
@article{flyvbjerg_error_1989,
  title = {Error estimates on averages of correlated data},
  volume = {91},
  issn = {00219606},
  doi = {doi:10.1063/1.457480},
  abstract = {We describe how the true statistical error on an average of correlated data can be obtained with ease and efficiency by a renormalization group method. The method is illustrated with numerical and analytical examples, having finite as well as infinite range correlations.},
  timestamp = {2016-08-06T11:32:24Z},
  number = {1},
  urldate = {2013-10-10},
  journal = {Journal of Chemical Physics},
  author = {Flyvbjerg, H. and Petersen, H. G.},
  month = jul,
  year = {1989},
  pages = {461}
}

@article{repetto_lensless_2004,
  title = {Lensless digital holographic microscope with light-emitting diode illumination},
  volume = {29},
  timestamp = {2012-10-08T18:40:28Z},
  number = {10},
  journal = {Optics Letters},
  author = {Repetto, L. and Piano, E. and Pontiggia, C.},
  year = {2004},
  keywords = {holo,holography,led},
  pages = {1132--1134},
  file = {repetto2004led_holo.pdf:/home/tdimiduk/documents/holography/repetto2004led_holo.pdf:application/pdf}
}

@article{zijlstra_rotational_2012,
  title = {Rotational diffusion and alignment of short gold nanorods in an external electric field},
  volume = {14},
  issn = {1463-9084},
  doi = {10.1039/C2CP24092K},
  abstract = {We present measurements of the polarized extinction of gold nanorod suspensions exposed to an external electric field. By employing an amplitude modulated field in combination with lock-in detection we resolve changes in the optical density as low as 10-6 in an integration time of 10 s. This sensitivity allo},
  language = {en},
  timestamp = {2016-08-06T11:28:59Z},
  number = {13},
  urldate = {2013-10-07},
  journal = {Phys. Chem. Chem. Phys.},
  author = {Zijlstra, Peter and {van Stee}, Marijn and Verhart, Nico and Gu, Ziyu and Orrit, Michel},
  month = mar,
  year = {2012},
  pages = {4584--4588}
}

@inproceedings{emery_dhm_2007,
  title = {{{DHM}} ({{Digital Holography Microscope}}) for imaging cells},
  volume = {61},
  timestamp = {2012-10-08T18:40:28Z},
  booktitle = {Journal of {{Physics}}: {{Conference Series}}},
  author = {Emery, Y. and Cuche, E. and Colomb, T. and Depeursinge, C. and Rappaz, B. and Marquet, P. and Magistretti, P.},
  year = {2007},
  keywords = {bio,holo,holography,lab_depeursinge,microscopy},
  pages = {1317--1321},
  file = {emery2007dhm_imaging_cells.pdf:/home/tdimiduk/documents/holography/emery2007dhm_imaging_cells.pdf:application/pdf}
}

@article{rivenson_recovery_2012,
  title = {Recovery of partially occluded objects by applying compressive {{Fresnel}} holography},
  volume = {37},
  doi = {10.1364/OL.37.001757},
  abstract = {A compressive Fresnel holography approach is suggested for the recovery of partially occluded objects. Reconstruction guarantees are analyzed and the effectiveness of the method is demonstrated using simulations and an experimental result showing the reconstruction of a partially occluded resolution chart.},
  timestamp = {2013-08-07T14:56:55Z},
  number = {10},
  urldate = {2013-08-07},
  journal = {Optics Letters},
  author = {Rivenson, Yair and Rot, Alon and Balber, Sergey and Stern, Adrian and Rosen, Joseph},
  month = may,
  year = {2012},
  keywords = {Computational imaging,Digital holography,Fourier optics and signal processing,Inverse problems},
  pages = {1757--1759},
  file = {Rivenson et al_2012_Recovery of partially occluded objects by applying compressive Fresnel.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/9DKRPZPC/Rivenson et al_2012_Recovery of partially occluded objects by applying compressive Fresnel.pdf:application/pdf;Opt. Lett. Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/RDXKBD3C/abstract.html:text/html}
}

@misc{_canon_????,
  title = {Canon {{Digital Rebel 300D IR Filter Removal Modification}} and {{Peltier Cooling Plans}} -by {{Gary Honis}}},
  timestamp = {2009-08-28T18:23:30Z},
  urldate = {2009-08-28},
  howpublished = {\url{http://ghonis2.ho8.com/rebelmodnew.html}},
  file = {Canon Digital Rebel 300D IR Filter Removal Modification and Peltier Cooling Plans -by Gary Honis:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/2JBE8SUM/rebelmodnew.html:text/html}
}

@article{seifi_three-dimensional_2012,
  title = {Three-dimensional reconstruction of particle holograms: a fast and accurate multiscale approach},
  volume = {29},
  shorttitle = {Three-dimensional reconstruction of particle holograms},
  doi = {10.1364/JOSAA.29.001808},
  abstract = {In-line digital holography is an imaging technique that is being increasingly used for studying three-dimensional flows. It has been previously shown that very accurate reconstructions of objects could be achieved with the use of an inverse problem framework. Such approaches, however, suffer from higher computational times compared to less accurate conventional reconstructions based on hologram backpropagation. To overcome this computational issue, we propose a coarse-to-fine multiscale approach to strongly reduce the algorithm complexity. We illustrate that an accuracy comparable to that of state-of-the-art methods can be reached while accelerating parameter-space scanning.},
  timestamp = {2016-08-06T11:19:33Z},
  number = {9},
  urldate = {2012-10-08},
  journal = {Journal of the Optical Society of America A},
  author = {Seifi, Mozhdeh and Fournier, Corinne and Denis, Loic and Chareyron, Delphine and Mari{\'e}, Jean-Louis},
  month = sep,
  year = {2012},
  keywords = {*update,algorithm,colloid,digital,fitting,holo,holography,inverse problem,Light scattering,microscopy,reconstruction,sampling},
  pages = {1808--1817},
  file = {Seifi et al_2012_Three-dimensional reconstruction of particle holograms.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/B2ETDTBQ/Seifi et al_2012_Three-dimensional reconstruction of particle holograms.pdf:application/pdf;J. Opt. Soc. Am. A Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/5N8QD6GX/abstract.html:text/html}
}

@article{morgan_dielectrophoretic_2001,
  title = {The dielectrophoretic and travelling wave forces generated by interdigitated electrode arrays: analytical solution using {{Fourier}} series},
  volume = {34},
  issn = {0022-3727},
  shorttitle = {The dielectrophoretic and travelling wave forces generated by interdigitated electrode arrays},
  timestamp = {2016-08-06T11:31:03Z},
  number = {10},
  journal = {J. Phys. D: Appl. Phys.},
  author = {Morgan, Hywel and Izquierdo, Alberto Garc{\'\i}a and Bakewell, David and Green, Nicolas G and Ramos, Antonio},
  month = may,
  year = {2001},
  pages = {1553--1561}
}

@article{ortega-arroyo_interferometric_2012,
  title = {Interferometric scattering microscopy ({{iSCAT}}): new frontiers in ultrafast and ultrasensitive optical microscopy},
  volume = {14},
  shorttitle = {Interferometric scattering microscopy ({{iSCAT}})},
  timestamp = {2016-08-11T00:02:03Z},
  number = {45},
  urldate = {2013-04-16},
  journal = {Physical Chemistry Chemical Physics},
  author = {Ortega-Arroyo, Jaime and Kukura, Philipp},
  year = {2012},
  pages = {15625--15636},
  file = {Ortega-Arroyo_Kukura_2012_Interferometric scattering microscopy (iSCAT).pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/CSTVE463/Ortega-Arroyo_Kukura_2012_Interferometric scattering microscopy (iSCAT).pdf:application/pdf;Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/P6B7KS87/c2cp41013c.html:text/html;Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/RVSJVCKA/c2cp41013c.html:text/html}
}

@article{dagostino_enhanced_2009,
  title = {Enhanced fluorescence by metal nanospheres on metal substrates},
  volume = {34},
  doi = {10.1364/OL.34.002381},
  abstract = {We investigate the metal enhanced fluorescence by silver nanospheres on a thin silver substrate. Experimental measurements for core/shell colloidal nanocrystals embedded in a polymer matrix show a fluorescence enhancement factor of about 9. We apply the discrete dipole approximation method to describe the local-field enhancement factor (LFEF). We find that the observed fluorescence enhancement is related to the broad LFEF profile induced by the substrate.},
  timestamp = {2016-08-06T11:32:33Z},
  number = {15},
  urldate = {2013-10-07},
  journal = {Opt. Lett.},
  author = {D'Agostino, Stefania and Pompa, Pier Paolo and Chiuri, Rocco and Phaneuf, Raymond J. and Britti, Dominic G. and Rinaldi, Rosaria and Cingolani, Roberto and {Della Sala}, Fabio},
  month = aug,
  year = {2009},
  keywords = {Computational electromagnetic methods,Fluorescence,Surface plasmons},
  pages = {2381--2383},
  file = {D'Agostino et al_2009_Enhanced fluorescence by metal nanospheres on metal substrates.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/BP8VBTW9/D'Agostino et al_2009_Enhanced fluorescence by metal nanospheres on metal substrates.pdf:application/pdf;Opt. Lett. Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/UCR437U2/abstract.html:text/html}
}

@article{herzig_bicontinuous_2007,
  title = {Bicontinuous emulsions stabilized solely by colloidal particles},
  volume = {6},
  issn = {1476-1122},
  timestamp = {2016-08-06T11:31:57Z},
  number = {12},
  journal = {Nat. Mater.},
  author = {Herzig, E. M. and White, K. A. and Schofield, A. B. and Poon, W. C. K. and Clegg, P. S.},
  month = dec,
  year = {2007},
  pages = {966--971}
}

@article{huang_introducing_1997,
  title = {Introducing dielectrophoresis as a new force field for field-flow fractionation},
  volume = {73},
  issn = {0006-3495},
  abstract = {We present the principle of cell characterization and separation by dielectrophoretic field-flow fractionation and show preliminary experimental results. The operational device takes the form of a thin chamber in which the bottom wall supports an array of microelectrodes. By applying appropriate AC voltage signals to these electrodes, dielectrophoretic forces are generated to levitate cells suspended in the chamber and to affect their equilibrium heights. A laminar flow profile is established in the chamber so that fluid flows faster with increasing distance from the chamber walls. A cell carried in the flow stream will attain an equilibrium height, and a corresponding velocity, based on the balance of dielectrophoretic, gravitational, and hydrodynamic lift forces it experiences. We describe a theoretical model for this system and show that the cell velocity is a function of the mean fluid velocity, the voltage and frequency of the signals applied to the electrodes, and, most significantly, the cell dielectric properties. The validity of the model is demonstrated with human leukemia (HL-60) cells subjected to a parallel electrode array, and application of the device to separating HL-60 cells from peripheral blood mononuclear cells is shown.},
  timestamp = {2016-08-06T11:31:51Z},
  number = {2},
  journal = {Biophys. J.},
  author = {Huang, Y. and Wang, X.B. and Becker, F.F. and Gascoyne, P.R.},
  month = aug,
  year = {1997},
  pages = {1118--1129}
}

@book{pawley_handbook_2006,
  address = {New York},
  edition = {3rd},
  title = {Handbook of {{Biological Confocal Microscopy}}},
  isbn = {0-387-25921-X 978-0-387-25921-5},
  timestamp = {2009-08-20T14:35:58Z},
  publisher = {{Springer}},
  author = {Pawley, James B.},
  year = {2006},
  keywords = {confocal}
}

@article{lim_sampling_2011,
  title = {Sampling and processing for compressive holography [{{Invited}}]},
  volume = {50},
  doi = {10.1364/AO.50.000H75},
  abstract = {Compressive holography applies sparsity priors to data acquired by digital
                holography to infer a small number of object features or basis vectors from a
                slightly larger number of discrete measurements. Compressive holography may be
                applied to reconstruct three-dimensional (3D) images from two-dimensional (2D)
                measurements or to reconstruct 2D images from sparse apertures. This paper is a
                tutorial covering practical compressive holography procedures, including field
                propagation, reference filtering, and inverse problems in compressive holography. We
                present as examples 3D tomography from a 2D hologram, 2D image reconstruction from a
                sparse aperture, and diffuse object estimation from diverse speckle
                realizations.},
  timestamp = {2013-08-07T13:41:03Z},
  number = {34},
  urldate = {2013-08-07},
  journal = {Applied Optics},
  author = {Lim, Sehoon and Marks, Daniel L. and Brady, David J.},
  month = dec,
  year = {2011},
  keywords = {compressed sensing,Computational imaging,Digital holography,holo,Speckle imaging,Tomographic image processing},
  pages = {H75--H86},
  file = {Lim et al_2011_Sampling and processing for compressive holography [Invited].pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/TT7JZ7BK/Lim et al_2011_Sampling and processing for compressive holography [Invited].pdf:application/pdf;Appl. Opt. Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/6J3UQXQK/abstract.html:text/html}
}

@book{mendenhall_statistics_1991,
  address = {San Francisco},
  edition = {3rd},
  title = {Statistics for engineering and the sciences},
  timestamp = {2016-08-06T11:31:26Z},
  publisher = {{Dellen Pub. Co.}},
  author = {Mendenhall, W. and Sincich, T.},
  year = {1991}
}

@article{ortega_hydrodynamic_2003,
  title = {Hydrodynamic properties of rodlike and disklike particles in dilute solution},
  volume = {119},
  issn = {00219606},
  doi = {doi:10.1063/1.1615967},
  abstract = {The hydrodynamic properties of cylindrical (rodlike and discoidal) particles in dilute solution have been computed using the bead-shell model treatment. Previous results [Tirado and Garc{\'\i}a de la Torre, J. Chem. Phys. 71, 2581 (1979); 73, 1993 (1980)] for rods with length-to-diameter ratio p\ensuremath{\backslash}textgreater2 are now extended to short cylinders and disks down to p = 0.1. The intrinsic viscosity is obtained for rods and disks, and results are presented for the three rotational relaxation times of a cylindrical particle. The hydrodynamic properties are expressed in forms that have a weak variation with p, and are therefore useful for the analysis of experimental values. We present examples of the determination of the length and diameter of the cylindrical particles, for DNA oligonucleotides and tobacco mosaic virus. \ensuremath{\backslash}copyright 2003 American Institute of Physics.},
  timestamp = {2016-08-06T11:30:28Z},
  number = {18},
  urldate = {2013-10-07},
  author = {Ortega, A. and {Garc{\'\i}a de la Torre}, J.},
  month = nov,
  year = {2003},
  pages = {9914},
  file = {Ortega_García de la Torre_2003_Hydrodynamic properties of rodlike and disklike particles in dilute solution.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/5Z3NQSPZ/Ortega_García de la Torre_2003_Hydrodynamic properties of rodlike and disklike particles in dilute solution.pdf:application/pdf;AIP Journal Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/S96CMZNT/p9914_s1.html:text/html}
}

@article{xu_tracking_2003,
  title = {Tracking particles in four dimensions with in-line holographic microscopy},
  volume = {28},
  doi = {10.1364/OL.28.000164},
  abstract = {We describe a simple holographic method that has enabled us to capture as a single data set the trajectories of micrometer-sized objects suspended in water. By subtracting consecutive holograms of a particle suspension and then adding these difference holograms, we constructed a final data set that contains the time evolution of the particle trajectories free from spurious background interference effects. The method is illustrated by a recording of the motion of 5\textendash{}10-\ensuremath{\mu}m diameter algae in water.},
  timestamp = {2012-10-08T18:40:28Z},
  number = {3},
  urldate = {2011-01-19},
  journal = {Optics Letters},
  author = {Xu, W. and Jericho, M. H. and Kreuzer, H. J. and Meinertzhagen, I. A.},
  month = feb,
  year = {2003},
  keywords = {holo,holography,lab_jericho,lab_kreuzer,tracking},
  pages = {164--166},
  file = {Opt. Lett. Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/XUFBS4ZG/abstract.html:text/html}
}

@article{tirado_comparison_1984-1,
  title = {Comparison of theories for the translational and rotational diffusion coefficients of rod-like macromolecules. {{Application}} to short {{DNA}} fragments},
  volume = {81},
  issn = {00219606},
  doi = {doi:10.1063/1.447827},
  abstract = {Two theories relating the translational and rotational diffusion coefficients Dt and Dr of a rod-like macromolecule to its length and diameter, proposed by Broersma [J. Chem. Phys. 74, 6989 (1981)], and Tirado and Garc{\'\i}a de la Torre [J. Chem. Phys. 71, 2581 (1979); 73, 1986 (1980)] are shown to predict different values of the coefficients for a particle of given dimensions. Next, we use the two theories to analyze existing experimental data of sedimentation coefficients s and translational and rotational diffusion coefficients of short DNA fragments, and obtain values of the hydrated diameter of DNA d which is treated as an adjustable parameter. The results are compared with the expected value, d\ensuremath{\ElsevierGlyph{2242}}26\AA{}. This comparison favors clearly the Tirado\textendash{}Garcia de la Torre theory in the case of Dt and s. For Dr, and using a rise per base pair r=3.4 \AA{}, this theory gives best agreement for all the data examined, while when r=3.3 \AA{}, the agreement depends on the source of data.},
  timestamp = {2016-08-06T11:27:19Z},
  number = {4},
  urldate = {2013-10-04},
  journal = {The Journal of Chemical Physics},
  author = {Tirado, M. Mercedes and Mart{\'\i}nez, Carmen L{\'o}pez and {de la Torre}, Jos{\'e} Garc{\'\i}a},
  month = aug,
  year = {1984},
  pages = {2047},
  file = {Tirado et al_1984_Comparison of theories for the translational and rotational diffusion.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/IEHE2AR9/Tirado et al_1984_Comparison of theories for the translational and rotational diffusion.pdf:application/pdf;Tirado et al_1984_Comparison of theories for the translational and rotational diffusion.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/WC7J5D5N/Tirado et al_1984_Comparison of theories for the translational and rotational diffusion.pdf:application/pdf;AIP Journal Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/8JFBWFJM/p2047_s1.html:text/html;AIP Journal Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/XP5MBABJ/p2047_s1.html:text/html}
}

@book{morse_methods_1953,
  address = {New York},
  title = {Methods of theoretical physics},
  timestamp = {2016-08-06T11:30:59Z},
  urldate = {2013-10-09},
  publisher = {{McGraw-Hill}},
  author = {Morse, Philip M. and Feshbach, Herman},
  year = {1953}
}

@article{lee_holographic_2007,
  title = {Holographic microscopy of holographically trapped three-dimensional structures},
  volume = {15},
  doi = {10.1364/OE.15.001505},
  abstract = {Holographic optical trapping uses forces exerted by computer-generated holograms to organize microscopic materials into three-dimensional structures. In a complementary manner, holographic video microscopy uses real-time recordings of in-line holograms to create time-resolved volumetric images of three-dimensional microstructures. The combination is exceptionally effective for organizing, inspecting and analyzing soft-matter systems.},
  timestamp = {2012-10-08T18:40:28Z},
  number = {4},
  urldate = {2011-01-17},
  journal = {Optics Express},
  author = {Lee, Sang-Hyuk and Grier, David G.},
  month = feb,
  year = {2007},
  keywords = {holo,holography,lab_grier,tweezers_holographic},
  pages = {1505--1512},
  file = {OSA Journals PDF:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/9KVCI933/view_article.html:text/html;Opt. Express Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/PTHRPS3Z/abstract.html:text/html}
}

@misc{_mayavi_????,
  title = {Mayavi - {{3D}} scientific data visualization and plotting:: {{Enthought}}, {{Inc}}.},
  timestamp = {2009-08-20T14:42:50Z},
  urldate = {2009-08-20},
  howpublished = {\url{http://code.enthought.com/projects/mayavi/}},
  file = {Mayavi - 3D scientific data visualization and plotting\:\: Enthought, Inc.:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/SG5N8TJ3/mayavi.html:text/html}
}

@article{liu_all--one_2008,
  title = {All-in-one multifunctional optical microscope with a single holographic measurement},
  volume = {47},
  timestamp = {2012-10-08T18:40:28Z},
  journal = {Optical Engineering},
  author = {Liu, C. and Bae, Y. S and Yang, W. and Kim, D. Y and others},
  year = {2008},
  keywords = {bio,holo,holography,lab_kim,off_axis},
  pages = {087001},
  file = {All-in-one multifunctional optical microscope with a single holographic measurement | Browse - Optical Engineering:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/V9QTBUGX/p087001_s1.html:text/html}
}

@article{kreuzer_digital_2001,
  title = {Digital in-line holography with photons and electrons},
  volume = {13},
  timestamp = {2016-08-11T01:59:15Z},
  number = {47},
  journal = {Journal of Physics: Condensed Matter},
  author = {Kreuzer, H. J. and Jericho, M. J. and Meinertzhagen, I. A. and Xu, W.},
  year = {2001},
  keywords = {holo,holography,lab_jericho,lab_kreuzer},
  pages = {10729--10741},
  file = {Kreuzer et al_2001_Digital in-line holography with photons and electrons.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/MHM3AF8B/Kreuzer et al_2001_Digital in-line holography with photons and electrons.pdf:application/pdf}
}

@article{biancaniello_line_2006,
  title = {Line optical tweezers instrument for measuring nanoscale interactions and kinetics},
  volume = {77},
  timestamp = {2016-08-06T11:33:17Z},
  journal = {Rev. Sci. Inst.},
  author = {Biancaniello, P. L and Crocker, J. C},
  year = {2006},
  pages = {113702}
}

@article{beard_unbiased_2003,
  title = {Unbiased {{Rotational Moves}} for {{Rigid-Body Dynamics}}},
  volume = {85},
  issn = {0006-3495},
  abstract = {We introduce an unbiased protocol for performing rotational moves in rigid-body dynamics simulations. This approach\textendash{}based on the analytic solution for the rotational equations of motion for an orthogonal coordinate system at constant angular velocity\textendash{}removes deficiencies that have been largely ignored in Brownian dynamics simulations, namely errors for finite rotations that result from applying the noncommuting rotational matrices in an arbitrary order. Our algorithm should thus replace standard approaches to rotate local coordinate frames in Langevin and Brownian dynamics simulations.},
  timestamp = {2016-08-06T11:33:22Z},
  number = {5},
  urldate = {2011-03-11},
  journal = {Biophysical Journal},
  author = {Beard, Daniel A. and Schlick, Tamar},
  month = nov,
  year = {2003},
  pages = {2973--2976}
}

@article{dubois_improved_1999,
  title = {Improved three-dimensional imaging with a digital holography microscope with a source of partial spatial coherence},
  volume = {38},
  timestamp = {2016-08-11T02:04:42Z},
  journal = {Applied Optics},
  author = {Dubois, F. and Joannes, L. and Legros, J. C},
  year = {1999},
  keywords = {partial},
  pages = {34},
  file = {dubois1999partial_coherence.pdf:/home/tdimiduk/documents/holography/dubois1999partial_coherence.pdf:application/pdf}
}

@article{dubois_digital_2006-1,
  title = {Digital holographic microscopy with reduced spatial coherence for three-dimensional particle flow analysis},
  volume = {45},
  doi = {10.1364/AO.45.000864},
  abstract = {We investigate the use of a digital holographic microscope working in partially coherent illumination to study in three dimensions a micrometer-size particle flow. The phenomenon under investigation rapidly varies in such a way that it is necessary to record, for every camera frame, the complete holographic information for further processing. For this purpose, we implement the Fourier-transform method for optical amplitude extraction. The suspension of particles is flowing in a split-flow lateral-transport thin separation cell that is usually used to separate the species by their sizes. Details of the optical implementation are provided. Examples of reconstructed images of different particle sizes are shown, and a particle-velocity measurement technique that is based on the blurred holographic image is exploited.},
  timestamp = {2012-10-08T18:40:28Z},
  number = {5},
  urldate = {2009-09-23},
  journal = {Applied Optics},
  author = {Dubois, Frank and Callens, Natacha and Yourassowsky, Catherine and Hoyos, Mauricio and Kurowski, Pascal and Monnom, Olivier},
  month = feb,
  year = {2006},
  keywords = {holo,holography,image_processing,reduced_coherence},
  pages = {864--871},
  file = {Dubois et al_2006_Digital holographic microscopy with reduced spatial coherence for.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/4JEQ3GH9/Dubois et al_2006_Digital holographic microscopy with reduced spatial coherence for.pdf:application/pdf;Appl. Opt. Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/SPPJK7CU/abstract.html:text/html}
}

@article{asakura_interaction_1958,
  title = {Interaction between particles suspended in solutions of macromolecules},
  volume = {33},
  abstract = {An attractive force appears between particles suspended in solutions of macromolecules when there is neither direct interaction between two particles nor energetic interaction between particles and solute macromolecules. The magnitude of this force is of the order of the osmotic pressure of the solution of macromolecules and the range is of the order of the diameter of macromolecules. This force is calculated as a function of concentration, shape, and charge of macromolecules, and it is shown that it becomes stronger in solutions of chain macromolecules or of macromolecules of dissymmetrical shape than in solutions of rigid spherical macromolecules at the same net concentration. If macromolecules have charge, the force can be greatly intensified. In every case numerical estimation is made, and it is found that actually this kind of force can have a remarkable influence on the state of suspended particles. Numerical examples of the critical concentration of particles at their macroscopic aggregation are given. Finally a short description is added on the effect of energetic interaction between particles and macromolecules.},
  timestamp = {2016-08-06T11:33:27Z},
  number = {126},
  journal = {J. Polymer Sci.},
  author = {Asakura, Sho and Oosawa, Fumio},
  year = {1958},
  pages = {183--192}
}

@article{fugal_practical_2009,
  title = {Practical methods for automated reconstruction and characterization of particles in digital in-line holograms},
  volume = {20},
  timestamp = {2016-08-25T19:51:58Z},
  number = {075501},
  journal = {Meas. Sci. Technol.},
  author = {Fugal, J. P and Schulz, T. J and Shaw, R. A},
  year = {2009},
  keywords = {holo,holography,sampling,todo},
  pages = {075501},
  file = {Fugal et al_2009_Practical methods for automated reconstruction and characterization of.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/WPX2T4A3/Fugal et al_2009_Practical methods for automated reconstruction and characterization of.pdf:application/pdf}
}

@article{koenig_brownian_1975,
  title = {Brownian motion of an ellipsoid. {{A}} correction to {{Perrin}}'s results},
  volume = {14},
  copyright = {Copyright \ensuremath{\backslash}copyright 1975 John Wiley \& Sons, Inc.},
  issn = {1097-0282},
  doi = {10.1002/bip.1975.360141115},
  language = {en},
  timestamp = {2016-08-06T11:31:43Z},
  number = {11},
  urldate = {2013-10-10},
  author = {Koenig, Seymour H.},
  year = {1975},
  pages = {2421--2423}
}

@article{vrij_polymers_1976,
  title = {Polymers at interfaces and the interactions in colloidal dispersions},
  volume = {48},
  timestamp = {2016-08-06T11:30:02Z},
  number = {4},
  journal = {Pure Appl. Chem.},
  author = {Vrij, A.},
  year = {1976},
  pages = {471}
}

@article{markx_dielectrophoretic_1997,
  title = {The dielectrophoretic levitation of latex beads, with reference to field-flow fractionation},
  volume = {30},
  issn = {0022-3727, 1361-6463},
  timestamp = {2016-08-06T11:31:32Z},
  number = {17},
  journal = {J. Phys D: Appl. Phys.},
  author = {Markx, Gerard H and Pethig, Ronald and Rousselet, Juliette},
  month = sep,
  year = {1997},
  pages = {2470--2477}
}

@article{donoho_compressed_2006,
  title = {Compressed sensing},
  volume = {52},
  issn = {0018-9448},
  doi = {10.1109/TIT.2006.871582},
  abstract = {Suppose x is an unknown vector in Ropfm (a digital image or signal); we plan to measure n general linear functionals of x and then reconstruct. If x is known to be compressible by transform coding with a known transform, and we reconstruct via the nonlinear procedure defined here, the number of measurements n can be dramatically smaller than the size m. Thus, certain natural classes of images with m pixels need only n=O(m1/4log5/2(m)) nonadaptive nonpixel samples for faithful recovery, as opposed to the usual m pixel samples. More specifically, suppose x has a sparse representation in some orthonormal basis (e.g., wavelet, Fourier) or tight frame (e.g., curvelet, Gabor)-so the coefficients belong to an lscrp ball for 0\ensuremath{<}ples1. The N most important coefficients in that expansion allow reconstruction with lscr2 error O(N1/2-1p/). It is possible to design n=O(Nlog(m)) nonadaptive measurements allowing reconstruction with accuracy comparable to that attainable with direct knowledge of the N most important coefficients. Moreover, a good approximation to those N important coefficients is extracted from the n measurements by solving a linear program-Basis Pursuit in signal processing. The nonadaptive measurements have the character of "random" linear combinations of basis/frame elements. Our results use the notions of optimal recovery, of n-widths, and information-based complexity. We estimate the Gel'fand n-widths of lscrp balls in high-dimensional Euclidean space in the case 0\ensuremath{<}ples1, and give a criterion identifying near- optimal subspaces for Gel'fand n-widths. We show that "most" subspaces are near-optimal, and show that convex optimization (Basis Pursuit) is a near-optimal way to extract information derived from these near-optimal subspaces},
  timestamp = {2013-07-24T15:40:39Z},
  number = {4},
  journal = {IEEE Transactions on Information Theory},
  author = {Donoho, D.L.},
  year = {2006},
  keywords = {Adaptive sampling,Basis Pursuit,Compressed sensing,compressed sensing,convex optimization,convex programming,data compression,Data mining,Digital images,eigenvalues of random matrices,Euclidean space,Gel'fand,general linear functional measurement,image coding,image reconstruction,image sampling,image sensors,information-based complexity,integrated sensing and processing,minimum,nonadaptive nonpixel sampling,optimal recovery,Pixel,Quotient-of-a-Subspace theorem,sensing compression,signal processing,Size measurement,sparse matrices,sparse representation,sparse solution of linear equations,transform coding,Vectors},
  pages = {1289--1306},
  file = {Donoho_2006_Compressed sensing.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/4AN3I52A/Donoho_2006_Compressed sensing.pdf:application/pdf;IEEE Xplore Abstract Record:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/S44MZAG2/articleDetails.html:text/html}
}

@article{song_assembled_2009,
  title = {Assembled {{Surface-Anisotropic Colloids}} as a {{Template}} for a {{Multistage Catalytic Membrane Reactor}}},
  volume = {1},
  issn = {1944-8244},
  doi = {10.1021/am900286k},
  abstract = {A polymeric catalytic membrane reactor (CMR) is fabricated using alternating assemblies of surface-anisotropic (sa-) and plain (p-) polystyrene (PS) colloids as a template. We report the preparation of TiO2 sa-PS colloids by physical vapor deposition of titanium onto a colloidal monolayer in an oxygen-rich environment and employ the modified colloids as a means to deliver the TiO2 catalyst to the CMR pores. sa-PS and p-PS colloids are assembled into alternating cylindrical sections inside a microcapillary followed by infiltration and curing of a liquid polymer precursor in the interstitial space of the assembly. Subsequent organic solvent treatment results in a cylindrical porous CMR with embedded TiO2 caps. TiO2 cap embedment, composition and surface morphology, surface pore structure, and cross-sectional integrity are analyzed using variable-pressure scanning electron microscopy, transmission electron microscopy, and X-ray photoelectron spectroscopy.},
  timestamp = {2016-08-06T11:30:12Z},
  number = {8},
  urldate = {2013-10-07},
  journal = {ACS Appl. Mater. Interfaces},
  author = {Song, Jung Hun (Kevin) and Kretzschmar, Ilona},
  month = aug,
  year = {2009},
  pages = {1747--1754},
  file = {Song_Kretzschmar_2009_Assembled Surface-Anisotropic Colloids as a Template for a Multistage Catalytic.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/H7J2KSE4/Song_Kretzschmar_2009_Assembled Surface-Anisotropic Colloids as a Template for a Multistage Catalytic.pdf:application/pdf;ACS Full Text Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/NTEHMMV8/am900286k.html:text/html}
}

@article{lewis_swimming_2006,
  title = {Swimming speed of three species of {{Alexandrium}} ({{Dinophyceae}}) as determined by digital in-line holography},
  volume = {45},
  issn = {0031-8884},
  doi = {10.2216/04-59.1},
  abstract = {Digital in-line holographic (DIH) microscopy Was Used to track motility in several related species of the marine dinoflagellate Alexandrium in response to temperature after acclimation at selected temperatures. Numerical reconstruction of DIH holograms yielded high-contrast three-dimensional images of the trajectories Of many Motile Cells swimming simultaneously throughtout the sample volume. Swimming speed and trajectory were determined for clonal isolates of A. ostenfeldii, A. minutum and A. tamarense within the temperature range front 8 to 24 degrees C. The strains of these species revealed difference in temperature optima for growth and tolerance that were a function of both acclimation responses and genetic factors reflecting the origin of the isolates. The fastest swimming, speeds were recorded at 24 degrees C for cells of A. minutum. Acclimated strains of all three species swam significantly slower at lower temperatures, although fastest swimming speeds did not always occur at temperature optima for growth. Aged cells from stationary phase cultures swain more slowly than cells in exponential growth phase. Doublets from a rapidly dividing culture swam faster than singlets from the same culture, confirming the propulsive advantage of paired cells. Holographic microscopy is a powerful tool for the acquisition of detailed observations of swimming behaviour of microalgal cells in the form of three-dimensional trajectories over the appropriate temporal (sub-second) and spatial (micrometer) scales.},
  timestamp = {2013-08-28T14:20:06Z},
  number = {1},
  urldate = {2009-09-23},
  journal = {Phycologia},
  author = {Lewis, NI and Xu, WB and Jericho, SK and Kreuzer, HJ and Jericho, MH and Cembella, AD},
  month = jan,
  year = {2006},
  keywords = {holo,holography,inline,lab_jericho,lab_kreuzer,lensless,microorganisms,tracking},
  pages = {61--70},
  file = {lewis_cembella2006swimming_speed.pdf:/home/tdimiduk/documents/holography/lewis_cembella2006swimming_speed.pdf:application/pdf;ISI Web of Knowledge Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/TKCSWNNP/full_record.html:text/html}
}

@misc{coffin_decoding_2010,
  title = {Decoding raw digital photos in {{Linux}}},
  timestamp = {2016-08-06T14:34:39Z},
  urldate = {2009-08-20},
  howpublished = {\url{http://www.cybercom.net/~dcoffin/dcraw/}},
  author = {Coffin, Dave},
  year = {2010},
  file = {Decoding raw digital photos in Linux:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/KE259TRQ/dcraw.html:text/html}
}

@article{meng_holographic_2004,
  title = {Holographic particle image velocimetry: from film to digital recording},
  volume = {15},
  issn = {0957-0233},
  shorttitle = {Holographic particle image velocimetry},
  doi = {10.1088/0957-0233/15/4/009},
  timestamp = {2016-08-06T11:33:48Z},
  number = {4},
  urldate = {2011-01-19},
  journal = {Measurement Science and Technology},
  author = {Meng, Hui and Pan, Gang and Pu, Ye and Woodward, Scott H},
  month = apr,
  year = {2004},
  keywords = {holo,holography,piv},
  pages = {673--685},
  file = {Holographic particle image velocimetry\: from film to digital recording:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/ME938U52/009.html:text/html}
}

@article{baraniuk_random_2009,
  title = {Random {{Projections}} of {{Smooth Manifolds}}},
  volume = {9},
  issn = {1615-3375, 1615-3383},
  doi = {10.1007/s10208-007-9011-z},
  abstract = {We propose a new approach for nonadaptive dimensionality reduction of manifold-modeled data, demonstrating that a small number of random linear projections can preserve key information about a manifold-modeled signal. We center our analysis on the effect of a random linear projection operator \ensuremath{\Phi}:\ensuremath{\mathbb{R}} N \ensuremath{\rightarrow{}\mathbb{R}} M , M\ensuremath{<}N, on a smooth well-conditioned K-dimensional submanifold \ensuremath{\mathscr{M}\subset{}\mathbb{R}} N . As our main theoretical contribution, we establish a sufficient number M of random projections to guarantee that, with high probability, all pairwise Euclidean and geodesic distances between points on \ensuremath{\mathscr{M}} are well preserved under the mapping \ensuremath{\Phi}. Our results bear strong resemblance to the emerging theory of Compressed Sensing (CS), in which sparse signals can be recovered from small numbers of random linear measurements. As in CS, the random measurements we propose can be used to recover the original data in \ensuremath{\mathbb{R}} N . Moreover, like the fundamental bound in CS, our requisite M is linear in the ``information level'' K and logarithmic in the ambient dimension N; we also identify a logarithmic dependence on the volume and conditioning of the manifold. In addition to recovering faithful approximations to manifold-modeled signals, however, the random projections we propose can also be used to discern key properties about the manifold. We discuss connections and contrasts with existing techniques in manifold learning, a setting where dimensionality reducing mappings are typically nonlinear and constructed adaptively from a set of sampled training data.},
  language = {en},
  timestamp = {2013-09-06T15:36:21Z},
  number = {1},
  urldate = {2013-09-06},
  journal = {Foundations of Computational Mathematics},
  author = {Baraniuk, Richard G. and Wakin, Michael B.},
  month = feb,
  year = {2009},
  keywords = {Applications of Mathematics,Compressed sensing,Computer Science; general,Dimensionality reduction,Johnson–Lindenstrauss lemma,Linear and Multilinear Algebras; Matrix Theory,Manifold learning,Manifolds,Math Applications in Computer Science,Numerical Analysis,Random projections,Sparsity},
  pages = {51--77},
  file = {Baraniuk_Wakin_2009_Random Projections of Smooth Manifolds.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/7QAUI7DK/Baraniuk_Wakin_2009_Random Projections of Smooth Manifolds.pdf:application/pdf;Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/S52NZ6UH/s10208-007-9011-z.html:text/html}
}

@article{mishchenko_t-matrix_1996,
  title = {T-matrix computations of light scattering by non-spherical particles: a review},
  volume = {55},
  shorttitle = {T-matrix computations of light scattering by non-spherical particles},
  timestamp = {2016-08-06T11:31:15Z},
  number = {5},
  journal = {J. Quant. Spectrosc. Radiat. Transfer},
  author = {Mishchenko, M. I and Travis, L. D and Mackowski, D. W},
  year = {1996},
  pages = {535--576}
}

@article{schnars_digital_2002,
  title = {Digital recording and numerical reconstruction of holograms},
  volume = {13},
  timestamp = {2012-10-08T18:40:28Z},
  number = {9},
  journal = {Measurement Science and Technology},
  author = {Schnars, U. and Juptner, W. P.O},
  year = {2002},
  keywords = {holo,holography,lab_juptner,lab_schnars,off_axis},
  pages = {85--101},
  file = {Schnars_Juptner_2002_Digital recording and numerical reconstruction of holograms.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/UZCAI4RP/Schnars_Juptner_2002_Digital recording and numerical reconstruction of holograms.pdf:application/pdf}
}

@book{bohren_absorption_1998,
  title = {Absorption and scattering of light by small particles},
  isbn = {0-471-29340-7},
  timestamp = {2016-08-06T11:33:09Z},
  publisher = {{Wiley-Interscience}},
  author = {Bohren, Craig F. and Huffman, Donald R},
  year = {1998}
}

@book{goodman_introduction_2005,
  address = {Englewood  Colo.},
  edition = {3rd ed.},
  title = {Introduction to {{Fourier}} optics},
  isbn = {978-0-9747077-2-3},
  timestamp = {2009-09-02T18:21:13Z},
  publisher = {{Roberts \& Co.}},
  author = {Goodman, Joseph},
  year = {2005}
}

@article{didonato_recurrence_1982,
  title = {Recurrence {{Relations}} for the {{Indefinite Integrals}} of the {{Associated Legendre Functions}}},
  volume = {38},
  issn = {00255718},
  timestamp = {2016-08-06T11:32:28Z},
  number = {158},
  urldate = {2013-10-09},
  journal = {Mathematics of Computation},
  author = {DiDonato, A. R.},
  month = apr,
  year = {1982},
  pages = {547}
}

@article{antl_preparation_1986,
  title = {The preparation of poly(methyl methacrylate) latices in non-aqueous media},
  volume = {17},
  issn = {0166-6622},
  abstract = {A single-stage method is described for preparing monodisperse poly(methyl methacrylate) latices stabilised by poly(12-hydroxy-stearic acid) in hydrocarbon media. By variation of solvency conditions, it was possible to obtain a variation in particle size. At high monomer concentrations, a range of particle diameters between 178 nm and 2.6 \ensuremath{\mu}m was obtained with a small coefficient of variation on the number average size. At low monomer concentrations, stable latices were obtained with diameters of \ensuremath{\sim} 80 nm. Some suggestions are made for the mechanism of particle formation and growth in non-aqueous latices.},
  timestamp = {2016-08-06T11:33:30Z},
  number = {1},
  journal = {Colloids. Surf.},
  author = {Antl, L. and Goodwin, J.W. and Hill, R.D. and Ottewill, R.H. and Owens, S.M. and Papworth, S. and Waters, J.A.},
  month = jan,
  year = {1986},
  pages = {67--78}
}

@article{meng_free-energy_2010,
  title = {The {{Free-Energy Landscape}} of {{Clusters}} of {{Attractive Hard Spheres}}},
  volume = {327},
  abstract = {The study of clusters has provided a tangible link between local geometry and bulk condensed matter, but experiments have not yet systematically explored the thermodynamics of the smallest clusters. Here we present experimental measurements of the structures and free energies of colloidal clusters in which the particles act as hard spheres with short-range attractions. We found that highly symmetric clusters are strongly suppressed by rotational entropy, whereas the most stable clusters have anharmonic vibrational modes or extra bonds. Many of these clusters are subsets of close-packed lattices. As the number of particles increases from 6 to 10, we observe the emergence of a complex free-energy landscape with a small number of ground states and many local minima.},
  timestamp = {2016-08-06T11:31:23Z},
  number = {5965},
  journal = {Science},
  author = {Meng, Guangnan and Arkus, Natalie and Brenner, Michael P. and Manoharan, Vinothan N.},
  month = jan,
  year = {2010},
  pages = {560--563}
}

@article{norisuye_wormlike_1979,
  title = {Wormlike {{Chains Near}} the {{Rod Limit}}: {{Translational Friction Coefficient}}},
  volume = {12},
  issn = {0024-9297},
  shorttitle = {Wormlike {{Chains Near}} the {{Rod Limit}}},
  doi = {10.1021/ma60068a032},
  timestamp = {2016-08-06T11:30:30Z},
  number = {2},
  urldate = {2013-10-10},
  journal = {Macromolecules},
  author = {Norisuye, Takashi and Motowoka, Masanori and Fujita, Hiroshi},
  month = mar,
  year = {1979},
  pages = {320--323}
}

@article{choi_three-dimensional_2009,
  title = {Three-dimensional volumetric measurement of red blood cell motion using digital holographic microscopy},
  volume = {48},
  doi = {10.1364/AO.48.002983},
  abstract = {Measurement of blood flow with high spatial and temporal resolutions in a three-dimensional (3D) volume is a challenge in biomedical research fields. In this study, digital holographic microscopy is used to measure the 3D motion of human red blood cells (RBCs) in a microscale volume. The cinematographic holography technique, which uses a high-speed camera, enabled the continuous tracking of individual RBCs in a microtube flow. Several autofocus functions that quantify the sharpness of reconstructed RBC images are evaluated to locate the accurate depthwise position of RBCs. In this study, the squared Laplacian function yields the smallest depth of focus and locates the depthwise positions of RBCs with a root mean square error of 2.3 \ensuremath{\mu}m. By applying this method, we demonstrate the measurement of four-dimensional (space and time) trajectories as well as 3D velocity profiles of RBCs. The measurement uncertainties of the present method are also discussed.},
  timestamp = {2012-10-08T18:40:28Z},
  number = {16},
  urldate = {2009-09-23},
  journal = {Applied Optics},
  author = {Choi, Yong-Seok and Lee, Sang-Joon},
  month = jun,
  year = {2009},
  keywords = {3d,autofocus,bio,blood,holo,holography,lab_lee_sj,microscopy,todo,tracking},
  pages = {2983--2990},
  file = {Choi_Lee_2009_Three-dimensional volumetric measurement of red blood cell motion using digital.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/GGWA92CR/Choi_Lee_2009_Three-dimensional volumetric measurement of red blood cell motion using digital.pdf:application/pdf;Appl. Opt. Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/BR4DCRT3/abstract.html:text/html}
}

@article{glotzer_self-assembly_2004,
  title = {Self-assembly: {{From}} nanoscale to microscale colloids},
  volume = {50},
  issn = {1547-5905},
  shorttitle = {Self-assembly},
  language = {en},
  timestamp = {2016-08-09T18:54:48Z},
  number = {12},
  urldate = {2013-10-14},
  journal = {AIChE Journal},
  author = {Glotzer, S. C. and Solomon, M. J. and Kotov, N. A.},
  year = {2004},
  keywords = {Brownian motion,colloid,diffusion,perspective,review,self-assembly},
  pages = {2978--2985}
}

@article{jericho_submersible_2006,
  title = {Submersible digital in-line holographic microscope},
  volume = {77},
  doi = {10.1063/1.2193827},
  timestamp = {2016-08-11T01:57:31Z},
  number = {4},
  urldate = {2009-08-26},
  journal = {Review of Scientific Instruments},
  author = {Jericho, S. K. and Garcia-Sucerquia, J. and Xu, Wenbo and Jericho, M. H. and Kreuzer, H. J.},
  month = apr,
  year = {2006},
  keywords = {bio,holo,holography,microorganisms,optical microscopy},
  pages = {043706--10},
  file = {jericho_2006_submersible_DIHM.pdf:/home/tdimiduk/documents/holography/jericho_2006_submersible_DIHM.pdf:application/pdf}
}

@article{chaudhary_janus_2012,
  title = {Janus {{Colloidal Matchsticks}}},
  volume = {134},
  issn = {0002-7863},
  doi = {10.1021/ja305067g},
  abstract = {We fabricated chemically and shape-anisotropic colloids composed of silica rods coated with gold tips using a multistep process involving electric-field alignment and crystallization, microcontact printing, and selective metallization. Through direct observation, we found that these ?Janus matchsticks? self-assemble into multipods (bi-, tri-, and tetrapods) of varying coordination number and patch angle in aqueous solution.},
  timestamp = {2016-08-06T11:33:05Z},
  number = {31},
  urldate = {2013-10-10},
  journal = {J. Am. Chem. Soc.},
  author = {Chaudhary, Kundan and Chen, Qian and Ju{\'a}rez, Jaime J. and Granick, Steve and Lewis, Jennifer A.},
  month = aug,
  year = {2012},
  pages = {12901--12903}
}

@article{perrin_mouvement_1934,
  title = {Mouvement brownien d'un ellipsoide - {{I}}. {{Dispersion}} di{\'e}lectrique pour des mol{\'e}cules ellipsoidales},
  volume = {5},
  issn = {0368-3842},
  doi = {10.1051/jphysrad:01934005010049700},
  timestamp = {2016-08-06T11:30:25Z},
  number = {10},
  urldate = {2013-10-07},
  author = {Perrin, Francis},
  year = {1934},
  pages = {497--511},
  file = {Brownian motion of an ellipsoid - I. Dielectric dispersion for ellipsoidal molecules.Mouvement brownien d'un ellipsoide - I. Dispersion diélectrique pour des molécules ellipsoidales | J. Phys. Radium:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/F87RNXJV/jphysrad_1934__5_10_497_0.html:text/html}
}

@inproceedings{markwardt_non-linear_2009,
  title = {Non-linear {{Least}}-squares {{Fitting}} in {{IDL}} with {{MPFIT}}},
  volume = {411},
  isbn = {1050-3390},
  abstract = {MPFIT is a port to IDL of the non-linear least squares fitting program MINPACK-1.  MPFIT inherits the robustness of the original FORTRAN version of MINPACK-1, but is optimized for performance and convenience in IDL.  In addition to the main fitting engine, MPFIT, several specialized functions are provided to fit 1-D curves and 2-D images, 1-D and 2-D peaks, and interactive fitting from the IDL command line. Several constraints can be applied to model parameters, including fixed constraints, simple bounding constraints, and ``tying'' the value to another parameter.  Several data-weighting methods are allowed, and the parameter covariance matrix is computed. Extensive diagnostic capabilities are available during the fit, via a call-back subroutine, and after the fit is complete.  Several different forms of documentation are provided, including a tutorial, reference pages, and frequently asked questions.  The package has been translated to C and Python as well.  The full IDL and C packages can be found at
http://purl.com/net/mpfit.},
  timestamp = {2016-08-06T16:16:18Z},
  urldate = {2013-10-25},
  booktitle = {Astronomical {{Data Analysis Software}} and {{Systems XVIII}}},
  author = {Markwardt, C. B.},
  year = {2009},
  pages = {251},
  file = {Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/IZ34BQBA/2009ASPC..411..html:text/html}
}

@incollection{fuller_electromagnetic_2000,
  title = {Electromagnetic scattering by compounded spherical particles},
  isbn = {978-0-12-498660-2},
  shorttitle = {Light scattering by nonspherical particles},
  timestamp = {2016-08-06T11:32:16Z},
  booktitle = {Light scattering by nonspherical particles: {{Theory}}, measurements, and applications},
  publisher = {{Academic Press}},
  author = {Fuller, Kirk A. and Mackowski, Daniel W.},
  editor = {Mishchenko, Michael I. and Hovenier, Joachim W. and Travis, Larry D.},
  year = {2000},
  keywords = {Electromagnetic waves,Light,Light - Scattering,Light/ Scattering,Mathematics / Functional Analysis,Nature / Weather,Particles,Radiation,Science / Applied Sciences,Science / Earth Sciences / General,Science / Earth Sciences / Meteorology \& Climatology,Science / Earth Sciences / Oceanography,Science / Geophysics,Science / Light,Science / Optics,Science / Physics},
  pages = {225--272}
}

@article{saragosti_modeling_2012,
  title = {Modeling {{E}}. coli {{Tumbles}} by {{Rotational Diffusion}}. {{Implications}} for {{Chemotaxis}}},
  volume = {7},
  abstract = {The bacterium Escherichia coli in suspension in a liquid medium swims by a succession of runs and tumbles, effectively describing a random walk. The tumbles randomize incompletely, i.e. with a directional persistence, the orientation taken by the bacterium. Here, we model these tumbles by an active rotational diffusion process characterized by a diffusion coefficient and a diffusion time. In homogeneous media, this description accounts well for the experimental reorientations. In shallow gradients of nutrients, tumbles are still described by a unique rotational diffusion coefficient. Together with an increase in the run length, these tumbles significantly contribute to the net chemotactic drift via a modulation of their duration as a function of the direction of the preceding run. Finally, we discuss the limits of this model in propagating concentration waves characterized by steep gradients. In that case, the effective rotational diffusion coefficient itself varies with the direction of the preceding run. We propose that this effect is related to the number of flagella involved in the reorientation process.},
  timestamp = {2016-08-06T11:30:19Z},
  number = {4},
  urldate = {2013-10-09},
  journal = {PLoS ONE},
  author = {Saragosti, Jonathan and Silberzan, Pascal and Buguin, Axel},
  month = apr,
  year = {2012},
  pages = {e35412}
}

@article{xiao_sorting_2010,
  title = {Sorting colloidal particles into multiple channels with optical forces: {{Prismatic}} optical fractionation},
  volume = {82},
  shorttitle = {Sorting colloidal particles into multiple channels with optical forces},
  abstract = {Brownian particles drifting through a periodically structured force landscape can become entrained by the landscape's symmetries. What direction a particular particle takes can depend strongly on subtle variations in its physical properties. Consequently, a homogeneously structured force field can sort a mixture of particles into spatially separated fractions, much as an optical prism refracts light into its component wavelengths. When the force landscape is implemented with structured light fields, such continuous multichannel sorting may be termed prismatic optical fractionation. We describe experimental and numerical studies of colloidal spheres' transport through periodic arrays of optical tweezers, which reveal an important role for three-dimensional motion in determining a drifting particle's fate. These studies also demonstrate sorting on the basis of statistically locked-in transport, in which Brownian fluctuations contribute to direction selection.},
  timestamp = {2016-08-06T11:29:46Z},
  number = {5},
  journal = {Phys. Rev. E},
  author = {Xiao, Ke and Grier, David G.},
  month = nov,
  year = {2010},
  pages = {051407}
}

@article{seo_lensfree_2009,
  title = {Lensfree holographic imaging for on-chip cytometry and diagnostics},
  volume = {9},
  timestamp = {2009-11-12T15:25:42Z},
  number = {6},
  journal = {Lab on a Chip},
  author = {Seo, S. and Su, T. W and Tseng, D. K and Erlinger, A. and Ozcan, A.},
  year = {2009},
  pages = {777--787}
}

@inproceedings{mcgorty_measuring_2008,
  series = {OSA Technical Digest (CD)},
  title = {Measuring {{Dynamics}} and {{Interactions}} of {{Colloidal Particles}} with {{Digital Holographic Microscopy}}},
  abstract = {Micrometer-sized colloidal particles are a model system for understanding self-assembly in condensed matter. Here I present the results of digital holographic microscopy experiments that probe the 3D structure and dynamics of these systems.},
  timestamp = {2016-08-06T11:31:28Z},
  booktitle = {Digital holography and three-dimensional imaging},
  publisher = {{Optical Society of America}},
  author = {McGorty, Ryan and Fung, Jerome and Kaz, David and Ahn, Steven and Manoharan, Vinothan N.},
  month = mar,
  year = {2008},
  keywords = {Digital holography,holography,Other areas of optics,Particles},
  pages = {DTuB1}
}

@article{cheong_strategies_2010,
  title = {Strategies for three-dimensional particle tracking with holographic video microscopy},
  volume = {18},
  doi = {10.1364/OE.18.013563},
  abstract = {The video stream captured by an in-line holographic microscope can be analyzed on a frame-by-frame basis to track individual colloidal particles' three-dimensional motions with nanometer resolution. In this work, we compare the performance of two complementary analysis techniques, one based on fitting to the exact Lorenz-Mie theory and the other based on phenomenological interpretation of the scattered light field reconstructed with Rayleigh-Sommerfeld back-propagation. Although Lorenz-Mie tracking provides more information and is inherently more precise, Rayleigh-Sommerfeld reconstruction is faster and more general. The two techniques agree quantitatively on colloidal spheres' in-plane positions. Their systematic differences in axial tracking can be explained in terms of the illuminated objects' light scattering properties.},
  timestamp = {2016-08-06T16:32:56Z},
  number = {13},
  urldate = {2011-02-28},
  journal = {Optics Express},
  author = {Cheong, Fook Chiong and Krishnatreya, Bhaskar Jyoti and Grier, David G.},
  month = jun,
  year = {2010},
  keywords = {3d,and metrology,colloid,Computer holography,digital,holo,holography,inline,Instrumentation,measurement,microscopy,mie,particle_tracking,particle tracking,reconstruction,scattering,Three-dimensional microscopy},
  pages = {13563--13573}
}

@article{moon_automated_2009,
  title = {Automated {{Three-Dimensional Identification}} and {{Tracking}} of {{Micro}}/{{Nanobiological Organisms}} by {{Computational Holographic Microscopy}}},
  volume = {97},
  issn = {0018-9219},
  doi = {10.1109/JPROC.2009.2017563},
  abstract = {The ability to sense, track, identify, and monitor biological micro/nanoorganisms in a real-time, automated, and integrated system is of great importance from both scientific and technological standpoints. Such a system and its possible variants would have numerous applications in a wide spectrum of fields, including defense against biological warfare, disease control, environmental health and safety, and medical treatments. In this paper, we review a comprehensive mixture of optical and computational tools developed in our group aiming at real-time sensing and recognition of biological microorganisms. Digital in-line holographic microscopy is used with both coherent and partially coherent illumination to probe the specimen interferometerically. The interference pattern is then recorded on an optoelectronic image sensor and transferred to a computer where special statistical algorithms are performed to segment, recognize, and track the microorganisms within the field of view of the microscope. The advantages of proposed holographic sensing are described compared to conventional two-dimensional imaging systems. in addition, the theoretical aspects and fundamental limitations of digital in-line holographic microscopy are discussed, which determine the relationship between system parameters and achievable performance. The proposed optical-digital integrated system for automated, real-time sensing and recognition of biological microorganisms has been deemed promising with the potential of widespread application. We demonstrate how the proposed techniques function together in a series of experiments.},
  timestamp = {2013-08-28T14:20:47Z},
  number = {6},
  urldate = {2009-09-23},
  journal = {Proceedings of the IEEE},
  author = {Moon, I and Daneshpanah, M and Javidi, B and Stern, A},
  month = jun,
  year = {2009},
  keywords = {3d,bio,holo,holography,inline,lab_javidi,lab_stern},
  pages = {990--1010},
  file = {moon_stern2009holo_identification.pdf:/home/tdimiduk/documents/holography/moon_stern2009holo_identification.pdf:application/pdf;ISI Web of Knowledge Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/3HSUQDHE/full_record.html:text/html}
}

@article{gittings_determination_1998,
  title = {The determination of hydrodynamic size and zeta potential from electrophoretic mobility and light scattering measurements},
  volume = {141},
  issn = {0927-7757},
  doi = {10.1016/S0927-7757(98)00207-6},
  abstract = {Colloidal particle diffusivities are usually measured by light scattering and \ensuremath{\zeta}-potentials determined from electrophoretic mobilities. A hydrodynamic size can be calculated from the diffusivity by use of the Stokes\textendash{}Einstein equation, although this ignores the influence of the surface charge and the ion cloud surrounding each particle. Similarly, \ensuremath{\zeta}-potentials are often calculated from a radius determined by transmission electron microscopy or light scattering. In either case, a false picture emerges since the \ensuremath{\zeta}-potential is defined as the potential at the electrokinetic shear surface. Here we show that a self-consistent picture emerges upon combining diffusivity and electrophoretic mobility measurements so as to include the effects of the diffuse layer in the hydrodynamic/electrokinetic particle size determination. The diffusivity and electrophoretic mobility of an anionic polystyrene latex were measured over a range of salt strengths. When diffuse layer effects were ignored, the particle diameter decreased monotonically from 180 nm to 158 nm as the salt concentration increased from (approximately) 10 \ensuremath{\mu}M to 10 mM. When diffuse layer effects were incorporated into the analysis by simultaneously calculating the particle size and charge, the ionic strength dependence weakened. Above an ionic strength of 10-4 M, the size varied by less than 1\% and exceeded the dry size (from transmission electron microscopy) by about 4\%. Although making use of the two experimental parameters has a significant impact on the calculated size, the effect on \ensuremath{\zeta}-potentials is small. Some evidence of a fuzzy layer was present at ionic strengths below 10-4 M since the particle size increased with diminishing ionic strength.},
  timestamp = {2016-08-06T11:32:00Z},
  number = {1},
  urldate = {2013-10-10},
  journal = {Colloids and Surfaces A: Physicochemical and Engineering Aspects},
  author = {Gittings, M.R and Saville, D.A},
  month = oct,
  year = {1998},
  keywords = {Electrophoretic mobility,Hydrodynamic size,Light scattering,Zeta potential},
  pages = {111--117}
}

@article{shor_minimization_1974,
  title = {A minimization method using the operation of extension of the space in the direction of the difference of two successive gradients},
  volume = {7},
  issn = {0011-4235, 1573-8337},
  timestamp = {2016-08-06T11:30:13Z},
  number = {3},
  journal = {Cybernetics},
  author = {Shor, N. Z. and Zhurbenko, N. G.},
  year = {1974},
  pages = {450--459}
}

@article{kuijk_synthesis_2011,
  title = {Synthesis of {{Monodisperse}}, {{Rodlike Silica Colloids}} with {{Tunable Aspect Ratio}}},
  volume = {133},
  issn = {0002-7863},
  doi = {10.1021/ja109524h},
  abstract = {Although the experimental study of spherical colloids has been extensive, similar studies on rodlike particles are rare because suitable model systems are scarcely available. To fulfill this need, we present the synthesis of monodisperse rodlike silica colloids with tunable dimensions. Rods were produced with diameters of 200 nm and greater and lengths up to 10 ?m, resulting in aspect ratios from 1 to ?25. The growth mechanism of these rods involves emulsion droplets inside which silica condensation takes place. Due to an anisotropic supply of reactants, the nucleus grows to one side only, resulting in rod formation. In concentrated dispersions, these rods self-assemble in liquid crystal phases, which can be studied quantitatively on the single particle level in three-dimensional real-space using confocal microscopy. Isotropic, paranematic, and smectic phases were observed for this system.},
  timestamp = {2016-08-06T11:31:38Z},
  number = {8},
  urldate = {2013-10-10},
  journal = {J. Am. Chem. Soc.},
  author = {Kuijk, Anke and {van Blaaderen}, Alfons and Imhof, Arnout},
  month = mar,
  year = {2011},
  pages = {2346--2349}
}

@article{yoshizaki_dynamics_1980-1,
  title = {Dynamics of spheroid-cylindrical molecules in dilute solution},
  volume = {72},
  issn = {00219606},
  doi = {doi:10.1063/1.438945},
  abstract = {The dilute solution dynamics of spheroid\textendash{}cylindrical molecules, i.e., straight cylinders with oblate, spherical, or prolate hemispheroid caps at the ends, is studied in detail. The translational and rotatory diffusion coefficients and the dynamic intrinsic viscosity are evaluated numerically for short cylinders by determining the frictional force by an orthodox method of classical hydrodynamics. For long cylinders, the Oseen\textendash{}Burgers procedure is shown to be valid, and the results previously obtained by it are still useful. Thus, empirical interpolation formulas for the transport coefficients above are also constructed to be applied to spheroid\textendash{}cylinders of arbitrary size. The end effects on the translational and rotatory diffusion coefficients are rather small, while the effect on the zero-frequency intrinsic viscosity is remarkable, depending appreciably on the shape of the ends, though for relatively short cylinders. In general, for a rigid body of revolution having a plane of symmetry perpendicular to its axis, it is shown that the dynamic intrinsic viscosity may be expressed in terms of the zero-frequency intrinsic viscosity, the rotatory diffusion coefficient about a principal axis in the symmetry plane, and a newly defined factor, which is also associated with the rotational motion about this axis.},
  timestamp = {2016-08-06T11:27:19Z},
  number = {1},
  urldate = {2013-10-10},
  author = {Yoshizaki, Takenao and Yamakawa, Hiromi},
  month = jan,
  year = {1980},
  pages = {57}
}

@article{rivenson_overview_2013,
  title = {Overview of compressive sensing techniques applied in holography [{{Invited}}]},
  volume = {52},
  doi = {10.1364/AO.52.00A423},
  abstract = {In recent years compressive sensing (CS) has been successfully introduced in digital holography (DH). Depending on the ability to sparsely represent an object, the CS paradigm provides an accurate object reconstruction framework from a relatively small number of encoded signal samples. DH has proven to be an efficient and physically realizable sensing modality that can exploit the benefits of CS. In this paper, we provide an overview of the theoretical guidelines for application of CS in DH and demonstrate the benefits of compressive digital holographic sensing.},
  timestamp = {2013-08-08T22:06:56Z},
  number = {1},
  urldate = {2013-08-08},
  journal = {Applied Optics},
  author = {Rivenson, Yair and Stern, Adrian and Javidi, Bahram},
  month = jan,
  year = {2013},
  keywords = {Computational imaging,Digital holography,Digital image processing,Fourier optics and signal processing,Inverse problems},
  pages = {A423--A432},
  file = {Rivenson et al_2013_Overview of compressive sensing techniques applied in holography [Invited].pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/6DFM96W6/Rivenson et al_2013_Overview of compressive sensing techniques applied in holography [Invited].pdf:application/pdf;Appl. Opt. Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/GGZRR2FW/abstract.html:text/html}
}

@article{pickering_cxcvi.emulsions_1907,
  title = {{{CXCVI}}.\textendash{}{{Emulsions}}},
  volume = {91},
  issn = {0368-1645},
  abstract = {PICKERING : EMULSIONS. 2001 CXCVI. By SPENCER UMFREVILLE PICKERING, M.A., F.R.S. IN the Sixth Report of the Woburn Experimental Fruit Farm (Eyre and Spottiswoode, 1906) were published the results of an examination of emulsions of paraffin oil in solutions of soft soap, such as are used for insecticidal purposes; t},
  language = {en},
  timestamp = {2016-08-06T11:56:39Z},
  urldate = {2013-10-11},
  journal = {J. Chem. Soc., Trans.},
  author = {Pickering, Spencer Umfreville},
  month = jan,
  year = {1907},
  pages = {2001--2021}
}

@article{mann_movies_2006,
  title = {Movies of cellular and sub-cellular motion by digital holographic microscopy},
  volume = {5},
  issn = {1475-925X},
  doi = {10.1186/1475-925X-5-21},
  abstract = {BACKGROUND:Many biological specimens, such as living cells and their intracellular components, often exhibit very little amplitude contrast, making it difficult for conventional bright field microscopes to distinguish them from their surroundings. To overcome this problem phase contrast techniques such as Zernike, Normarsky and dark-field microscopies have been developed to improve specimen visibility without chemically or physically altering them by the process of staining. These techniques have proven to be invaluable tools for studying living cells and furthering scientific understanding of fundamental cellular processes such as mitosis. However a drawback of these techniques is that direct quantitative phase imaging is not possible. Quantitative phase imaging is important because it enables determination of either the refractive index or optical thickness variations from the measured optical path length with sub-wavelength accuracy.Digital holography is an emergent phase contrast technique that offers an excellent approach in obtaining both qualitative and quantitative phase information from the hologram. A CCD camera is used to record a hologram onto a computer and numerical methods are subsequently applied to reconstruct the hologram to enable direct access to both phase and amplitude information. Another attractive feature of digital holography is the ability to focus on multiple focal planes from a single hologram, emulating the focusing control of a conventional microscope.METHODS:A modified Mach-Zender off-axis setup in transmission is used to record and reconstruct a number of holographic amplitude and phase images of cellular and sub-cellular features.RESULTS:Both cellular and sub-cellular features are imaged with sub-micron, diffraction-limited resolution. Movies of holographic amplitude and phase images of living microbes and cells are created from a series of holograms and reconstructed with numerically adjustable focus, so that the moving object can be accurately tracked with a reconstruction rate of 300ms for each hologram. The holographic movies show paramecium swimming among other microbes as well as displaying some of their intracellular processes. A time lapse movie is also shown for fibroblast cells in the process of migration.CONCLUSION:Digital holography and movies of digital holography are seen to be useful new tools for visualization of dynamic processes in biological microscopy. Phase imaging digital holography is a promising technique in terms of the lack of coherent noise and the precision with which the optical thickness of a sample can be profiled, which can lead to images with an axial resolution of a few nanometres.},
  timestamp = {2012-10-08T18:40:28Z},
  number = {1},
  urldate = {2009-09-23},
  journal = {BioMedical Engineering OnLine},
  author = {Mann, Christopher and Yu, Lingfeng and Kim, Myung},
  year = {2006},
  keywords = {holo,holography,off_axis,phase_unwrapping},
  pages = {21},
  file = {Mann et al_2006_Movies of cellular and sub-cellular motion by digital holographic microscopy.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/TIU3AVMU/Mann et al_2006_Movies of cellular and sub-cellular motion by digital holographic microscopy.pdf:application/pdf;biomedical-engineering-online Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/RJ89HNVI/21.html:text/html}
}

@article{satake_measurements_2006,
  title = {Measurements of {{3D}} flow in a micro-pipe via micro digital holographic particle tracking velocimetry},
  volume = {17},
  timestamp = {2013-08-28T14:25:46Z},
  number = {7},
  journal = {Measurement Science and Technology},
  author = {Satake, S. and Kunugi, T. and Sato, K. and Ito, T. and Kanamori, H. and Taniguchi, J.},
  year = {2006},
  keywords = {holo,holography},
  pages = {1647--1651},
  file = {satake2006flow_tracking.pdf:/home/tdimiduk/documents/holography/satake2006flow_tracking.pdf:application/pdf}
}

@article{pampaloni_third_2007,
  title = {The third dimension bridges the gap between cell culture and live tissue},
  volume = {8},
  issn = {1471-0072},
  doi = {10.1038/nrm2236},
  timestamp = {2010-07-16T21:36:54Z},
  number = {10},
  urldate = {2010-07-16},
  journal = {Nat. Rev. Mol. Cell Biol.},
  author = {Pampaloni, Francesco and Reynaud, Emmanuel G. and Stelzer, Ernst H. K.},
  month = oct,
  year = {2007},
  pages = {839--845},
  file = {Nature Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/GZQIXCUD/nrm2236.html:text/html}
}

@article{sokolova_enhanced_2013,
  title = {Enhanced transcription rates in membrane-free protocells formed by coacervation of cell lysate},
  volume = {110},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1222321110},
  abstract = {Liquid\textendash{}liquid phase transitions in complex mixtures of proteins and other molecules produce crowded compartments supporting in vitro transcription and translation. We developed a method based on picoliter water-in-oil droplets to induce coacervation in Escherichia coli cell lysate and follow gene expression under crowded and noncrowded conditions. Coacervation creates an artificial cell-like environment in which the rate of mRNA production is increased significantly. Fits to the measured transcription rates show a two orders of magnitude larger binding constant between DNA and T7 RNA polymerase, and five to six times larger rate constant for transcription in crowded environments, strikingly similar to in vivo rates. The effect of crowding on interactions and kinetics of the fundamental machinery of gene expression has a direct impact on our understanding of biochemical networks in vivo. Moreover, our results show the intrinsic potential of cellular components to facilitate macromolecular organization into membrane-free compartments by phase separation.},
  language = {en},
  timestamp = {2013-08-19T15:01:44Z},
  number = {29},
  urldate = {2013-08-19},
  journal = {Proceedings of the National Academy of Sciences},
  author = {Sokolova, Ekaterina and Spruijt, Evan and Hansen, Maike M. K. and Dubuc, Emilien and Groen, Joost and Chokkalingam, Venkatachalam and Piruska, Aigars and Heus, Hans A. and Huck, Wilhelm T. S.},
  month = jul,
  year = {2013},
  keywords = {macromolecular crowding,microdroplets},
  pages = {11692--11697},
  file = {Sokolova et al_2013_Enhanced transcription rates in membrane-free protocells formed by coacervation.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/CBCMMUXK/Sokolova et al_2013_Enhanced transcription rates in membrane-free protocells formed by coacervation.pdf:application/pdf;Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/TRTD2NVM/11692.html:text/html},
  pmid = {23818642}
}

@article{xu_digital_2002,
  title = {Digital in-line holography of microspheres},
  volume = {41},
  timestamp = {2013-08-28T14:21:49Z},
  number = {25},
  journal = {Applied Optics},
  author = {Xu, W. and Jericho, MH and Meinertzhagen, IA and Kreuzer, HJ},
  year = {2002},
  keywords = {holo,holography,inline,lab_kreuzer},
  pages = {5367--5375},
  file = {Xu et al_2002_Digital in-line holography of microspheres.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/KJW986H3/Xu et al_2002_Digital in-line holography of microspheres.pdf:application/pdf}
}

@article{sheng_digital_2006,
  title = {Digital holographic microscope for measuring three-dimensional particle distributions and motions},
  volume = {45},
  timestamp = {2012-10-08T18:40:28Z},
  number = {16},
  journal = {Applied Optics},
  author = {Sheng, J. and Malkiel, E. and Katz, J.},
  year = {2006},
  keywords = {holo,holography,lens,microscopy},
  pages = {3893--3901},
  file = {sheng_dhm_3d_distro.pdf:/home/tdimiduk/documents/holography/sheng_dhm_3d_distro.pdf:application/pdf}
}

@article{fung_holographic_2013,
  title = {Holographic measurements of anisotropic three-dimensional diffusion of colloidal clusters},
  volume = {88},
  doi = {10.1103/PhysRevE.88.020302},
  abstract = {We measure all nonzero elements of the three-dimensional diffusion tensor D for clusters of colloidal spheres to a precision of 1\% or better using digital holographic microscopy. We study both dimers and triangular trimers of spheres, for which no analytical calculations of the diffusion tensor exist. We observe anisotropic rotational and translational diffusion arising from the asymmetries of the clusters. In the case of the three-particle triangular cluster, we also detect a small but statistically significant difference in the rotational diffusion about the two in-plane axes. We attribute this difference to weak breaking of threefold rotational symmetry due to a small amount of particle polydispersity. Our experimental measurements agree well with numerical calculations and show how diffusion constants can be measured under conditions relevant to colloidal self-assembly, where theoretical and even numerical prediction is difficult.},
  timestamp = {2016-08-06T11:32:09Z},
  number = {2},
  urldate = {2013-10-07},
  journal = {Phys. Rev. E},
  author = {Fung, Jerome and Manoharan, Vinothan N.},
  month = aug,
  year = {2013},
  pages = {020302},
  file = {Fung_Manoharan_2013_Holographic measurements of anisotropic three-dimensional diffusion of.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/7SXCZCK4/Fung_Manoharan_2013_Holographic measurements of anisotropic three-dimensional diffusion of.pdf:application/pdf;APS Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/PXTQ5UH6/PhysRevE.88.html:text/html}
}

@article{yurkin_discrete-dipole-approximation_2011,
  series = {Polarimetric Detection, Characterization, and Remote Sensing},
  title = {The Discrete-Dipole-Approximation Code {{ADDA}}: {{Capabilities}} and Known Limitations},
  volume = {112},
  issn = {0022-4073},
  shorttitle = {The Discrete-Dipole-Approximation Code {{ADDA}}},
  doi = {10.1016/j.jqsrt.2011.01.031},
  abstract = {The open-source code ADDA is described, which implements the discrete dipole approximation (DDA), a method to simulate light scattering by finite 3D objects of arbitrary shape and composition. Besides standard sequential execution, ADDA can run on a multiprocessor distributed-memory system, parallelizing a single DDA calculation. Hence the size parameter of the scatterer is in principle limited only by total available memory and computational speed. ADDA is written in C99 and is highly portable. It provides full control over the scattering geometry (particle morphology and orientation, and incident beam) and allows one to calculate a wide variety of integral and angle-resolved scattering quantities (cross sections, the Mueller matrix, etc.). Moreover, ADDA incorporates a range of state-of-the-art DDA improvements, aimed at increasing the accuracy and computational speed of the method. We discuss both physical and computational aspects of the DDA simulations and provide a practical introduction into performing such simulations with the ADDA code. We also present several simulation results, in particular, for a sphere with size parameter 320 (100-wavelength diameter) and refractive index 1.05.},
  timestamp = {2016-08-29T22:18:59Z},
  number = {13},
  urldate = {2016-08-29},
  journal = {Journal of Quantitative Spectroscopy and Radiative Transfer},
  author = {Yurkin, Maxim A. and Hoekstra, Alfons G.},
  month = sep,
  year = {2011},
  keywords = {Computer program,Discrete dipole approximation,Light scattering simulation,Very large particles},
  pages = {2234--2247},
  file = {ScienceDirect Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/2IVFZ4ZG/S0022407311000562.html:text/html}
}

@article{martchenko_hydrodynamic_2011,
  title = {Hydrodynamic {{Properties}} of {{Magnetic Nanoparticles}} with {{Tunable Shape Anisotropy}}: {{Prediction}} and {{Experimental Verification}}},
  volume = {115},
  issn = {1520-6106},
  shorttitle = {Hydrodynamic {{Properties}} of {{Magnetic Nanoparticles}} with {{Tunable Shape Anisotropy}}},
  doi = {10.1021/jp2078264},
  abstract = {We describe the characterization of the hydrodynamic properties of anisotropic magnetic nanoparticles using a combination of transmission electron microscopy (TEM) and dynamic as well as depolarized dynamic light scattering (DLS/DDLS). The particles used are nearly monodisperse hematite spindles with an average length of 280 nm and a minor axis of 57 nm, coated with a layer of silica of variable thickness that allows us to tune the particle aspect ratio between 5 and 2. Their geometrical dimensions can thus be determined easily and quantitatively from TEM. Moreover, their size is ideal to employ DLS and DDLS to measure the translational and rotational diffusion coefficients DT and DR, while the presence of a magnetic core opens a plethora of opportunities for future studies and applications. We demonstrate that we can successfully predict the hydrodynamic properties of the different particles based on a TEM characterization of their size distribution and using established theoretical models for the hydrodynamic properties of anisotropic particles. When compared with the theoretical predictions, our light scattering measurements are in quantitative agreement. This agreement between theory and experiment is achieved without having to invoke any adjustable free parameter, as the TEM results are used to calculate the corresponding diffusion coefficients on an absolute scale. We demonstrate that this is achieved due to a new and simple method for the statistical weighting of the TEM information, and the use of the correct hydrodynamic models for the observed particle shape. In addition, we also demonstrate an enhanced sensitivity of the rotational diffusion for the surface properties of ellipsoidal nanoparticles, and point out that this may serve as an ideal tool toward characterizing functionalized surfaces.},
  timestamp = {2016-08-06T11:31:30Z},
  number = {49},
  urldate = {2013-10-10},
  journal = {J. Phys. Chem. B},
  author = {Martchenko, Ilya and Dietsch, Herv{\'e} and Moitzi, Christian and Schurtenberger, Peter},
  month = dec,
  year = {2011},
  pages = {14838--14845}
}

@article{gabor_new_1948,
  title = {A new microscopic principle},
  volume = {161},
  timestamp = {2013-04-22T14:03:24Z},
  number = {4098},
  journal = {Nature},
  author = {Gabor, D.},
  year = {1948},
  keywords = {holo,holography},
  pages = {777--778},
  file = {Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/T43RASEX/index.html:text/html}
}

@article{xiao_multidimensional_2010,
  title = {Multidimensional {{Optical Fractionation}} of {{Colloidal Particles}} with {{Holographic Verification}}},
  volume = {104},
  abstract = {The trajectories of colloidal particles driven through a periodic potential energy landscape can become kinetically locked-in to directions dictated by the landscape's symmetries. When the landscape is realized with a structured light field, the path a given particle follows has been predicted to depend exquisitely sensitively on such properties as the particle's size and refractive index. We confirm these predictions by measuring the transport of colloidal silica spheres through arrays of holographic optical traps, using holographic video microscopy to track individual spheres' motions in three dimensions and simultaneously to measure each sphere's radius and refractive index with part-per-thousand resolution. These measurements demonstrate optical fractionation's ability to sort with part-per-thousand resolution on multiple characteristics simultaneously.},
  timestamp = {2016-08-06T11:29:49Z},
  number = {2},
  journal = {Phys. Rev. Lett.},
  author = {Xiao, Ke and Grier, David G.},
  month = jan,
  year = {2010},
  pages = {028302}
}

@inproceedings{mantiuk_high_????,
  title = {High dynamic range imaging pipeline: {{Perception}}-motivated representation of visual content},
  shorttitle = {High dynamic range imaging pipeline},
  timestamp = {2009-08-21T17:17:37Z},
  booktitle = {in {{Proc}}. of {{Human Vision}} and {{Electronic Imaging XII}}, {{IS}}\&T/{{SPIE}}'s {{Annual Symposium}} on {{Electronic Imaging}} (2007)},
  author = {Mantiuk, R. and Krawczyk, G. and Mantiuk, R. and Seidel, H. P},
  file = {Mantiuk et al_High dynamic range imaging pipeline.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/JJMF69R9/Mantiuk et al_High dynamic range imaging pipeline.pdf:application/pdf}
}

@article{xu_digital_2001,
  title = {Digital in-line holography for biological applications},
  volume = {98},
  timestamp = {2012-10-08T18:40:28Z},
  number = {20},
  journal = {Proceedings of the National Academy of Sciences},
  author = {Xu, W. and Jericho, M. H. and Meinertzhagen, I. A. and Kreuzer, H. J.},
  year = {2001},
  keywords = {3d,bio,holo,holography,inline,lab_kreuzer,microscopy},
  pages = {11301},
  file = {xu_2001_DIH_for_bio.pdf:/home/tdimiduk/documents/holography/xu_2001_DIH_for_bio.pdf:application/pdf}
}

@misc{oliphant_scipy_2001,
  title = {{{SciPy}}: {{Open}} source scientific tools for {{Python}}},
  timestamp = {2016-08-06T17:24:56Z},
  urldate = {2016-08-06},
  author = {Oliphant, Travis and Peterson, Pearu and Eric, Jones and others},
  year = {2001},
  file = {SciPy -:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/WUJWBEGU/www.scipy.org.html:text/html}
}

@article{kreis_frequency_2002,
  title = {Frequency analysis of digital holography with reconstruction by convolution},
  volume = {41},
  issn = {00913286},
  timestamp = {2016-08-06T11:31:40Z},
  number = {8},
  journal = {Opt. Eng.},
  author = {Kreis, Thomas M.},
  year = {2002},
  pages = {1829--1839}
}

@article{satake_three-dimensional_2005,
  title = {Three-{{Dimensional Flow Tracking}} in a {{Micro Channel}} with {{High Time Resolution Using Micro Digital-Holographic Particle-Tracking Velocimetry}}},
  volume = {12},
  issn = {1340-6000},
  doi = {10.1007/s10043-005-0442-y},
  timestamp = {2013-08-28T14:32:39Z},
  number = {6},
  urldate = {2011-01-19},
  journal = {Optical Review},
  author = {Satake, S. and Kunugi, Tomoaki and Sato, Kazuho and Ito, Tomoyoshi and Taniguchi, Jun},
  month = nov,
  year = {2005},
  keywords = {fast,holo,holography,piv},
  pages = {442--444},
  file = {Satake et al_2005_Three-Dimensional Flow Tracking in a Micro Channel with High Time Resolution.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/I7M928S2/Satake et al_2005_Three-Dimensional Flow Tracking in a Micro Channel with High Time Resolution.pdf:application/pdf;SpringerLink - Optical Review, Volume 12, Number 6:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/8ZTBZSVW/7330117607371k5n.html:text/html}
}

@book{berne_dynamic_1976,
  title = {Dynamic light scattering: with applications to chemistry, biology, and physics},
  isbn = {978-0-471-07100-6},
  shorttitle = {Dynamic light scattering},
  timestamp = {2016-08-06T11:33:20Z},
  publisher = {{Wiley}},
  author = {Berne, Bruce J. and Pecora, Robert},
  year = {1976},
  keywords = {Light,Molecules,Science / Molecular Physics,Science / Optics}
}

@article{cheong_rotational_2010,
  title = {Rotational and translational diffusion of copper oxide nanorods measured with holographic video microscopy},
  volume = {18},
  doi = {10.1364/OE.18.006555},
  abstract = {We use holographic video microscopy to track the three-imensional translational and rotational diffusion of copper oxide nanorods suspended in water. Rayleigh-Sommerfeld back-propagation of a single holographic snapshot yields a volumetric reconstruction of the nanorod's optical scattering pattern, from which we estimate both its dimensions and also its instantaneous position and orientation. Analyzing a video sequence yields measurements of the freely diffusing nanorod's dynamics, from which we estimate the technique's resolution.},
  timestamp = {2016-08-06T11:33:57Z},
  number = {7},
  urldate = {2013-10-07},
  journal = {Opt. Express},
  author = {Cheong, Fook C. and Grier, David G.},
  month = mar,
  year = {2010},
  keywords = {Digital holography,Particles,Three-dimensional microscopy},
  pages = {6555--6562},
  file = {Cheong_Grier_2010_Rotational and translational diffusion of copper oxide nanorods measured with.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/FGMMTSB9/Cheong_Grier_2010_Rotational and translational diffusion of copper oxide nanorods measured with.pdf:application/pdf;Opt. Express Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/SP4TS8FD/abstract.html:text/html}
}

@article{mackowski_calculation_1996,
  title = {Calculation of the {{T}} matrix and the scattering matrix for ensembles of spheres},
  volume = {13},
  doi = {10.1364/JOSAA.13.002266},
  abstract = {We present a method for determination of the random-orientation polarimetric scattering properties of an arbitrary, nonsymmetric cluster of spheres. The method is based on calculation of the cluster T matrix, from which the orientation-averaged scattering matrix and total cross sections can be analytically obtained. An efficient numerical method is developed for the T-matrix calculation, which is faster and requires less computer memory than the alternative approach based on matrix inversion. The method also allows calculation of the random-orientation scattering properties of a cluster in a fraction of the time required for numerical quadrature. Numerical results for the random-orientation scattering matrix are presented for sphere ensembles in the form of densely packed clusters and linear chains.},
  timestamp = {2016-08-06T11:31:34Z},
  number = {11},
  urldate = {2013-05-10},
  journal = {Journal of the Optical Society of America A},
  author = {Mackowski, Daniel W. and Mishchenko, Michael I.},
  month = nov,
  year = {1996},
  pages = {2266--2278},
  file = {J. Opt. Soc. Am. A Full Text PDF:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/QIIQIDQS/Mackowski and Mishchenko - 1996 - Calculation of the T matrix and the scattering mat.pdf:application/pdf;Mackowski_Mishchenko_1996_Calculation of the T matrix and the scattering matrix for ensembles of spheres.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/SCGF49X6/Mackowski_Mishchenko_1996_Calculation of the T matrix and the scattering matrix for ensembles of spheres.pdf:application/pdf;J. Opt. Soc. Am. A Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/ECEWT2MP/abstract.html:text/html;J. Opt. Soc. Am. A Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/G2GM6CA3/abstract.html:text/html}
}

@article{yeom_real-time_2006,
  title = {Real-{{Time}} 3-{{D Sensing}}, {{Visualization}} and {{Recognition}} of {{Dynamic Biological Microorganisms}}},
  volume = {94},
  issn = {0018-9219},
  doi = {10.1109/JPROC.2006.870691},
  abstract = {We introduce optical imaging techniques for three-dimensional (3-D)visualization and identification of microorganisms. Three-dimensional sensing and reconstruction is performed by single-exposure on-line (SEOL)digital holography. A coherent microscope-based Mach-Zehnder interferometer records Fresnel digital holograms of microorganisms. Complex amplitude holographic images are computationally reconstructed at different depths by an inverse Fresnel transformation. For pattern recognition/identification, two approaches are addressed. One is 3-D morphology-based recognition and the other is shape-tolerant 3-D recognition. In the first approach, a series of image recognition techniques is used to analyze 3-D geometrical shapes of microorganisms, which is composed of magnitude and phase distributions. Segmentation, feature extraction, graph matching, feature selection, training, and decision rules are presented. For the second approach, a number of sampling segments are arbitrarily extracted from the reconstructed 3-D biological microorganism. These samples are processed using a number of cost functions and statistical inference theory for the equality of means and equality of variances between the sampling segments. Experimental results with sphacelaria alga, tribonema aequale alga, and polysiphonia alga are presented.},
  timestamp = {2012-10-08T18:40:28Z},
  number = {3},
  journal = {Proceedings of the IEEE},
  author = {Yeom, S. and Moon, I and Javidi, B.},
  year = {2006},
  keywords = {holo,holography,lab_javidi,segmentation},
  pages = {550--566},
  file = {Yeom et al_2006_Real-Time 3-D Sensing, Visualization and Recognition of Dynamic Biological.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/WZG2ANRB/Yeom et al_2006_Real-Time 3-D Sensing, Visualization and Recognition of Dynamic Biological.pdf:application/pdf}
}

@article{nikolaides_electric-field-induced_2002,
  title = {Electric-field-induced capillary attraction between like-charged particles at liquid interfaces},
  volume = {420},
  issn = {0028-0836},
  timestamp = {2016-08-06T11:30:32Z},
  number = {6913},
  journal = {Nature},
  author = {Nikolaides, M. G. and Bausch, A. R. and Hsu, M. F. and Dinsmore, A. D. and Brenner, M. P. and Gay, C. and Weitz, D. A.},
  month = nov,
  year = {2002},
  pages = {299--301}
}

@book{mysels_critical_1971,
  address = {Washington},
  series = {NSRDS-NBS, 36},
  title = {Critical micelle concentrations of aqueous surfactant systems},
  timestamp = {2016-08-06T11:30:56Z},
  publisher = {{U.S. National Bureau of Standards}},
  author = {Mysels, Karol J and Mukerjee, Pasupati},
  year = {1971}
}

@article{lee_characterizing_2007,
  title = {Characterizing and tracking single colloidal particles with video holographic microscopy},
  volume = {15},
  doi = {10.1364/OE.15.018275},
  abstract = {We use digital holographic microscopy and Mie scattering theory to simultaneously characterize and track individual colloidal particles. Each holographic snapshot provides enough information to measure a colloidal sphere's radius and refractive index to within 1\%, and simultaneously to measure its three-dimensional position with nanometer in-plane precision and 10 nanometer axial resolution.},
  timestamp = {2016-08-06T16:33:56Z},
  number = {26},
  urldate = {2012-10-08},
  journal = {Optics Express},
  author = {Lee, Sang-Hyuk and Roichman, Yohai and Yi, Gi-Ra and Kim, Shin-Hyun and Yang, Seung-Man and {van Blaaderen}, Alfons and {van Oostrum}, Peter and Grier, David G.},
  month = dec,
  year = {2007},
  pages = {18275--18282},
  file = {Lee et al_2007_Characterizing and tracking single colloidal particles with video holographic.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/KHS3P7ZT/Lee et al_2007_Characterizing and tracking single colloidal particles with video holographic.pdf:application/pdf;Opt. Express Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/JFQTDJ7M/abstract.html:text/html}
}

@article{seebergh_evidence_1995,
  title = {Evidence of a hairy layer at the surface of polystyrene latex particles},
  volume = {100},
  issn = {0927-7757},
  doi = {10.1016/0927-7757(95)03155-7},
  abstract = {Polystyrene latexes are treated as model colloids, yet the observed electrokinetic and size behavior do not conform to the predictions of theory. Upon the addition of low concentrations of electrolyte, the electrophoretic mobility and zeta potential of the latex increase, while the hydrodynamic size decreases. One explanation for the anomalous behavior is the presence of a hairy layer at the latex surface. According to the hairy layer model, flexible polymer chains, or hairs, at the surface extend into solution, owing to electrostatic repulsion between the ionic groups which terminate the hairs and the ionic groups which are anchored at the surface. The thickness of the hairy layer is altered by the presence of electrolyte owing to charge shielding. As such, the size and electrokinetic parameters are functions of ionic strength. This model is frequently invoked in the literature; however, to the author's knowledge, no previous studies have attempted to verify the presence of a hairy layer via simultaneous measurement of both the size and electrokinetic characteristics of a given latex over a range of conditions. Evidence from other investigators indicates that heating a latex to its glass transition temperature yields particles whose electrokinetic behavior is more nearly ideal. Interpreted in terms of the hairy layer model, such results suggest that heat treatment smoothes or removes the hairs. In the current study, the presence of a hairy layer is investigated by comparing size, mobility, critical coagulation concentration, and surface charge density measurements for three different surfactant-free latexes before and after heat treatment. The new results strongly support the existence of a hairy layer. Light scattering measurements indicate that the thickness of the layer may be as great as 7 nm.},
  timestamp = {2016-08-06T11:30:14Z},
  urldate = {2013-10-10},
  journal = {Colloids and Surfaces A: Physicochemical and Engineering Aspects},
  author = {Seebergh, Jill E. and Berg, John C.},
  month = jul,
  year = {1995},
  keywords = {Electrokinetics of latexes,Hairy layer model,Heat treatment of latexes,Hydrodynamic size of latexes,Polymer latexes},
  pages = {139--153}
}

@article{soulez_inverse_2007,
  title = {Inverse problem approach in particle digital holography: out-of-field particle detection made possible},
  volume = {24},
  issn = {1084-7529},
  shorttitle = {Inverse problem approach in particle digital holography},
  doi = {10.1364/JOSAA.24.003708},
  timestamp = {2016-08-06T11:20:13Z},
  number = {12},
  urldate = {2009-09-22},
  journal = {Journal of the Optical Society of America A},
  author = {Soulez, Ferr{\'e}ol and Denis, Lo{\"\i}c and Thi{\'e}baut, Eric and Fournier, Corinne and Goepfert, Charles},
  year = {2007},
  keywords = {fitting,holo,holography,particle_tracking},
  pages = {3708},
  file = {Soulez et al_2007_Inverse problem approach in particle digital holography.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/QRRTG3BK/Soulez et al_2007_Inverse problem approach in particle digital holography.pdf:application/pdf;HAL - INSU \:\: [ujm-00192619, version 1] Inverse problem approach in Particle Digital Holography \: out-of-field particle detection made possible:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/JQFKBQ52/ujm-00192619.html:text/html}
}

@inproceedings{depeursinge_digital_2007,
  title = {Digital holographic microscopy applied to life sciences},
  volume = {2007},
  doi = {10.1109/IEMBS.2007.4353782},
  abstract = {Digital holographic microscopy (DHM) is applied to life sciences applications and demonstrate its capability of real-time imaging and quantitative measurements of physiological parameters such as cell volume or mean cell hemoglobin concentration (MCHC) of erythrocyte cells. DHM has the advantage to be non-invasive (no phototoxicity, no contrast agents) and allows a high throughput measurements.},
  timestamp = {2016-08-11T02:03:43Z},
  urldate = {2009-08-28},
  booktitle = {Annual {{International Conference}} of the {{IEEE Engineering}} in {{Medicine}} and {{Biology Society}}},
  author = {Depeursinge, Christian and Colomb, Tristan and Emery, Yves and K{\"u}hn, Jonas and Charri{\`e}re, Florian and Rappaz, Benjamin and Marquet, Pierre},
  year = {2007},
  keywords = {bio,holo,holography,image_processing,lab_depeursinge,lab_marquet,microscopy},
  pages = {6244--6247},
  file = {depeursinge_2007_dhm_bio.pdf:/home/tdimiduk/documents/holography/depeursinge_2007_dhm_bio.pdf:application/pdf;PubMed Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/ZAJBK264/18003448.html:text/html},
  pmid = {18003448}
}

@article{burr_determination_2011,
  title = {Determination of the soot aggregate size distribution from elastic light scattering through {{Bayesian}} inference},
  volume = {112},
  issn = {0022-4073},
  doi = {10.1016/j.jqsrt.2010.12.001},
  abstract = {Recovering the size distribution of aerosolized soot aggregates from multiangle elastic light scattering data requires the inversion of an integral equation, which is a mathematically ill-posed problem. This paper demonstrates how maximum a posteriori (MAP) inference can be used to stabilize the inversion by introducing prior information about the size distribution of the soot aggregates. Results show that the size distribution can be recovered using only simple smoothness and non-negativity priors if the aggregate number density is known, but otherwise it is necessary to specify additional information about the presumed distribution shape.},
  timestamp = {2016-08-06T11:20:27Z},
  number = {6},
  urldate = {2016-02-12},
  journal = {Journal of Quantitative Spectroscopy and Radiative Transfer},
  author = {Burr, D. W. and Daun, K. J. and Link, O. and Thomson, K. A. and Smallwood, G. J.},
  month = apr,
  year = {2011},
  keywords = {Elastic light scattering,Elastic light scattering,MAP,MAP,Particle sizing,Particle sizing,Soot,Soot,Tikhonov regularization,Tikhonov regularization},
  pages = {1099--1107}
}

@article{dixon_holographic_2011,
  title = {Holographic deconvolution microscopy for high-resolution particle tracking},
  volume = {19},
  copyright = {\textcopyright{} 2011 OSA},
  issn = {1094-4087},
  doi = {10.1364/OE.19.016410},
  abstract = {Rayleigh-Sommerfeld back-propagation can be used to reconstruct the three-dimensional light field responsible for the recorded intensity in an in-line hologram. Deconvolving the volumetric reconstruction with an optimal kernel derived from the Rayleigh-Sommerfeld propagator itself emphasizes the objects responsible for the scattering pattern while suppressing both the propagating light and also such artifacts as the twin image. Bright features in the deconvolved volume may be identified with such objects as colloidal spheres and nanorods. Tracking their thermally-driven Brownian motion through multiple holographic video images provides estimates of the tracking resolution, which approaches 1 nm in all three dimensions.},
  language = {EN},
  timestamp = {2016-08-06T16:16:00Z},
  number = {17},
  urldate = {2016-03-28},
  journal = {Optics Express},
  author = {Dixon, Lisa and Cheong, Fook Chiong and Grier, David G.},
  month = aug,
  year = {2011},
  keywords = {deconvolution,holo,holography,lab_grier},
  pages = {16410--16417},
  file = {Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/JTKR6D25/abstract.html:text/html}
}

@article{sivia_analysis_1991,
  title = {Analysis of neutron reflectivity data: maximum entropy, {{Bayesian}} spectral analysis and speckle holography},
  volume = {173},
  issn = {0921-4526},
  shorttitle = {Analysis of neutron reflectivity data},
  doi = {10.1016/0921-4526(91)90042-D},
  abstract = {The analysis of neutron reflectivity data to obtain nuclear scattering length density profiles is akin to the notorious phaseless Fourier problem, well known in many fields such as crystallography. Current methods of analysis culminate in the refinement of a few parameters of a functional model, and are often preceded by a long and laborious process of trial and error. We start by discussing the use of maximum entropy for obtaining ``free-form'' solutions of the density profile, as an alternative to the trail and error phase when a functional model is not available. Next we consider a Bayesian spectral analysis approach, which is appropriate for optimising the parameters of a simple (but adequate) type of model when the number of parameters is not known. Finally, we suggest a novel experimental procedure, the analogue of astronomical speckle holography, designed to alleviate the ambiguity problems inherent in traditional reflectivity measurements.},
  timestamp = {2016-08-06T11:20:31Z},
  number = {1\textendash{}2},
  urldate = {2016-02-12},
  journal = {Physica B: Condensed Matter},
  author = {Sivia, D. S. and Hamilton, W. A. and Smith, G. S.},
  month = aug,
  year = {1991},
  pages = {121--138}
}

@article{cheong_flow_2009,
  title = {Flow visualization and flow cytometry with holographic video microscopy},
  volume = {17},
  issn = {1094-4087},
  doi = {10.1364/OE.17.013071},
  language = {en},
  timestamp = {2016-08-06T16:15:54Z},
  number = {15},
  urldate = {2016-07-27},
  journal = {Optics Express},
  author = {Cheong, Fook Chiong and {R{\'e}mi Dreyfus}, Bo Sun and Amato-Grill, Jesse and Xiao, Ke and Dixon, Lisa and Grier, David G.},
  month = jul,
  year = {2009},
  keywords = {Digital holography,Image analysis,Three-dimensional microscopy,Velocimetry},
  pages = {13071}
}

@article{dimiduk_random-subset_2014,
  title = {Random-subset fitting of digital holograms for fast three-dimensional particle tracking},
  volume = {53},
  doi = {10.1364/AO.53.00G177},
  abstract = {Fitting scattering solutions to time series of digital holograms is a precise way to measure three-dimensional dynamics of microscale objects such as colloidal particles. However, this inverse-problem approach is computationally expensive. We show that the computational time can be reduced by an order of magnitude or more by fitting to a random subset of the pixels in a hologram. We demonstrate our algorithm on experimentally measured holograms of micrometer-scale colloidal particles, and we show that 20-fold increases in speed, relative to fitting full frames, can be attained while introducing errors in the particle positions of 10 nm or less. The method is straightforward to implement and works for any scattering model. It also enables a parallelization strategy wherein random-subset fitting is used to quickly determine initial guesses that are subsequently used to fit full frames in parallel. This approach may prove particularly useful for studying rare events, such as nucleation, that can only be captured with high frame rates over long times.},
  timestamp = {2016-08-06T16:33:19Z},
  number = {27},
  urldate = {2014-08-26},
  journal = {Applied Optics},
  author = {Dimiduk, Thomas G. and Perry, Rebecca W. and Fung, Jerome and Manoharan, Vinothan N.},
  month = sep,
  year = {2014},
  keywords = {+Holographic,microscopy},
  pages = {G177--G183},
  file = {Dimiduk et al_2014_Random-subset fitting of digital holograms for fast three-dimensional particle.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/T8BG6KFW/Dimiduk et al_2014_Random-subset fitting of digital holograms for fast three-dimensional particle.pdf:application/pdf;Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/E5EW345V/12748673.html:text/html}
}

@article{denis_inline_2009,
  title = {Inline hologram reconstruction with sparsity constraints},
  volume = {34},
  issn = {1539-4794},
  doi = {10.1364/OL.34.003475},
  abstract = {Inline digital holograms are classically reconstructed using linear operators to model diffraction. It has long been recognized that such reconstruction operators do not invert the hologram formation operator. Classical linear reconstructions yield images with artifacts such as distortions near the field-of-view boundaries or twin images. When objects located at different depths are reconstructed from a hologram, in-focus and out-of-focus images of all objects superimpose upon each other. Additional processing, such as maximum-of-focus detection, is thus unavoidable for any successful use of the reconstructed volume. In this Letter, we consider inverting the hologram formation model in a Bayesian framework. We suggest the use of a sparsity-promoting prior, verified in many inline holography applications, and present a simple iterative algorithm for 3D object reconstruction under sparsity and positivity constraints. Preliminary results with both simulated and experimental holograms are highly promising.},
  language = {EN},
  timestamp = {2016-08-06T16:33:07Z},
  number = {22},
  urldate = {2016-02-12},
  journal = {Optics Letters},
  author = {Denis, L{\"o}ic and Lorenz, Dirk and Thi{\'e}baut, Eric and Fournier, Corinne and Trede, Dennis},
  month = nov,
  year = {2009},
  keywords = {Bayes' theorem,holography,reconstruction},
  pages = {3475--3477}
}

@article{perry_real-space_2012,
  title = {Real-space studies of the structure and dynamics of self-assembled colloidal clusters},
  issn = {1359-6640, 1364-5498},
  doi = {10.1039/c2fd20061a},
  timestamp = {2016-08-06T16:34:06Z},
  urldate = {2012-08-31},
  journal = {Faraday Discussions},
  author = {Perry, Rebecca W. and Meng, Guangnan and Dimiduk, Thomas G. and Fung, Jerome and Manoharan, Vinothan N.},
  year = {2012},
  file = {c2fd20061a.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/234H2ACI/c2fd20061a.pdf:application/pdf;Perry et al_2012_Real-space studies of the structure and dynamics of self-assembled colloidal.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/JJQK4SJ6/Perry et al_2012_Real-space studies of the structure and dynamics of self-assembled colloidal.pdf:application/pdf;Real-space studies of the structure and dynamics of self-assembled colloidal clusters - Faraday Discussions (RSC Publishing):/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/7AMWNDDA/C2FD20061A.html:text/html;Real-space studies of the structure and dynamics of self-assembled colloidal clusters - Faraday Discussions (RSC Publishing):/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/7HSKVXCK/C2FD20061A.html:text/html}
}

@article{ovryn_three-dimensional_2000,
  title = {Three-dimensional forward scattering particle image velocimetry applied to a microscopic field-of-view},
  volume = {29},
  issn = {0723-4864, 1432-1114},
  doi = {10.1007/s003480070019},
  abstract = {We have completed a model to predict the three-dimensional position of a spherical particle from the image formed by a high numerical aperture microscope. Although this information may be exploited in a number of different ways, we are particularly interested in determining the three components of velocity for seed particles following a flow. The basis of the model is to use Mie theory to determine the complete electromagnetic field scattered by a spherical particle and then to propagate the scattered field across the interface between sample and air and then through a high aperture microscope and ultimately to a detector.},
  language = {en},
  timestamp = {2016-08-06T11:19:37Z},
  number = {1},
  urldate = {2014-04-07},
  journal = {Experiments in Fluids},
  author = {Ovryn, B.},
  month = dec,
  year = {2000},
  keywords = {*read,holography,Light scattering,mie,propagation},
  pages = {S175--S184}
}

@article{wang_celebrating_2015,
  title = {Celebrating {{Soft Matter}}'s 10th {{Anniversary}}: {{Monitoring}} colloidal growth with holographic microscopy},
  volume = {11},
  issn = {1744-6848},
  shorttitle = {Celebrating {{Soft Mattertextquoterights}} 10th {{Anniversary}}},
  doi = {10.1039/C4SM01979B},
  abstract = {Holographic video microscopy offers valuable and previously unavailable insights into the progress of colloidal synthesis by providing measurements of the size and refractive index of individual colloidal particles in the dispersion. These measurements are precise enough to track subtle changes in particles' properties and rapid enough for real-time process control. We demonstrate this technique by applying it to the synthesis of monodisperse samples of crosslinked polydimethysiloxane (PDMS) spheres. The measured time dependence of these spheres' most probable radius is consistent with the LaMer model for colloidal growth. The joint distribution of size and refractive index, however, also reveals a small proportion of undersize, lower-density spheres. Trends in the distribution's time evolution offer insights into their origin. Applied over longer time periods, holographic characterization also tracks how the newly-synthesized spheres age, and illuminates the aging mechanism.},
  language = {en},
  timestamp = {2016-08-06T16:34:22Z},
  number = {6},
  urldate = {2016-07-26},
  journal = {Soft Matter},
  author = {Wang, Chen and Shpaisman, Hagay and Hollingsworth, Andrew D. and Grier, David G.},
  year = {2015},
  pages = {1062--1066}
}

@article{yevick_machine-learning_2014,
  title = {Machine-learning approach to holographic particle characterization},
  volume = {22},
  copyright = {\textcopyright{} 2014 Optical Society of America},
  issn = {1094-4087},
  doi = {10.1364/OE.22.026884},
  abstract = {Holograms of colloidal dispersions encode comprehensive information about individual particlestextquoteright three-dimensional positions, sizes and optical properties. Extracting that information typically is computationally intensive, and thus slow. Here, we demonstrate that machine-learning techniques based on support vector machines (SVMs) can analyze holographic video microscopy data in real time on low-power computers. The resulting stream of precise particle-resolved tracking and characterization data provides unparalleled insights into the composition and dynamics of colloidal dispersions and enables applications ranging from basic research to process control and quality assurance.},
  language = {EN},
  timestamp = {2016-08-06T11:19:11Z},
  number = {22},
  urldate = {2016-02-09},
  journal = {Optics Express},
  author = {Yevick, Aaron and Hannel, Mark and Grier, David G.},
  month = nov,
  year = {2014},
  pages = {26884--26890}
}

@article{wang_holographic_2016,
  title = {Holographic {{Characterization}} of {{Protein Aggregates}}},
  volume = {105},
  issn = {0022-3549},
  doi = {10.1016/j.xphs.2015.12.018},
  abstract = {We demonstrate how holographic video microscopy can be used to detect, count, and characterize individual micrometer-scale protein aggregates as they flow down a microfluidic channel in their native buffer. Holographic characterization directly measures the radius and refractive index of subvisible protein aggregates and offers insights into their morphologies. The measurement proceeds fast enough to build up population averages for time-resolved studies and lends itself to tracking trends in protein aggregation arising from changing environmental factors. Information on individual particle's refractive indexes can be used to differentiate protein aggregates from such contaminants as silicone droplets. These capabilities are demonstrated through measurements on samples of bovine pancreas insulin aggregated through centrifugation and of bovine serum albumin aggregated by complexation with a polyelectrolyte. Differentiation is demonstrated with samples that have been spiked with separately characterized silicone spheres. Holographic characterization measurements are compared with results obtained with microflow imaging and dynamic light scattering.},
  timestamp = {2016-08-06T16:34:25Z},
  number = {3},
  urldate = {2016-07-26},
  journal = {Journal of Pharmaceutical Sciences},
  author = {Wang, Chen and Zhong, Xiao and Ruffner, David B. and Stutt, Alexandra and Philips, Laura A. and Ward, Michael D. and Grier, David G.},
  month = mar,
  year = {2016},
  keywords = {aggregation,biopharmaceuticals characterization,biopharmaceuticals characterization,Colloids,Colloids,digital,holography,Light scattering,Light scattering,microfluidic,microparticles,microparticles,Microscopy,microscopy,particle size,particle size,particle size measurement,protein,protein aggregation,protein aggregation},
  pages = {1074--1085},
  file = {Wang et al_Holographic Characterization of Protein Aggregates.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/JNTUDSVX/Wang et al_Holographic Characterization of Protein Aggregates.pdf:application/pdf;ScienceDirect Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/WFMAQXFK/S0022354915002488.html:text/html}
}

@article{soulez_inverse-problem_2007,
  title = {Inverse-problem approach for particle digital holography: accurate location based on local optimization},
  volume = {24},
  issn = {1520-8532},
  shorttitle = {Inverse-problem approach for particle digital holography},
  doi = {10.1364/JOSAA.24.001164},
  language = {EN},
  timestamp = {2016-08-06T16:34:17Z},
  number = {4},
  urldate = {2016-02-12},
  journal = {JOSA A},
  author = {Soulez, Ferr{\'e}ol and Denis, L{\"o}ic and Fournier, Corinne and Thi{\'e}baut, {\'E}ric and Goepfert, Charles},
  month = apr,
  year = {2007},
  keywords = {fitting,holo,holography},
  pages = {1164--1171},
  file = {Soulez et al_2007_Inverse-problem approach for particle digital holography.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/7S7F77BS/Soulez et al_2007_Inverse-problem approach for particle digital holography.pdf:application/pdf;J. Opt. Soc. Am. A Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/MAFD8ISI/abstract.html:text/html}
}

@article{rahmani_colloidal_2016,
  title = {Colloidal particle adsorption at liquid interfaces: {{Capillary}} driven dynamics and thermally activated kinetics},
  shorttitle = {Colloidal particle adsorption at liquid interfaces},
  abstract = {The adsorption of single colloidal microparticles (0.5--1 \$\ensuremath{\backslash}mu\$m radius) at a water-oil interface has been recently studied experimentally using digital holographic microscopy [Kaz \ensuremath{\backslash}textit\{et al., Nat. Mater.\}, 2012, \ensuremath{\backslash}textbf\{11\}, 138--142]. An initially fast adsorption dynamics driven by capillary forces is followed by an unexpectedly slow relaxation to equilibrium that is logarithmic in time and can span hours or days. The slow relaxation kinetics has been attributed to the presence of surface "defects" with nanoscale dimensions (1--5\ensuremath{\backslash},nm) that induce multiple metastable configurations of the contact line perimeter. A kinetic model considering thermally activated transitions between such metastable configurations has been proposed [Colosqui \ensuremath{\backslash}textit\{et al., Phys. Rev. Lett.\}, 2013, \ensuremath{\backslash}textbf\{111\}, 028302] to predict both the relaxation rate and the crossover point to the slow logarithmic regime. However, the adsorption dynamics observed experimentally before the crossover point has remained unstudied. In this work, we propose a Langevin model that is able to describe the entire adsorption process of single colloidal particles by considering metastable states produced by surface defects and thermal motion of the particle and liquid interface. Invoking the fluctuation dissipation theorem, we introduce a drag term that considers significant dissipative forces induced by thermal fluctuations of the liquid interface. Langevin dynamics simulations based on the proposed adsorption model yield close agreement with experimental observations for different microparticles, capturing the crossover from (fast) capillary driven dynamics to (slow) thermally activated kinetics.},
  timestamp = {2016-08-06T16:34:15Z},
  archivePrefix = {arXiv},
  eprinttype = {arxiv},
  eprint = {1604.06836},
  urldate = {2016-07-27},
  journal = {arXiv:1604.06836 [cond-mat]},
  author = {Rahmani, Amir M. and Wang, Anna and Manoharan, Vinothan N. and Colosqui, Carlos E.},
  month = apr,
  year = {2016},
  keywords = {-,Condensed,Matter,Soft}
}

@article{kaz_physical_2012,
  title = {Physical ageing of the contact line on colloidal particles at liquid interfaces},
  volume = {11},
  copyright = {\textcopyright{} 2011 Nature Publishing Group},
  issn = {1476-1122},
  doi = {10.1038/nmat3190},
  abstract = {Youngtextquoterights law predicts that a colloidal sphere in equilibrium with a liquid interface will straddle the two fluids, its height above the interface defined by an equilibrium contact angle. This has been used to explain why colloids often bind to liquid interfaces, and has been exploited in emulsification, water purification, mineral recovery, encapsulation and the making of nanostructured materials. However, little is known about the dynamics of binding. Here we show that the adsorption of polystyrene microspheres to a water/oil interface is characterized by a sudden breach and an unexpectedly slow relaxation. The relaxation appears logarithmic in time, indicating that complete equilibration may take months. Surprisingly, viscous dissipation appears to play little role. Instead, the observed dynamics, which bear strong resemblance to ageing in glassy systems, agree well with a model describing activated hopping of the contact line over nanoscale surface heterogeneities. These results may provide clues to longstanding questions on colloidal interactions at an interface.},
  language = {en},
  timestamp = {2016-08-06T16:33:45Z},
  number = {2},
  urldate = {2016-02-23},
  journal = {Nature Materials},
  author = {Kaz, David M. and McGorty, Ryan and Mani, Madhav and Brenner, Michael P. and Manoharan, Vinothan N.},
  month = feb,
  year = {2012},
  keywords = {Colloids,Colloids,Computation,interfaces and thin films,modelling and theory,Surfaces,Theory and computation},
  pages = {138--142},
  file = {[PDF] from harvard.edu:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/FT7KHP98/Kaz et al. - 2011 - Physical ageing of the contact line on colloidal p.pdf:application/pdf;Full Text PDF:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/WEXBEECA/Kaz et al. - 2012 - Physical ageing of the contact line on colloidal p.pdf:application/pdf;Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/G4ARXEJK/nmat3190.html:text/html;Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/NXQSJHNQ/nmat3190.html:text/html}
}

@article{foreman-mackey_emcee:_2013,
  title = {emcee: {{The MCMC Hammer}}},
  volume = {125},
  issn = {00046280, 15383873},
  shorttitle = {emcee},
  doi = {10.1086/670067},
  abstract = {We introduce a stable, well tested Python implementation of the affine-invariant ensemble sampler for Markov chain Monte Carlo (MCMC) proposed by Goodman \& Weare (2010). The code is open source and has already been used in several published projects in the astrophysics literature. The algorithm behind emcee has several advantages over traditional MCMC sampling methods and it has excellent performance as measured by the autocorrelation time (or function calls per independent sample). One major advantage of the algorithm is that it requires hand-tuning of only 1 or 2 parameters compared to \$\ensuremath{\backslash}sim Ntextasciicircum2\$ for a traditional algorithm in an N-dimensional parameter space. In this document, we describe the algorithm and the details of our implementation and API. Exploiting the parallelism of the ensemble method, emcee permits any user to take advantage of multiple CPU cores without extra effort. The code is available online at http://dan.iel.fm/emcee under the MIT License.},
  timestamp = {2016-08-06T11:20:15Z},
  number = {925},
  urldate = {2016-07-26},
  journal = {Publications of the Astronomical Society of the Pacific},
  author = {Foreman-Mackey, Daniel and Hogg, David W. and Lang, Dustin and Goodman, Jonathan},
  month = mar,
  year = {2013},
  keywords = {Astrophysics - Instrumentation and Methods for Astrophysics,Physics - Computational Physics,Statistics - Computation},
  pages = {306--312}
}

@article{fung_imaging_2012,
  title = {Imaging {{Multiple Colloidal Particles}} by {{Fitting Electromagnetic Scattering Solutions}} to {{Digital Holograms}}},
  volume = {113},
  doi = {10.1016/j.jqsrt.2012.06.007},
  abstract = {Digital holographic microscopy is a fast three-dimensional (3D) imaging tool with many applications in soft matter physics. Recent studies have shown that electromagnetic scattering solutions can be fit to digital holograms to obtain the 3D positions of isolated colloidal spheres with nanometer precision and millisecond temporal resolution. Here we describe the results of new techniques that extend the range of systems that can be studied with fitting. We show that an exact multisphere superposition scattering solution can fit holograms of colloidal clusters containing up to six spheres. We also introduce an approximate and computationally simpler solution, Mie superposition, that is valid for multiple spheres spaced several wavelengths or more from one another. We show that this method can be used to analyze holograms of several spheres on an emulsion droplet, and we give a quantitative criterion for assessing its validity.},
  timestamp = {2016-08-06T16:33:37Z},
  number = {18},
  journal = {Journal of Quantitative Spectroscopy and Radiative Transfer},
  author = {Fung, Jerome and Perry, Rebecca W. and Dimiduk, Thomas G. and Manoharan, Vinothan N.},
  month = dec,
  year = {2012},
  keywords = {+Holographic,microscopy},
  pages = {2482--2489},
  file = {ScienceDirect Full Text PDF:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/EW8VQTJN/Fung et al. - Imaging multiple colloidal particles by fitting el.pdf:application/pdf;Fung et al_2012_Imaging multiple colloidal particles by fitting electromagnetic scattering.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/T4QZW3N9/Fung et al_2012_Imaging multiple colloidal particles by fitting electromagnetic scattering.pdf:application/pdf;ScienceDirect Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/2US9VNWB/S0022407312002890.html:text/html}
}

@article{cheong_holographic_2009,
  title = {Holographic microrheology of polysaccharides from {{Streptococcus}} mutans biofilms},
  volume = {48},
  issn = {0035-4511, 1435-1528},
  doi = {10.1007/s00397-008-0320-1},
  abstract = {We use three-dimensional holographic particle tracking to perform microrheological measurements of model gelled media, including the polysaccharide pellicle of dental biofilms created by the common cariogenic oral pathogen Streptococcus mutans. Nanometer-resolution video-rate holographic tracking of embedded colloidal spheres provides accurate measurements of the gelstextquoteright complex viscoelastic moduli, including insights into these propertiestextquoteright heterogeneity. When applied to polysaccharides of S. mutans biofilms, these techniques promise quantitative microscopic assays for candidate therapeutic agents against cariogenic dental biofilms.},
  language = {en},
  timestamp = {2016-08-06T16:32:51Z},
  number = {1},
  urldate = {2013-10-13},
  journal = {Rheologica Acta},
  author = {Cheong, Fook Chiong and Duarte, Simone and Lee, Sang-Hyuk and Grier, David G.},
  month = jan,
  year = {2009},
  keywords = {bacteria,biofilm,gel,holography,microrheology,microscopy},
  pages = {109--115}
}

@article{ovryn_imaging_2000,
  title = {Imaging of transparent spheres through a planar interface using a high-numerical-aperture optical microscope},
  volume = {17},
  doi = {10.1364/JOSAA.17.001202},
  abstract = {The details of a model used to predict the scattering of a plane polarized wave by a spherical particle as observed with a microscope are presented. The model accounts for the effect of a refractive interface on the outgoing scattered field and determines the image produced by a lens with high numerical aperture. The predictions of the model are verified by direct comparison with the experimentally observed scattering from polystyrene spheres in a fluid.},
  timestamp = {2016-08-06T16:16:34Z},
  number = {7},
  urldate = {2014-02-19},
  journal = {Journal of the Optical Society of America A},
  author = {Ovryn, Ben and Izen, Steven H.},
  month = jul,
  year = {2000},
  keywords = {Mie theory,Mie theory,Modulation transfer function,Modulation transfer function,Scattering measurements,Scattering measurements,Three-dimensional microscopy,Three-dimensional microscopy},
  pages = {1202--1213}
}

@article{marquardt_algorithm_1963,
  title = {An {{Algorithm}} for {{Least-Squares Estimation}} of {{Nonlinear Parameters}}},
  volume = {11},
  issn = {0368-4245},
  timestamp = {2016-08-06T16:33:59Z},
  number = {2},
  urldate = {2016-07-28},
  journal = {Journal of the Society for Industrial and Applied Mathematics},
  author = {Marquardt, Donald W.},
  year = {1963},
  keywords = {algorithm,inference,maximum likelihood,nonlinear,optimization},
  pages = {431--441}
}

@article{wang_using_2014,
  series = {Electromagnetic and Light Scattering by Nonspherical Particles XIV},
  title = {Using the discrete dipole approximation and holographic microscopy to measure rotational dynamics of non-spherical colloidal particles},
  volume = {146},
  issn = {0022-4073},
  doi = {10.1016/j.jqsrt.2013.12.019},
  abstract = {We present a new, high-speed technique to track the three-dimensional translation and rotation of non-spherical colloidal particles. We capture digital holograms of micrometer-scale silica rods and sub-micrometer-scale Janus particles freely diffusing in water, and then fit numerical scattering models based on the discrete dipole approximation to the measured holograms. This inverse-scattering approach allows us to extract the position and orientation of the particles as a function of time, along with static parameters including the size, shape, and refractive index. The best-fit sizes and refractive indices of both particles agree well with expected values. The technique is able to track the center of mass of the rod to a precision of 35 nm and its orientation to a precision of 1.5\ensuremath{^\circ}, comparable to or better than the precision of other 3D diffusion measurements on non-spherical particles. Furthermore, the measured translational and rotational diffusion coefficients for the silica rods agree with hydrodynamic predictions for a spherocylinder to within 0.3\%. We also show that although the Janus particles have only weak optical asymmetry, the technique can track their 2D translation and azimuthal rotation over a depth of field of several micrometers, yielding independent measurements of the effective hydrodynamic radius that agree to within 0.2\%. The internal and external consistency of these measurements validate the technique. Because the discrete dipole approximation can model scattering from arbitrarily shaped particles, our technique could be used in a range of applications, including particle tracking, microrheology, and fundamental studies of colloidal self-assembly or microbial motion.},
  timestamp = {2016-08-09T19:51:21Z},
  urldate = {2016-02-10},
  journal = {Journal of Quantitative Spectroscopy and Radiative Transfer},
  author = {Wang, Anna and Dimiduk, Thomas G. and Fung, Jerome and Razavi, Sepideh and Kretzschmar, Ilona and Chaudhary, Kundan and Manoharan, Vinothan N.},
  month = oct,
  year = {2014},
  keywords = {Colloids,Colloids,Diffusion,diffusion,Digital holography,Digital holography,Discrete dipole approximation,Discrete dipole approximation,Light scattering,Light scattering,Non-spherical,Non-spherical},
  pages = {499--509},
  file = {Wang et al_Using the discrete dipole approximation and holographic microscopy to measure.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/U4QISS5G/Wang et al_Using the discrete dipole approximation and holographic microscopy to measure.pdf:application/pdf;ScienceDirect Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/AJ2FMR5W/S0022407314000028.html:text/html}
}

@book{gregory_bayesian_2005,
  title = {Bayesian {{Logical Data Analysis}} for the {{Physical Sciences}}: {{A Comparative Approach}} with {{Mathematica}}\textsuperscript{\textregistered{}} {{Support}}},
  isbn = {978-0-521-84150-4},
  shorttitle = {Bayesian {{Logical Data Analysis}} for the {{Physical Sciences}}},
  abstract = {Bayesian inference provides a simple and unified approach to data analysis, allowing experimenters to assign probabilities to competing hypotheses of interest, on the basis of the current state of knowledge. By incorporating relevant prior information, it can sometimes improve model parameter estimates by many orders of magnitude. This book provides a clear exposition of the underlying concepts with many worked examples and problem sets. It also discusses implementation, including an introduction to Markov chain Monte-Carlo integration and linear and nonlinear model fitting. Particularly extensive coverage of spectral analysis (detecting and measuring periodic signals) includes a self-contained introduction to Fourier and discrete Fourier methods. There is a chapter devoted to Bayesian inference with Poisson sampling, and three chapters on frequentist methods help to bridge the gap between the frequentist and Bayesian approaches. Supporting Mathematica\textregistered{} notebooks with solutions to selected problems, additional worked examples, and a Mathematica tutorial are available at www.cambridge.org/9780521150125.},
  language = {en},
  timestamp = {2016-08-25T20:01:00Z},
  publisher = {{Cambridge University Press}},
  author = {Gregory, Phil},
  month = apr,
  year = {2005},
  keywords = {Mathematics / Geometry / General,Mathematics / Probability \& Statistics / Bayesian Analysis,Mathematics / Probability \& Statistics / General,Science / Physics / Astrophysics}
}

@article{fung_measuring_2011,
  title = {Measuring translational, rotational, and vibrational dynamics in colloids with digital holographic microscopy},
  volume = {19},
  issn = {1094-4087},
  doi = {10.1364/OE.19.008051},
  language = {en},
  timestamp = {2016-08-06T16:33:26Z},
  number = {9},
  urldate = {2016-07-26},
  journal = {Optics Express},
  author = {Fung, Jerome and Martin, K. Eric and Perry, Rebecca W. and Kaz, David M. and McGorty, Ryan and Manoharan, Vinothan N.},
  month = apr,
  year = {2011},
  keywords = {Digital holography,Digital holography,Scattering measurements,Scattering measurements,Three-dimensional microscopy,Three-dimensional microscopy},
  pages = {8051}
}

@article{stober_controlled_1968,
  title = {Controlled growth of monodisperse silica spheres in the micron size range},
  volume = {26},
  issn = {0021-9797},
  doi = {10.1016/0021-9797(68)90272-5},
  abstract = {A system of chemical reactions has been developed which permits the controlled growth of spherical silica particles of uniform size by means of hydrolysis of alkyl silicates and subsequent condensation of silicic acid in alcoholic solutions. Ammonia is used as a morphological catalyst. Particle sizes obtained in suspension range from less than 0.05 \ensuremath{\mu} to 2 \ensuremath{\mu} in diameter.},
  timestamp = {2016-08-06T11:30:10Z},
  number = {1},
  urldate = {2013-10-14},
  journal = {Journal of Colloid and Interface Science},
  author = {St{\"o}ber, Werner and Fink, Arthur and Bohn, Ernst},
  month = jan,
  year = {1968},
  pages = {62--69}
}

@article{chen_rheological_2003,
  title = {Rheological {{Microscopy}}: {{Local Mechanical Properties}} from {{Microrheology}}},
  volume = {90},
  shorttitle = {Rheological {{Microscopy}}},
  doi = {10.1103/PhysRevLett.90.108301},
  abstract = {We demonstrate how tracer microrheology methods can be extended to study submicron scale variations in the viscoelastic response of soft materials; in particular, a semidilute solution of \ensuremath{\lambda}-DNA. The polymer concentration is depleted near the surfaces of the tracer particles, within a distance comparable to the polymer correlation length. The rheology of this microscopic layer alters the tracers' motion and can be precisely quantified using one- and two-point microrheology. Interestingly, we found this mechanically distinct layer to be twice as thick as the layer of depleted concentration, likely due to solvent drainage through the locally perturbed polymer structure.},
  timestamp = {2016-08-06T11:33:02Z},
  number = {10},
  urldate = {2013-10-11},
  journal = {Physical Review Letters},
  author = {Chen, D. T. and Weeks, E. R. and Crocker, J. C. and Islam, M. F. and Verma, R. and Gruber, J. and Levine, A. J. and Lubensky, T. C. and Yodh, A. G.},
  month = mar,
  year = {2003},
  pages = {108301}
}

@article{sheng_digital_2007,
  title = {Digital holographic microscopy reveals prey-induced changes in swimming behavior of predatory dinoflagellates},
  volume = {104},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.0704658104},
  abstract = {The shallow depth of field of conventional microscopy hampers analyses of 3D swimming behavior of fast dinoflagellates, whose motility influences macroassemblages of these cells into often-observed dense ``blooms.'' The present analysis of cinematic digital holographic microscopy data enables simultaneous tracking and characterization of swimming of thousands of cells within dense suspensions. We focus on Karlodinium veneficum and Pfiesteria piscicida, mixotrophic and heterotrophic dinoflagellates, respectively, and their preys. Nearest-neighbor distance analysis shows that predator and prey cells are randomly distributed relative to themselves, but, in mixed culture, each predator clusters around its respective prey. Both dinoflagellate species exhibit complex highly variable swimming behavior as characterized by radius and pitch of helical swimming trajectories and by translational and angular velocity. K. veneficum moves in both left- and right-hand helices, whereas P. piscicida swims only in right-hand helices. When presented with its prey (Storeatula major), the slower K. veneficum reduces its velocity, radius, and pitch but increases its angular velocity, changes that reduce its hydrodynamic signature while still scanning its environment as ``a spinning antenna.'' Conversely, the faster P. piscicida increases its speed, radius, and angular velocity but slightly reduces its pitch when exposed to prey (Rhodomonas sp.), suggesting the preferred predation tactics of an ``active hunter.''},
  language = {en},
  timestamp = {2016-08-06T16:16:46Z},
  number = {44},
  urldate = {2014-04-21},
  journal = {Proceedings of the National Academy of Sciences},
  author = {Sheng, Jian and Malkiel, Edwin and Katz, Joseph and Adolf, Jason and Belas, Robert and Place, Allen R.},
  month = oct,
  year = {2007},
  keywords = {autofocus,bio,holo,holography,lab_katz,microscopy,z_elongation},
  pages = {17512--17517},
  file = {sheng2007dhm_swimming_behavior.pdf:/home/tdimiduk/documents/holography/sheng2007dhm_swimming_behavior.pdf:application/pdf;Digital holographic microscopy reveals prey-induced changes in swimming behavior of predatory dinoflagellates — PNAS:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/BT84NGR4/17512.full.html:text/html}
}

@article{pu_intrinsic_2003,
  title = {Intrinsic aberrations due to {{Mie}} scattering in particle holography},
  volume = {20},
  doi = {10.1364/JOSAA.20.001920},
  abstract = {Holography of small particles is a newly revived topic because of its importance in holographic particle image velocimetry (HPIV). However, the property of particle images formed through holography remains largely unexplored. This fact undermines the measurement reliability of HPIV techniques and has become one of the obstacles in the full deployment of HPIV. We study the intrinsic aberrations in the holographic particle image introduced by particle light scattering and investigate how accurately holography can deliver information about the particles that are being imaged. Consistent with our experimental observations, simulations based on Mie scattering theory show that even with a perfect hologram the reconstructed particle images demonstrate complex three-dimensional morphologies and bodily shifts. These characteristics, manifested as image aberrations, result from uneven scattering amplitude and phase distributions across the finite aperture of the hologram. Such aberrations degrade the signal-to-noise ratio in the reconstructed image as well as introducing systematic errors in detected particle image positions. We examine the effect of these aberrations on HPIV measurements.},
  timestamp = {2016-08-06T16:34:12Z},
  number = {10},
  urldate = {2013-10-11},
  journal = {Journal of the Optical Society of America A},
  author = {Pu, Ye and Meng, Hui},
  month = oct,
  year = {2003},
  keywords = {aberration,Diffraction,Diffraction,digital,holography,holography,Light scattering,mie,Mie theory,Mie theory,particle tracking,piv},
  pages = {1920--1932}
}

@article{earl_parallel_2005,
  title = {Parallel tempering: {{Theory}}, applications, and new perspectives},
  volume = {7},
  issn = {1463-9076},
  shorttitle = {Parallel tempering},
  doi = {10.1039/B509983H},
  abstract = {We review the history of the parallel tempering simulation method. From its origins in data analysis, the parallel tempering method has become a standard workhorse of physiochemical simulations. We discuss the theory behind the method and its various generalizations. We mention a selected set of the many applications that have become possible with the
introduction of parallel tempering and we suggest several promising avenues for future research.},
  timestamp = {2016-08-06T16:32:42Z},
  urldate = {2016-08-03},
  journal = {Physical Chemistry Chemical Physics (Incorporating Faraday Transactions)},
  author = {Earl, David J. and Deem, Michael W.},
  year = {2005},
  pages = {3910}
}

@book{einstein_investigations_1956,
  title = {Investigations on the {{Theory}} of the {{Brownian Movement}}},
  timestamp = {2016-08-06T11:28:02Z},
  publisher = {{Dover, New York}},
  author = {Einstein, Albert},
  year = {1956}
}

@article{weitz_dynamics_1984,
  title = {Dynamics of {{Diffusion-Limited Kinetic Aggregation}}},
  volume = {53},
  abstract = {We study the dynamics of diffusion-limited cluster-cluster aggregation of aqueous colloids using quasielastic light scattering. Scaling behavior is found for the dependence of the mean cluster size on both time and initial concentration, and limits are placed on the scaling exponents of the cluster mass distribution. The fractal nature of the resultant clusters directly affects the exponents, illustrating the inherent relationship between the dynamic and static properties of kinetic aggregation processes.},
  timestamp = {2016-08-06T11:29:59Z},
  number = {17},
  urldate = {2013-10-13},
  journal = {Physical Review Letters},
  author = {Weitz, D. A. and Huang, J. S. and Lin, M. Y. and Sung, J.},
  month = oct,
  year = {1984},
  keywords = {aggregation,cluster,colloid,diffusion,dynamics,fractal,Light scattering},
  pages = {1657--1660}
}

@article{yoshizaki_dynamics_1980,
  title = {Dynamics of spheroid-cylindrical molecules in dilute solution},
  volume = {72},
  issn = {00219606},
  abstract = {The dilute solution dynamics of spheroid\textendash{}cylindrical molecules, i.e., straight cylinders with oblate, spherical, or prolate hemispheroid caps at the ends, is studied in detail. The translational and rotatory diffusion coefficients and the dynamic intrinsic viscosity are evaluated numerically for short cylinders by determining the frictional force by an orthodox method of classical hydrodynamics. For long cylinders, the Oseen\textendash{}Burgers procedure is shown to be valid, and the results previously obtained by it are still useful. Thus, empirical interpolation formulas for the transport coefficients above are also constructed to be applied to spheroid\textendash{}cylinders of arbitrary size. The end effects on the translational and rotatory diffusion coefficients are rather small, while the effect on the zero-frequency intrinsic viscosity is remarkable, depending appreciably on the shape of the ends, though for relatively short cylinders. In general, for a rigid body of revolution having a plane of symmetry perpendicular to its axis, it is shown that the dynamic intrinsic viscosity may be expressed in terms of the zero-frequency intrinsic viscosity, the rotatory diffusion coefficient about a principal axis in the symmetry plane, and a newly defined factor, which is also associated with the rotational motion about this axis.},
  timestamp = {2016-08-06T11:28:02Z},
  number = {1},
  urldate = {2013-10-10},
  journal = {Journal of Chemical Physics},
  author = {Yoshizaki, Takenao and Yamakawa, Hiromi},
  month = jan,
  year = {1980},
  pages = {57},
  @url = {http://jcp.aip.org/resource/1/jcpsa6/v72/i1/p57<sub>s</sub>1},
  @doi = {doi:10.1063/1.438945}
}

@article{latychevskaia_depth-resolved_2010,
  title = {Depth-resolved holographic reconstructions by three-dimensional deconvolution},
  volume = {18},
  doi = {10.1364/OE.18.022527},
  abstract = {Methods of three-dimensional deconvolution with a point-spread function as frequently employed in optical microscopy to reconstruct true three-dimensional distribution of objects are extended to holographic reconstructions. Two such schemes have been developed and are discussed: an instant deconvolution using the Wiener filter as well as an iterative deconvolution routine. The instant 3d-deconvolution can be applied to restore the positions of volume-spread objects such as small particles. The iterative deconvolution can be applied to restore the distribution of complex and extended objects. Simulated and experimental examples are presented and demonstrate artifact and noise free three-dimensional reconstructions from a single two-dimensional holographic record.},
  timestamp = {2016-08-06T16:33:52Z},
  number = {21},
  urldate = {2011-06-27},
  journal = {Optics Express},
  author = {Latychevskaia, Tatiana and Gehri, Fabian and Fink, Hans-Werner},
  month = oct,
  year = {2010},
  keywords = {3d,deconvolution,digital,holo,holography,image processing,reconstruction,sectioning},
  pages = {22527--22544}
}

@article{purcell_scattering_1973,
  title = {Scattering and {{Absorption}} of {{Light}} by {{Nonspherical Dielectric Grains}}},
  volume = {186},
  issn = {0004-637X, 1538-4357},
  abstract = {A method is described for calculating approximate extinction, absorption, and scattering cross-sections for dielectric grains of arbitrary shape, with dimensions comparable to or smaller than the wavelength of the incident radiation. The grain is modeled by an array of N polarizable elements in vacuum. The elements are located on a simple cubic lattice, and N is of order of magnitude 100. The polarizability of an element is such that an unbounded array would exhibit, according to the Clausius-Mosotti relation, the bulk dielectric constant of the grain material. The complex vector amplitude of each oscillator in the array, which is driven by the field of the incident wave and the fields of all the other oscillators, is determimed by an iterative procedure. From the N amplitudes all the cross-sections, including differential cross-sections, are obtained. The method was tested by comparing the cross-sections computed for "spherical" clusters of oscillators with exact Mie theory values for the corresponding dielectric spheres. Computed cross-sections are presented for five different grain shapes and three different complex refractive indices.},
  timestamp = {2016-08-11T00:02:05Z},
  urldate = {2013-10-14},
  journal = {The Astrophysical Journal},
  author = {Purcell, Edward M. and Pennypacker, Carlton R.},
  month = dec,
  year = {1973},
  pages = {705--714},
  file = {[HTML] harvard.edu:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/52NKWW7S/0000706.000.html:text/html},
  @url = {http://adsabs.harvard.edu.ezp-prod1.hul.harvard.edu/doi/10.1086/152538},
  @doi = {10.1086/152538}
}

@article{pickering_cxcvi.emulsions_1907-1,
  title = {{{CXCVI}}.\textemdash{}{{Emulsions}}},
  volume = {91},
  issn = {0368-1645},
  doi = {10.1039/CT9079102001},
  abstract = {PICKERING : EMULSIONS. 2001 CXCVI. By SPENCER UMFREVILLE PICKERING, M.A., F.R.S. IN the Sixth Report of the Woburn Experimental Fruit Farm (Eyre and Spottiswoode, 1906) were published the results of an examination of emulsions of paraffin oil in solutions of soft soap, such as are used for insecticidal purposes; t},
  language = {en},
  timestamp = {2016-08-06T10:18:00Z},
  number = {0},
  urldate = {2013-10-11},
  journal = {Journal of the Chemical Society, Transactions},
  author = {Pickering, Spencer Umfreville},
  month = jan,
  year = {1907},
  pages = {2001--2021}
}

@article{mackowski_calculation_1994,
  title = {Calculation of total cross sections of multiple-sphere clusters},
  volume = {11},
  timestamp = {2016-08-06T15:57:32Z},
  number = {11},
  urldate = {2014-04-19},
  journal = {Journal of the Optical Society of America A},
  author = {Mackowski, Daniel W.},
  year = {1994},
  pages = {2851--2861}
}

@article{tirado_comparison_1984,
  title = {Comparison of theories for the translational and rotational diffusion coefficients of rod-like macromolecules. {{Application}} to short {{DNA}} fragments},
  volume = {81},
  issn = {00219606},
  abstract = {Two theories relating the translational and rotational diffusion coefficients Dt and Dr of a rod-like macromolecule to its length and diameter, proposed by Broersma [J. Chem. Phys. 74, 6989 (1981)], and Tirado and Garc{\'\i}a de la Torre [J. Chem. Phys. 71, 2581 (1979); 73, 1986 (1980)] are shown to predict different values of the coefficients for a particle of given dimensions. Next, we use the two theories to analyze existing experimental data of sedimentation coefficients s and translational and rotational diffusion coefficients of short DNA fragments, and obtain values of the hydrated diameter of DNA d which is treated as an adjustable parameter. The results are compared with the expected value, d\ensuremath{\ElsevierGlyph{2242}}26\AA{}. This comparison favors clearly the Tirado\textendash{}Garcia de la Torre theory in the case of Dt and s. For Dr, and using a rise per base pair r=3.4 \AA{}, this theory gives best agreement for all the data examined, while when r=3.3 \AA{}, the agreement depends on the source of data.},
  timestamp = {2016-08-06T11:28:02Z},
  number = {4},
  journal = {Journal of Chemical Physics},
  author = {Tirado, M. Mercedes and Mart\'inez, Carmen L{\'o}pez and {de la Torre}, Jos{\'e} Gar{\'c}ia},
  month = aug,
  year = {1984},
  pages = {2047},
  @url = {http://jcp.aip.org/resource/1/jcpsa6/v81/i4/p2047<sub>s</sub>1},
  @doi = {doi:10.1063/1.447827}
}

@article{goodman_ensemble_2010,
  title = {Ensemble samplers with affine invariance},
  volume = {5},
  issn = {2157-5452, 1559-3940},
  doi = {10.2140/camcos.2010.5.65},
  language = {en},
  timestamp = {2016-08-06T16:32:42Z},
  number = {1},
  urldate = {2016-08-03},
  journal = {Communications in Applied Mathematics and Computational Science},
  author = {Goodman, Jonathan and Weare, Jonathan},
  month = jan,
  year = {2010},
  pages = {65--80}
}

@article{hoffmann_3d_2009,
  title = {{{3D Brownian Diffusion}} of {{Submicron-Sized Particle Clusters}}},
  volume = {3},
  issn = {1936-0851},
  abstract = {We report on the translation and rotation of particle clusters made through the combination of spherical building blocks. These clusters present ideal model systems to study the motion of objects with complex shape. Since they could be separated into fractions of well-defined configurations on a sufficient scale and because their overall dimensions were below 300 nm, the translational and rotational diffusion coefficients of particle doublets, triplets, and tetrahedrons could be determined by a combination of polarized dynamic light scattering (DLS) and depolarized dynamic light scattering (DDLS). The use of colloidal clusters for DDLS experiments overcomes the limitation of earlier experiments on the diffusion of complex objects near surfaces because the true 3D diffusion can be studied. When the exact geometry of the complex assemblies is known, different hydrodynamic models for calculating the diffusion coefficients for objects with complex shapes could be applied. Because hydrodynamic friction must be restricted to the cluster surface, the so-called shell model, in which the surface is represented as a shell of small friction elements, was most suitable to describe the dynamics. A quantitative comparison of the predictions from theoretical modeling with the results obtained by DDLS showed an excellent agreement between experiment and theory.},
  timestamp = {2016-08-06T11:28:38Z},
  number = {10},
  urldate = {2013-10-13},
  journal = {ACS Nano},
  author = {Hoffmann, Martin and Wagner, Claudia S. and Harnau, Ludger and Wittemann, Alexander},
  month = oct,
  year = {2009},
  keywords = {3d,Brownian motion,cluster,colloid,diffusion,dynamics,hydrodynamics,Light scattering},
  pages = {3326--3334}
}

@article{fricks_time-domain_2009,
  title = {Time-domain methods for diffusive transport in soft matter},
  volume = {69},
  timestamp = {2016-08-06T11:33:43Z},
  number = {5},
  urldate = {2013-12-19},
  journal = {SIAM Journal on Applied Mathematics},
  author = {Fricks, John and Yao, Lingxing and Elston, Timothy C. and Forest, M. Gregory},
  year = {2009},
  pages = {1277--1308}
}

@article{pickering_cxcvi.emulsions_1907,
  title = {{{CXCVI}}.--{{Emulsions}}},
  volume = {91},
  issn = {0368-1645},
  abstract = {PICKERING : EMULSIONS. 2001 CXCVI. By SPENCER UMFREVILLE PICKERING, M.A., F.R.S. IN the Sixth Report of the Woburn Experimental Fruit Farm (Eyre and Spottiswoode, 1906) were published the results of an examination of emulsions of paraffin oil in solutions of soft soap, such as are used for insecticidal purposes; t},
  language = {en},
  timestamp = {2016-08-06T11:28:02Z},
  urldate = {2013-10-11},
  journal = {Journal of the Chemical Society, Transactions},
  author = {Pickering, Spencer Umfreville},
  month = jan,
  year = {1907},
  pages = {2001--2021},
  @url = {http://pubs.rsc.org/en/content/articlelanding/1907/ct/ct9079102001},
  @doi = {10.1039/CT9079102001}
}

@article{brenner_taylor_1979,
  title = {Taylor dispersion in systems of sedimenting nonspherical brownian particles. {{I}}. {{Homogeneous}}, centrosymmetric, axisymmetric particles},
  volume = {71},
  issn = {0021-9797},
  doi = {10.1016/0021-9797(79)90232-7},
  abstract = {A recent theory of generalized Taylor dispersion phenomena is applied to the sedimentation of identical, nonneutrally buoyant, axisymmetric, Brownian particles settling in the Stokes-law regime. General expressions are derived for the mean (orientation-averaged) settling velocity {\=U}\ensuremath{_\ast} of the particles and the dispersion about this mean in the general case where the axisymmetric particles may lack fore-aft symmetry and where they may possess an inhomogeneous mass distribution. Specific calculations are carried out for the case where the particles possess a center of symmetry (as, for example, in the case of prolate and oblate spheroids) and are homogeneous. In such circumstances no gravitational couple acts upon the particles and they therefore possess no preferred orientations relative to the direction of the gravity field. The dispersion coefficients, D\=\ensuremath{\Vert{}{_\ast}} and D\=\ensuremath{\perp{}{_\ast}}, for motion of the particles parallel and perpendicular, respectively, to the direction of the gravity field are found to be of the forms D\ensuremath{_\ast}i = D + Ki\ensuremath{\lambda}2(U\ensuremath{_\ast})2dr with {\=U}\ensuremath{_\ast} the mean settling velocity of the particle, dr its rotary diffusion coefficient, and D\= = (13) \texttimes{} (D\ensuremath{\Vert} + 2D\ensuremath{\perp}) the mean translational diffusion coefficient of the particle\textemdash{}wherein D\ensuremath{\Vert} and D\ensuremath{\perp} are the orientation-specific molecular diffusivities of the particle for translation parallel and perpendicular, respectively, to its symmetry axis. In addition, \ensuremath{\lambda} is the dimensionless parameter \ensuremath{\lambda} = |D\ensuremath{\Vert} - D\ensuremath{\perp} |/D\=12, and \ensuremath{\kappa{}\Vert} = 2135 and \ensuremath{\kappa{}\perp} = 190. The forms of these transversely isotropic dispersivities agree with those recently obtained by Goren via a Langevin scheme, but the \ensuremath{\kappa}i values differ from his. A fundamental error in Goren's analysis is shown to be the source of the discrepancy. On the basis of these calculations, Smoluchowski's well-known equation for diffusion in an external field of force is shown to be generally inapplicable to nonspherical particles. Potential applications of the dispersion results are discussed.},
  timestamp = {2016-08-06T11:33:07Z},
  number = {2},
  urldate = {2013-10-10},
  journal = {Journal of Colloid and Interface Science},
  author = {Brenner, Howard},
  month = sep,
  year = {1979},
  pages = {189--208}
}

@article{seifi_accurate_2013,
  title = {Accurate {{3D}} tracking and size measurement of evaporating droplets using in-line digital holography and ``inverse problems'' reconstruction approach},
  volume = {21},
  shorttitle = {Accurate {{3D}} tracking and size measurement of evaporating droplets using in-linedigital holography and ?},
  doi = {10.1364/OE.21.027964},
  abstract = {Digital in-line holography was used to study a fast dynamic 3D phenomenon: the evaporation of
free-falling diethyl ether droplets. We describe an unsupervised reconstruction algorithm based on
an ``inverse problems'' approach previously developed by our team to accurately
reconstruct 3D trajectories and to estimate the droplets' size in a field of view of 7
\texttimes{} 11 \texttimes{} 20  mm 3 . A first experiment with non-evaporating droplets established that the radius
estimates were accurate to better than 0.1  \ensuremath{\mu}m . With evaporating
droplets, the vapor around the droplet distorts the diffraction patterns in the holograms. We showed
that areas with the strongest distortions can be discarded using an exclusion mask. We achieved
radius estimates better than 0.5  \ensuremath{\mu}m accuracy for evaporating droplets.
Our estimates of the evaporation rate fell within the range predicted by theoretical models.},
  timestamp = {2016-08-25T19:52:49Z},
  number = {23},
  urldate = {2014-03-07},
  journal = {Optics Express},
  author = {Seifi, Mozhdeh and Fournier, Corinne and Grosjean, Nathalie and M{\'e}{\`e}s, Loic and Mari{\'e}, Jean-Louis and Denis, Loic},
  month = nov,
  year = {2013},
  keywords = {Digital holography,Flow diagnostics,Image reconstruction techniques,Inverse problems,Metrology,Superresolution},
  pages = {27964--27980}
}

@misc{dimiduk_holopy_2016,
  title = {{{HoloPy}} - {{Hologram Processing}} and {{Light Scattering}} in {{Python}}},
  abstract = {holopy - Hologram processing and light scattering in python},
  timestamp = {2016-08-06T16:32:42Z},
  urldate = {2016-07-27},
  howpublished = {\url{https://github.com/manoharan-lab/holopy}},
  journal = {GitHub},
  author = {Dimiduk, Thomas G. and Fung, Jerome and Perry, Rebecca W. and Manoharan, Vinothan N.},
  year = {2016}
}

@article{candes_near-optimal_2006,
  title = {Near-{{Optimal Signal Recovery From Random Projections}}: {{Universal Encoding Strategies}}?},
  volume = {52},
  issn = {0018-9448},
  shorttitle = {Near-{{Optimal Signal Recovery From Random Projections}}},
  doi = {10.1109/TIT.2006.885507},
  abstract = {Suppose we are given a vector f in a class FsubeRopfN , e.g., a class of digital signals or digital images. How many linear measurements do we need to make about f to be able to recover f to within precision epsi in the Euclidean (lscr2) metric? This paper shows that if the objects of interest are sparse in a fixed basis or compressible, then it is possible to reconstruct f to within very high accuracy from a small number of random measurements by solving a simple linear program. More precisely, suppose that the nth largest entry of the vector |f| (or of its coefficients in a fixed basis) obeys |f|(n)lesRmiddotn-1p/, where R\ensuremath{>}0 and p\ensuremath{>}0. Suppose that we take measurements yk=langf\# ,Xkrang,k=1,...,K, where the Xk are N-dimensional Gaussian vectors with independent standard normal entries. Then for each f obeying the decay estimate above for some 0\ensuremath{<}p\ensuremath{<}1 and with overwhelming probability, our reconstruction ft, defined as the solution to the constraints yk=langf\# ,Xkrang with minimal lscr1 norm, obeys parf-f\#parlscr2lesCp middotRmiddot(K/logN)-r, r=1/p-1/2. There is a sense in which this result is optimal; it is generally impossible to obtain a higher accuracy from any set of K measurements whatsoever. The methodology extends to various other random measurement ensembles; for example, we show that similar results hold if one observes a few randomly sampled Fourier coefficients of f. In fact, the results are quite general and require only two hypotheses on the measurement ensemble which are detailed},
  timestamp = {2016-08-06T15:57:32Z},
  number = {12},
  journal = {IEEE Transactions on Information Theory},
  author = {Candes, E.J. and Tao, T.},
  month = dec,
  year = {2006},
  keywords = {Concentration of measure,Concrete,convex optimization,Digital images,duality in optimization,encoding,Geometry,image coding,image reconstruction,linear measurement,linear program,linear programming,Mathematics,Measurement standards,N-dimensional Gaussian vector,random matrices,random projection,Random projections,signal reconstruction,signal recovery,singular values of random matrices,Sparsity,trigonometric expansions,uncertainty principle,universal encoding strategy,Vectors},
  pages = {5406--5425}
}

@article{hunter_tracking_2011,
  title = {Tracking rotational diffusion of colloidal clusters},
  volume = {19},
  abstract = {We describe a novel method of tracking the rotational motion of clusters of colloidal particles. Our method utilizes rigid body transformations to determine the rotations of a cluster and extends conventional proven particle tracking techniques in a simple way, thus facilitating the study of rotational dynamics in systems containing or composed of colloidal clusters. We test our method by measuring dynamical properties of simulated Brownian clusters under conditions relevant to microscopy experiments. We then use the technique to track and describe the motions of a real colloidal cluster imaged with confocal microscopy.},
  timestamp = {2016-08-06T11:31:48Z},
  number = {18},
  urldate = {2013-10-13},
  journal = {Optics Express},
  author = {Hunter, Gary L. and Edmond, Kazem V. and Elsesser, Mark T. and Weeks, Eric R.},
  month = aug,
  year = {2011},
  keywords = {3d,cluster,colloid,confocal,diffusion,microscopy,rotation,technique},
  pages = {17189--17202}
}

@book{debye_polar_1929,
  title = {Polar molecules},
  timestamp = {2016-08-06T11:28:02Z},
  publisher = {{Dover, New York}},
  author = {Debye, Peter},
  year = {1929}
}

@article{anthony_single-particle_2006,
  title = {Single-{{Particle Colloid Tracking}} in {{Four Dimensions}}},
  volume = {22},
  issn = {0743-7463},
  doi = {10.1021/la062094h},
  abstract = {Coating a close-packed fluorescent colloid monolayer with a nanometer-thick metal film followed by sonication in liquid produces modulated optical nanoprobes. The metal coating modulates the fluorescence as these structures rotate in suspension, enabling the use of these particles as probes to monitor both rotational and center-of-mass (translational) dynamics in complex environments. Here, we demonstrate methods to simultaneously measure two translational and two rotational degrees of freedom, with excellent agreement to theory. The capability to determine two angles of rotation opens several new avenues of future research.},
  timestamp = {2016-08-06T11:33:33Z},
  number = {24},
  urldate = {2013-10-15},
  journal = {Langmuir},
  author = {Anthony, Stephen M. and Hong, Liang and Kim, Minsu and Granick, Steve},
  month = nov,
  year = {2006},
  pages = {9812--9815}
}

@article{schnars_direct_1994,
  title = {Direct recording of holograms by a {{CCD}} target and numerical reconstruction},
  volume = {33},
  doi = {10.1364/AO.33.000179},
  abstract = {The principle of recording holograms directly on a CCD target is described. A real image of the object is reconstructed from the digitally sampled hologram by means of numerical methods.},
  timestamp = {2016-08-06T11:30:17Z},
  number = {2},
  urldate = {2013-10-11},
  journal = {Applied Optics},
  author = {Schnars, U. and J{\"u}ptner, W.},
  month = jan,
  year = {1994},
  keywords = {holo,holography},
  pages = {179--181},
  file = {Appl. Opt. Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/JK25TQTT/abstract.html:text/html}
}

@article{bishop_optical_2004,
  title = {Optical {{Microrheology Using Rotating Laser-Trapped Particles}}},
  volume = {92},
  doi = {10.1103/PhysRevLett.92.198104},
  abstract = {We demonstrate an optical system that can apply and accurately measure the torque exerted by the trapping beam on a rotating birefringent probe particle. This allows the viscosity and surface effects within liquid media to be measured quantitatively on a micron-size scale using a trapped rotating spherical probe particle. We use the system to measure the viscosity inside a prototype cellular structure.},
  timestamp = {2016-08-06T11:33:11Z},
  number = {19},
  urldate = {2013-10-11},
  journal = {Physical Review Letters},
  author = {Bishop, Alexis I. and Nieminen, Timo A. and Heckenberg, Norman R. and Rubinsztein-Dunlop, Halina},
  month = may,
  year = {2004},
  pages = {198104}
}

@misc{nobelprize_physics_2014,
  title = {All {{Nobel Prizes}} in {{Physics}}},
  timestamp = {2016-08-11T01:55:46Z},
  urldate = {2016-08-09},
  howpublished = {\url{http://www.nobelprize.org/nobel_prizes/physics/laureates/}},
  journal = {nobelprize.org},
  author = {{Nobel Media AB 2015}},
  year = {2016},
  file = {All Nobel Prizes in Physics:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/RBHP3WEH/laureates.html:text/html}
}

@article{dubois_digital_2006,
  title = {Digital holographic microscopy for the three-dimensional dynamic analysis of in vitro cancer cell migration},
  volume = {11},
  issn = {10833668},
  doi = {10.1117/1.2357174},
  timestamp = {2016-08-09T17:39:02Z},
  number = {5},
  urldate = {2010-09-11},
  journal = {Journal of Biomedical Optics},
  author = {Dubois, Frank and Yourassowsky, Catherine and Monnom, Olivier and Legros, Jean-Claude and Debeir, Olivier and {Van Ham}, Philippe and Kiss, Robert and Decaestecker, Christine},
  year = {2006},
  keywords = {*read,3d,cancer,holography,microscopy,sectioning},
  pages = {054032},
  file = {Dubois et al_2006_Digital holographic microscopy for the three-dimensional dynamic analysis of in.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/X5GWQR5R/Dubois et al_2006_Digital holographic microscopy for the three-dimensional dynamic analysis of in.pdf:application/pdf}
}

@article{hannel_holographic_2015,
  title = {Holographic characterization of imperfect colloidal spheres},
  volume = {107},
  issn = {0003-6951, 1077-3118},
  doi = {10.1063/1.4932948},
  abstract = {We demonstrate precise measurements of the size and refractive index of individual dimpled colloidal spheres using holographic characterization techniques developed for ideal spheres.},
  timestamp = {2016-08-09T17:42:54Z},
  number = {14},
  urldate = {2016-08-09},
  journal = {Applied Physics Letters},
  author = {Hannel, Mark and Middleton, Christine and Grier, David G.},
  month = oct,
  year = {2015},
  keywords = {Colloidal systems,holography,Light scattering,Particle scattering,Refractive index},
  pages = {141905},
  file = {Hannel et al_2015_Holographic characterization of imperfect colloidal spheres.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/HRMX83J7/Hannel et al_2015_Holographic characterization of imperfect colloidal spheres.pdf:application/pdf;Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/TH7WEPNH/1.html:text/html}
}

@article{wang_stimulus-responsive_2015,
  title = {Stimulus-responsive colloidal sensors with fast holographic readout},
  volume = {107},
  issn = {0003-6951, 1077-3118},
  doi = {10.1063/1.4928178},
  abstract = {Colloidal spheres synthesized from polymer gels swell by absorbing molecules from solution. The resulting change in size can be monitored with nanometer precision using holographic video microscopy. When the absorbate is chemically similar to the polymer matrix, swelling is driven primarily by the entropy of mixing, and is limited by the surface tension of the swelling sphere and by the elastic energy of the polymer matrix. We demonstrate through a combination of optical micromanipulation and holographic particle characterization that the degree of swelling of a single polymer bead can be used to measure the monomer concentration in situ with spatial resolution comparable to the size of the sphere.},
  timestamp = {2016-08-09T17:43:56Z},
  number = {5},
  urldate = {2016-08-09},
  journal = {Applied Physics Letters},
  author = {Wang, Chen and Moyses, Henrique W. and Grier, David G.},
  month = aug,
  year = {2015},
  keywords = {holography,Polymers,Refractive index,Scanning electron microscopy,Silica},
  pages = {051903},
  file = {Wang et al_2015_Stimulus-responsive colloidal sensors with fast holographic readout.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/QIKAFGQC/Wang et al_2015_Stimulus-responsive colloidal sensors with fast holographic readout.pdf:application/pdf;Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/5FIEDRNE/1.html:text/html}
}

@article{moyses_robustness_2013,
  title = {Robustness of {{Lorenz-Mie}} microscopy against defects in illumination},
  volume = {21},
  issn = {1094-4087},
  doi = {10.1364/OE.21.005968},
  language = {en},
  timestamp = {2016-08-09T17:48:43Z},
  number = {5},
  urldate = {2016-08-09},
  journal = {Optics Express},
  author = {Moyses, Henrique W. and Krishnatreya, Bhaskar J. and Grier, David G.},
  month = mar,
  year = {2013},
  pages = {5968},
  file = {Moyses et al_2013_Robustness of Lorenz-Mie microscopy against defects in illumination.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/8JKZDHHT/Moyses et al_2013_Robustness of Lorenz-Mie microscopy against defects in illumination.pdf:application/pdf}
}

@article{shpaisman_holographic_2012,
  title = {Holographic microrefractometer},
  volume = {101},
  issn = {0003-6951, 1077-3118},
  doi = {10.1063/1.4747168},
  abstract = {In-line holographic microscopy of micrometer-scale colloidal spheres yields heterodyne scattering patterns that may be interpreted with Lorenz-Mie theory to obtain precise time-resolved information on the refractive index of the suspending medium. We demonstrate this approach to spatially resolved refractometry with measurements on calibrated refractive index standards and use it to monitor chemical concentration in a microfluidic channel. Using commercially available colloidal spheres as probe particles and a standard video camera for detection yields values for the fluid's refractive index at the position of each probe particle in each holographic snapshot with a demonstrated resolution of refractive index units (RIU) and a potential resolution surpassing . The combination of spatial resolution, temporal resolution, multi-point in situ access, and technical simplicity recommends this technique for cost-effective lab-on-a-chip applications. 2 \texttimes{} 10 - 3 10 - 4 RIU},
  timestamp = {2016-08-09T17:48:47Z},
  number = {9},
  urldate = {2016-08-09},
  journal = {Applied Physics Letters},
  author = {Shpaisman, Hagay and Krishnatreya, Bhaskar Jyoti and Grier, David G.},
  month = aug,
  year = {2012},
  keywords = {Cameras,Colloidal systems,holography,microfluidics,Refractive index},
  pages = {091102},
  file = {Shpaisman et al_2012_Holographic microrefractometer.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/JU6IN2M7/Shpaisman et al_2012_Holographic microrefractometer.pdf:application/pdf;Shpaisman et al_2012_Holographic microrefractometer.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/UDNNBW43/Shpaisman et al_2012_Holographic microrefractometer.pdf:application/pdf;Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/BVBRP6QM/freeabs_all.html:text/html;Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/GF2WMSPH/1.html:text/html}
}

@article{cheong_holographic_2011,
  title = {Holographic characterization of individual colloidal spheres' porosities},
  volume = {7},
  issn = {1744-6848},
  doi = {10.1039/C1SM05577A},
  abstract = {Holograms of colloidal spheres recorded through holographic video microscopy can be analyzed with the theory of light scattering to measure individual spheres' sizes and refractive indexes with part-per-thousand resolution. This information, in turn, can be interpreted to estimate each sphere's porosity.},
  language = {en},
  timestamp = {2016-08-09T17:46:37Z},
  number = {15},
  urldate = {2016-08-09},
  journal = {Soft Matter},
  author = {Cheong, Fook Chiong and Xiao, Ke and Pine, David J. and Grier, David G.},
  month = jul,
  year = {2011},
  pages = {6816--6819},
  file = {Cheong et al_2011_Holographic characterization of individual colloidal spheres' porosities.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/K3GVZVM6/Cheong et al_2011_Holographic characterization of individual colloidal spheres' porosities.pdf:application/pdf;Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/CT2R6NH6/c1sm05577a.html:text/html}
}

@article{cheong_technical_2009-1,
  title = {Technical note: {{Characterizing}} individual milk fat globules with holographic video microscopy},
  volume = {92},
  issn = {0022-0302},
  shorttitle = {Technical note},
  doi = {10.3168/jds.2008-1361},
  abstract = {We used in-line holography to create images of individual milk fat globules in diluted samples of milk. Analyzing these images with the exact Lorenz-Mie light scattering theory then yields the droplets' radii with nanometer resolution and their refractive indexes to within one part in a thousand. This procedure rapidly and directly characterizes both the quantity and quality of fat in milk.},
  timestamp = {2016-08-09T17:48:33Z},
  number = {1},
  urldate = {2016-08-09},
  journal = {Journal of Dairy Science},
  author = {Cheong, F. C. and Xiao, K. and Grier, D. G.},
  month = jan,
  year = {2009},
  keywords = {globule,globule,holography,holography,milk fat,milk fat},
  pages = {95--99},
  file = {ScienceDirect Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/N9HKJPM7/S0022030209703133.html:text/html}
}

@article{nadeau_use_2015,
  title = {Use of dyes to increase phase contrast for biological holographic microscopy},
  volume = {40},
  issn = {0146-9592, 1539-4794},
  doi = {10.1364/OL.40.004114},
  language = {en},
  timestamp = {2016-08-11T00:02:07Z},
  number = {17},
  urldate = {2016-08-09},
  journal = {Optics Letters},
  author = {Nadeau, Jay L. and Cho, Yong Bin and Lindensmith, Christian A.},
  month = sep,
  year = {2015},
  pages = {4114}
}

@article{carpio_noninvasive_2016,
  title = {Noninvasive imaging of {{3D}} micro and nanostructures by topological methods},
  copyright = {\{:status:in press\}},
  timestamp = {2016-08-09T19:09:47Z},
  journal = {SIAM Journal on Imaging Sciences},
  author = {Carpio, Ana and Dimiduk, Thomas G. and Rap{\'u}n, Mar{\'\i}a Luisa and Selgas, Virginia},
  year = {In Press}
}

@article{pham_digital_2012,
  title = {Digital holographic microscope with low-frequency attenuation filter for position measurement of a nanoparticle},
  volume = {37},
  issn = {0146-9592, 1539-4794},
  doi = {10.1364/OL.37.004119},
  language = {en},
  timestamp = {2016-08-09T19:27:52Z},
  number = {19},
  urldate = {2016-08-09},
  journal = {Optics Letters},
  author = {Pham, Quang Duc and Kusumi, Yuichi and Hasegawa, Satoshi and Hayasaki, Yoshio},
  month = oct,
  year = {2012},
  pages = {4119}
}

@article{goto_three-dimensional_2015,
  title = {Three-dimensional motion detection of a 20-nm gold nanoparticle using twilight-field digital holography with coherence regulation},
  volume = {40},
  issn = {0146-9592, 1539-4794},
  doi = {10.1364/OL.40.003344},
  language = {en},
  timestamp = {2016-08-09T19:28:18Z},
  number = {14},
  urldate = {2016-08-09},
  journal = {Optics Letters},
  author = {Goto, Kazufumi and Hayasaki, Yoshio},
  month = jul,
  year = {2015},
  pages = {3344}
}

@article{jacobsen_interferometric_2006,
  title = {Interferometric optical detection and tracking of very small gold nanoparticles at a water-glass interface},
  volume = {14},
  issn = {1094-4087},
  doi = {10.1364/OPEX.14.000405},
  language = {en},
  timestamp = {2016-08-09T19:28:58Z},
  number = {1},
  urldate = {2016-08-09},
  journal = {Optics Express},
  author = {Jacobsen, Volker and Stoller, Patrick and Brunner, Christian and Vogel, Viola and Sandoghdar, Vahid},
  year = {2006},
  pages = {405}
}

@article{piliarik_direct_2014,
  title = {Direct optical sensing of single unlabelled proteins and super-resolution imaging of their binding sites},
  volume = {5},
  copyright = {\textcopyright{} 2014 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  doi = {10.1038/ncomms5495},
  abstract = {Detection of single analyte molecules without the use of any label would improve the sensitivity of current biosensors by orders of magnitude to the ultimate graininess of biological matter. Over two decades, scientists have succeeded in pushing the limits of optical detection to single molecules using fluorescence. However, restrictions in photophysics and labelling protocols make this technique less attractive for biosensing. Recently, mechanisms based on vibrational spectroscopy, photothermal detection, plasmonics and microcavities have been explored for fluorescence-free detection of single biomolecules. Here, we show that interferometric detection of scattering (iSCAT) can achieve this goal in a direct and label-free fashion. In particular, we demonstrate detection of cancer marker proteins in buffer solution and in the presence of other abundant proteins. Furthermore, we present super-resolution imaging of protein binding with nanometer localization precision. The ease of iSCAT instrumentation promises a breakthrough for label-free studies of interactions involving proteins and other small biomolecules.
View full text},
  language = {en},
  timestamp = {2016-08-09T19:29:50Z},
  urldate = {2016-08-09},
  journal = {Nature Communications},
  author = {Piliarik, Marek and Sandoghdar, Vahid},
  month = jul,
  year = {2014},
  keywords = {Biological sciences,Biophysics,Optical physics},
  pages = {4495},
  file = {Piliarik_Sandoghdar_2014_Direct optical sensing of single unlabelled proteins and super-resolution.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/Q3EX8788/Piliarik_Sandoghdar_2014_Direct optical sensing of single unlabelled proteins and super-resolution.pdf:application/pdf;Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/P6RCRM2D/ncomms5495.html:text/html}
}

@article{kukura_high-speed_2009,
  title = {High-speed nanoscopic tracking of the position and orientation of a single virus},
  volume = {6},
  copyright = {\textcopyright{} 2009 Nature Publishing Group},
  issn = {1548-7091},
  doi = {10.1038/nmeth.1395},
  abstract = {Optical studies have revealed that, after binding, virions move laterally on the plasma membrane, but the complexity of the cellular environment and the drawbacks of fluorescence microscopy have prevented access to the molecular dynamics of early virus-host couplings, which are important for cell infection. Here we present a colocalization methodology that combines scattering interferometry and single-molecule fluorescence microscopy to visualize both position and orientation of single quantum dot\textendash{}labeled Simian virus 40 (SV40) particles. By achieving nanometer spatial and 8 ms temporal resolution, we observed sliding and tumbling motions during rapid lateral diffusion on supported lipid bilayers, and repeated back and forth rocking between nanoscopic regions separated by 9 nm. Our findings suggest recurrent swap of receptors and viral pentamers as well as receptor aggregation in nanodomains. We discuss the prospects of our technique for studying virus-membrane interactions and for resolving nanoscopic dynamics of individual biological nano-objects.},
  language = {en},
  timestamp = {2016-08-09T19:30:08Z},
  number = {12},
  urldate = {2016-08-09},
  journal = {Nature Methods},
  author = {Kukura, Philipp and Ewers, Helge and M{\"u}ller, Christian and Renn, Alois and Helenius, Ari and Sandoghdar, Vahid},
  month = dec,
  year = {2009},
  pages = {923--927},
  file = {Kukura et al_2009_High-speed nanoscopic tracking of the position and orientation of a single virus.pdf:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/24AJFGMG/Kukura et al_2009_High-speed nanoscopic tracking of the position and orientation of a single virus.pdf:application/pdf;Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/CBI2D47D/nmeth.1395.html:text/html}
}

@article{goldfain_dynamic_2016,
  title = {Dynamic {{Measurements}} of the {{Position}}, {{Orientation}}, and {{DNA Content}} of {{Individual Unlabeled Bacteriophages}}},
  volume = {120},
  issn = {1520-6106, 1520-5207},
  doi = {10.1021/acs.jpcb.6b02153},
  language = {en},
  timestamp = {2016-08-09T19:31:39Z},
  number = {26},
  urldate = {2016-08-09},
  journal = {The Journal of Physical Chemistry B},
  author = {Goldfain, Aaron M. and Garmann, Rees F. and Jin, Yan and Lahini, Yoav and Manoharan, Vinothan N.},
  month = jul,
  year = {2016},
  pages = {6130--6138}
}

@article{goodman_application_1991,
  title = {Application of fast-{{Fourier}}-transform techniques to the discrete-dipole approximation},
  volume = {16},
  issn = {0146-9592, 1539-4794},
  doi = {10.1364/OL.16.001198},
  language = {en},
  timestamp = {2016-08-14T18:44:14Z},
  number = {15},
  urldate = {2016-08-14},
  journal = {Optics Letters},
  author = {Goodman, J. J. and Flatau, P. J. and Draine, B. T.},
  month = aug,
  year = {1991},
  pages = {1198}
}

@article{kraft_brownian_2013,
  title = {Brownian motion and the hydrodynamic friction tensor for colloidal particles of complex shape},
  volume = {88},
  doi = {10.1103/PhysRevE.88.050301},
  abstract = {We synthesize colloidal particles with various anisotropic shapes and track their orientationally resolved Brownian trajectories using confocal microscopy. An analysis of appropriate short-time correlation functions provides direct access to the hydrodynamic friction tensor of the particles revealing nontrivial couplings between the translational and rotational degrees of freedom. The results are consistent with calculations of the hydrodynamic friction tensor in the low-Reynolds-number regime for the experimentally determined particle shapes.},
  timestamp = {2016-08-25T19:51:29Z},
  number = {5},
  urldate = {2016-08-25},
  journal = {Physical Review E},
  author = {Kraft, Daniela J. and Wittkowski, Raphael and {ten Hagen}, Borge and Edmond, Kazem V. and Pine, David J. and L{\"o}wen, Hartmut},
  month = nov,
  year = {2013},
  pages = {050301},
  file = {APS Snapshot:/home/tdimiduk/.mozilla/firefox/47kjlgp8.Tom/zotero/storage/T7PI6RRM/PhysRevE.88.html:text/html}
}


