#lorenzmie

Python routines for producing and analyzing in-line holographic video microscopy (HVM) images

lorenzmie provides a set of routines for producing and analyzing holographic images of transparent dielectric spheres (pretty niche, huh?). An example image is given below:

The methods used to produce this image can be explained by the physical processes they are supposed to simulate:

1. Illumination in the form of polarized, coherent plane waves (laser light) strikes a micron-sized sphere (eg- a micron sized glass bead).
2. The illuminated sphere produces a scattered wave according to the Lorenz-Mie theory.
3. The plane waves and scattered wave interfere with each other at the camera plane, thus producing the above image.

What's special about these images? The image produced is very sensitive to the physical parameters of the sphere. For example, a slightly larger sphere might have made very different rings. It is this senstivity that makes these images so special.

For instance, suppose you have a sphere with unknown physical properties. You can illuminate the sphere with a known laser source, record the scattering pattern, and indirectly measure the physical properties of the sphere. In particular, the radius, refractive index, and 3D position of the sphere can be measured. And because the electric fields at all points in the volume above the image can be approximately determined, we say that the image is holographic (ie - the 2D image contains all the information of a 3D volume). lorenzmie provides the means for fitting experimental holographic snapshots.

The methods provided here have been adopted, utilized and incrementally improved by David Grier's physics lab in the Center for Soft Matter research at NYU. For many of the exciting applications, see the references below.

Mark Hannel - Physics PhD Student at NYU University

Mark Hannel's Github Repository

1.svr - Calculating holograms is computationally expensive. Instead, support vector machines can offer a less precise, yet computational cheap method for analyzing holographic images.

2.debyewolf - Current implementations of HVM assume the fields produced at the focal plane of an object are the same fields that arrive in the camera plane. debyewolf will utilize the Debye-Wolf integral (along with the abbe-sine condition and the conservation of energy) to account for the changes in amplitude, phase and direction imparted on the field present at the camera.

GPLv3

1. S.-H. Lee, Y. Roichman, G.-R. Yi, S.-H. Kim, S.-M. 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).

2. 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).

3. F. C. Cheong, B. J. Krishnatreya and D. G. Grier, "Strategies for three-dimensional particle tracking with holographic video microscopy," Optics Express 18, 13563-13573 (2010).

4. H. Moyses, B. J. Krishnatreya and D. G. Grier, Optics Express 21 5968-5973 (2013).

5. C. F. Bohren and D. R. Huffman, Absorption and Scattering of Light by Small Particles (New York, Wiley 1983).

6. W. Yang, "Improved recurstive algorithm for light scattering by a multilayered sphere," Applied Optics 42, 1710--1720 (2003).

7. O. Pena and U. Pal, "Scattering of electromagnetic radiation by a multilayered sphere," Computer Physics Communications 180, 2348-2354 (2009).

8. P. Messmer, P. J. Mullowney and B. E. Granger, "GPULib: GPU computing in high-level languages," Computer Science and Engineering 10, 70-73 (2008)