius from the center.
utility.tgzGzipped tar archive

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

Last Modified: Thu Nov 12 09:00:29 EST 2009