References and credits
The following references describe applications of HoloPy and technical advances.
If you use HoloPy, we ask that you cite the articles that are relevant to your
application.
| [Dimiduk2016] | Dimiduk, Thomas G., and Vinothan N. Manoharan. “Bayesian Approach to Analyzing Holograms of Colloidal Particles.” Optics Express 24, no. 21 (October 17, 2016): 24045–60. doi:10.1364/OE.24.024045. |
| [Wang2016] | Wang, Anna, Rees F. Garmann, and Vinothan N. Manoharan. “Tracking E. Coli Runs and Tumbles with Scattering Solutions and Digital Holographic Microscopy.” Optics Express 24, no. 21 (October 17, 2016): 23719–25. doi:10.1364/OE.24.023719. |
| [Dimiduk2014] | Dimiduk, Thomas G., Rebecca W. Perry, Jerome Fung, and Vinothan N. Manoharan. “Random-Subset Fitting of Digital Holograms for Fast Three-Dimensional Particle Tracking.” Applied Optics 53, no. 27 (September 20, 2014): G177–83. doi:10.1364/AO.53.00G177. |
| [Wang2014] | Wang, Anna, Thomas G. Dimiduk, Jerome Fung, Sepideh Razavi, Ilona Kretzschmar, Kundan Chaudhary, and Vinothan N. Manoharan. “Using the Discrete Dipole Approximation and Holographic Microscopy to Measure Rotational Dynamics of Non-Spherical Colloidal Particles.” Journal of Quantitative Spectroscopy and Radiative Transfer 146 (October 2014): 499–509. doi:10.1016/j.jqsrt.2013.12.019. |
| [Fung2013] | Fung, Jerome, and Vinothan N. Manoharan. “Holographic Measurements of Anisotropic Three-Dimensional Diffusion of Colloidal Clusters.” Physical Review E 88, no. 2 (August 30, 2013): 020302. doi:10.1103/PhysRevE.88.020302. |
| [Fung2012] | Fung, Jerome, Rebecca W. Perry, Thomas G. Dimiduk, and Vinothan N. Manoharan. “Imaging Multiple Colloidal Particles by Fitting Electromagnetic Scattering Solutions to Digital Holograms.” Journal of Quantitative Spectroscopy and Radiative Transfer 113, no. 18 (December 2012): 2482–89. doi:10.1016/j.jqsrt.2012.06.007. |
| [Kaz2012] | Kaz, David M., Ryan McGorty, Madhav Mani, Michael P. Brenner, and Vinothan N. Manoharan. “Physical Ageing of the Contact Line on Colloidal Particles at Liquid Interfaces.” Nature Materials 11, no. 2 (February 2012): 138–42. doi:10.1038/nmat3190. |
| [Perry2012] | Perry, Rebecca W., Guangnan Meng, Thomas G. Dimiduk, Jerome Fung, and Vinothan N. Manoharan. “Real-Space Studies of the Structure and Dynamics of Self-Assembled Colloidal Clusters.” Faraday Discussions 159, no. 1 (June 7, 2012): 211–34. doi:10.1039/C2FD20061A. |
| [Fung2011] | Fung, Jerome, K. Eric Martin, Rebecca W. Perry, David M. Kaz, Ryan McGorty, and Vinothan N. Manoharan. “Measuring Translational, Rotational, and Vibrational Dynamics in Colloids with Digital Holographic Microscopy.” Optics Express 19, no. 9 (April 25, 2011): 8051–65. doi:10.1364/OE.19.008051. |
| [Leahy2020] | Leahy, Brian, Ronald Alexander, Caroline Martin, Solomon Barkley, and Vinothan N. Manoharan. “Large depth-of-field tracking of colloidal spheres in holographic microscopy by modeling the objective lens.” Optics Express 28, no. 2 (2020): 1061-1075. doi:10.1364/OE.382159 |
Ovryn and Izen and Lee and coworkers were the first to develop methods to fit scattering models to digital holograms:
| [Ovryn2000] | Ovryn, Ben, and Steven H. Izen. “Imaging of Transparent Spheres through a Planar Interface Using a High-Numerical-Aperture Optical Microscope.” Journal of the Optical Society of America A 17, no. 7 (July 1, 2000): 1202–13. doi:10.1364/JOSAA.17.001202. |
| [Lee2007] | Lee, Sang-Hyuk, Yohai Roichman, Gi-Ra Yi, Shin-Hyun Kim, Seung-Man Yang, Alfons van Blaaderen, Peter van Oostrum, and David G. Grier. “Characterizing and Tracking Single Colloidal Particles with Video Holographic Microscopy.” Optics Express 15, no. 26 (December 24, 2007): 18275–82. doi:10.1364/OE.15.018275. |
The following papers describe different methods for calculating scattering and various
algorithms that HoloPy uses in its calculations:
| [Yurkin2011] | Yurkin, Maxim A., and Alfons G. Hoekstra. “The Discrete-Dipole-Approximation Code ADDA: Capabilities and Known Limitations.” Journal of Quantitative Spectroscopy and Radiative Transfer 112, no. 13 (September 2011): 2234–47. doi:10.1016/j.jqsrt.2011.01.031. |
| [Mackowski1990] | Mackowski, D. W., Altenkirch, R. A., and Menguc, M. P. “Internal absorption cross sections in a stratified sphere.” Applied Optics 29, no. 10 (1990). do:10.1364/AO.29.001551. |
| [Mackowski1996] | Mackowski, Daniel W., and Michael I. Mishchenko. “Calculation of the T Matrix and the Scattering Matrix for Ensembles of Spheres.” Journal of the Optical Society of America A 13, no. 11 (November 1, 1996): 2266. doi:10.1364/JOSAA.13.002266. |
| [Wiscombe1996] | Wiscombe, J. “Mie Scattering Calculations: Advances in Technique and Fast, Vector-Speed Computer Codes,” 1979. doi:10.5065/D6ZP4414. |
| [Wiscombe1980] | Wiscombe, W. J. “Improved Mie scattering algorithms.” Applied Optics 19, no. 9 (May 1, 1980): 1505. doi:10.1364/AO.19.001505. |
| [Yang2003] | Yang, Wen. “Improved Recursive Algorithm for Light Scattering by a Multilayered Sphere.” Applied Optics 42, no. 9 (March 20, 2003): 1710–20. doi:10.1364/AO.42.001710. |
| [Lentz1976] | Lentz, William J. “Generating Bessel Functions in Mie Scattering Calculations Using Continued Fractions.” Applied Optics 15, no. 3 (March 1, 1976): 668–71. doi:10.1364/AO.15.000668. |
For scattering calculations and formalism, we draw heavily on the treatise of
Bohren & Huffman. We generally follow their conventions except where noted.
| [Bohren1983] | C. F. Bohren and D. R. Huffman, Absorption and Scattering of Light by Small Particles, Wiley (1983). |
For an introduction to Bayesian analysis of experimental data, we recommend
| [Gregory2010] | P. Gregory, Bayesian Logical Data Analysis for the Physical Sciences, Cambridge University Press (2010) |
The package includes code from several sources. We thank Daniel Mackowski for
allowing us to include his T-Matrix code, which computes scattering from
clusters of spheres: SCSMFO1B.
We also make use of a modified version of the Python version of mpfit,
originally developed by Craig Markwardt. The modified version we use is drawn
from the stsci_python package.
We thank A. Ross Barnett for permitting us to use his routine SBESJY.FOR, which
computes spherical Bessel functions.