pylorenzmie

Python routines for tracking and characterizing colloidal particles with in-line holographic video microscopy (HVM)

What pylorenzmie does

pylorenzmie provides a set of python classes for interacting with and analyzing holographic microscopy data. The hologram of a colloidal particle encodes comprehensive information about the particle's size, composition, and location in three dimensions. This package extracts that information by fitting a recorded hologram to a generative model based on the Lorenz-Mie theory of light scattering.

Documentation

The documentation is on Read the Docs:

• the quickstart shows how to compute and fit holograms,
• the API reference describes the classes, and
• the changelog lists what changed in each release and how to update.

The tutorial notebooks are rendered on GitHub: fitting a hologram, analyzing a frame, fitting a single frame, holograms of several spheres, video analysis and the building blocks of the model. The documentation of the development version is here.

To report a problem or to contribute, see CONTRIBUTING.md.

Installation

pylorenzmie requires Python 3.11 or later:

pip install pylorenzmie

Optional extras add faster calculators: pip install pylorenzmie[numba] (recommended: a fast CPU calculator), pylorenzmie[torch] (GPUs, including Apple silicon), pylorenzmie[gpu] (NVIDIA GPUs with CuPy), pylorenzmie[jax] and pylorenzmie[gui] (PyQt6 and PyTables, which the lmtool application needs). Extras can be combined, as in pip install pylorenzmie[numba,torch].

Example

Compute the hologram of a polystyrene sphere that is 1 micrometer in radius and 200 pixels from the focal plane:

from pylorenzmie.theory import LorenzMie, Sphere

model = LorenzMie()
model.coordinates = model.meshgrid((201, 201))
model.particle = Sphere(a_p=1., n_p=1.59, x_p=100., y_p=100., z_p=200.)
hologram = model.hologram().reshape(201, 201)

The quickstart goes on to fit recorded holograms.

Interactive particle tracking and characterization

pylorenzmie includes a GUI application called lmtool for interacting with experimentally recorded holograms.

Authors

David G. Grier (New York University), Lauren Altman, Fook Chiong Cheong, Mark D. Hannel, Sanghyuk Lee, Michael O'Brien, Sarah Odeh, Kaitlynn Snyder, Jackie Sustiel

Licensing.

GPLv3

References:

Lorenz-Mie analysis of colloidal particles

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. C. Martin, L. E. Altman, S. Rawat, A. Wang, D. G. Grier and V. N. Manoharan, "In-line holographic microscopy with model-based analysis," Nature Reviews Methods Primers 2, 83 (2022).

Lorenz-Mie theory of light scattering

1. C. F. Bohren and D. R. Huffman, Absorption and Scattering of Light by Small Particles (Wiley 1983).
2. M. I. Mishchenko, L. D. Travis and A. A. Lacis, Scattering Absorption and Emission of Light by Small Particles (Cambridge University Press, 2002).
3. G. Gouesbet and G. Gréhan, Generalized Lorenz-Mie Theories (Springer, 2011).

Computational methods

1. W. Yang, "Improved recursive algorithm for light scattering by a multilayered sphere," Applied Optics 42, 1710--1720 (2003).
2. O. Pena and U. Pal, "Scattering of electromagnetic radiation by a multilayered sphere," Computer Physics Communications 180, 2348-2354 (2009).
3. W. J. Wiscombe, "Improved Mie scattering algorithms," Applied Optics 19, 1505-1509 (1980).
4. A. A. R. Neves and D. Pisignano, "Effect of finite terms on the truncation error of Mie series," Optics Letters 37, 2481-2420 (2012).

Acknowledgements

Work on this project at New York University is supported by the National Science Foundation of the United States under award number DMR-2428983.