544 research outputs found
Ultrasonic dispersion (delta V/V) determined from mechanical resonance frequency shifts
With standing wave ultrasonic techniques, small changes in phase velocity which result from changes in some external parameter (e.g., temperature or magnetic field) have traditionally been determined by observing shifts in the mechanical resonance frequency of a composite resonator. Some previous investigators have assumed that the fractional change in velocity is equal to the fractional change in frequency. Substantially improved formulas for determining the dispersion are presented and one of these is shown to be much more accurate than all previous approximations. The results of simulated and actual experiments over wide ranges of dispersion, transducer loading parameter, and frequency are analyzed in order to compare the errors inherent in the various approximations
Robust Hypothesis Tests for Detecting Statistical Evidence of 2D and 3D Interactions in Single-Molecule Measurements
A variety of experimental techniques have improved the 2D and 3D spatial
resolution that can be extracted from \emph{in vivo} single-molecule
measurements. This enables researchers to quantitatively infer the magnitude
and directionality of forces experienced by biomolecules in their native
cellular environments. Situations where such forces are biologically relevant
range from mitosis to directed transport of protein cargo along cytoskeletal
structures. Models commonly applied to quantify single-molecule dynamics assume
that effective forces and velocity in the (or ) directions are
statistically independent, but this assumption is physically unrealistic in
many situations. We present a hypothesis testing approach capable of
determining if there is evidence of statistical dependence between positional
coordinates in experimentally measured trajectories; if the hypothesis of
independence between spatial coordinates is rejected, then a new model
accounting for 2D (3D) interactions should be considered to more faithfully
represent the underlying experimental kinetics. The technique is robust in the
sense that 2D (3D) interactions can be detected via statistical hypothesis
testing even if there is substantial inconsistency between the physical
particle's actual noise sources and the simplified model's assumed noise
structure. For example, 2D (3D) interactions can be reliably detected even if
the researcher assumes normal diffusion, but the experimental data experiences
"anomalous diffusion" and/or is subjected to a measurement noise characterized
by a distribution differing from that assumed by the fitted model. The approach
is demonstrated on control simulations and on experimental data (IFT88 directed
transport in the primary cilium).Comment: 7 pages, 6 figure
Two transducer formula for more precise determination of ultrasonic phase velocity from standing wave measurements
A two transducer correction formula valid for both solid and liquid specimens is presented. Using computer simulations of velocity measurements, the accuracy and range of validity of the results are discussed and are compared with previous approximations
Addressing systematic errors in axial distance measurements in single-emitter localization microscopy
Nanoscale localization of point emitters is critical to several methods in
optical fluorescence microscopy, including single-molecule super-resolution
imaging and tracking. While the precision of the localization procedure has
been the topic of extensive study, localization accuracy has been less
emphasized, in part due to the challenge of producing an experimental sample
containing unperturbed point emitters at known three-dimensional positions in a
relevant geometry. We report a new experimental system which reproduces a
widely-adopted geometry in high-numerical aperture localization microscopy, in
which molecules are situated in an aqueous medium above a glass coverslip
imaged with an oil-immersion objective. We demonstrate a calibration procedure
that enables measurement of the depth-dependent point spread function (PSF) for
open aperture imaging as well as imaging with engineered PSFs with index
mismatch. We reveal the complicated, depth-varying behavior of the focal plane
position in this system and discuss the axial localization biases incurred by
common approximations of this behavior. We compare our results to theoretical
calculations.Comment: 16 pages, 10 figure
Interferometric scattering enables fluorescence-free electrokinetic trapping of single nanoparticles in free solution
Anti-Brownian traps confine single particles in free solution by closed-loop
feedback forces that directly counteract Brownian motion. The extended-duration
measurement of trapped objects allows detailed characterization of
photophysical and transport properties, as well as observation of infrequent or
rare dynamics. However, this approach has been generally limited to particles
that can be tracked by fluorescent emission. Here we present the
Interferometric Scattering Anti-Brownian ELectrokinetic trap (ISABEL trap),
which uses interferometric scattering rather than fluorescence to monitor
particle position. By decoupling the ability to track (and therefore trap) a
particle from collection of its spectroscopic data, the ISABEL trap enables
confinement and extended study of single particles that do not fluoresce, that
only weakly fluoresce, or which exhibit intermittent fluorescence or
photobleaching. This new technique significantly expands the range of nanoscale
objects that may be investigated at the single-particle level in free solution.Comment: Manuscript and SI; videos available upon reques
Control and coherence of the optical transition of single defect centers in diamond
We demonstrate coherent control of the optical transition of single
Nitrogen-Vacancy defect centers in diamond. On applying short resonant laser
pulses, we observe optical Rabi oscillations with a half-period as short as 1
nanosecond, an order of magnitude shorter than the spontaneous emission time.
By studying the decay of Rabi oscillations, we find that the decoherence is
dominated by laser-induced spectral jumps. By using a low-power probe pulse as
a detuning sensor and applying post-selection, we demonstrate that spectral
diffusion can be overcome in this system to generate coherent photons.Comment: 5 pages,4 figure
BGnet: Accurate and rapid background estimation in single-molecule localization microscopy with deep neural nets
Background fluorescence, especially when it exhibits undesired spatial
features, is a primary factor for reduced image quality in optical microscopy.
Structured background is particularly detrimental when analyzing
single-molecule images for 3D localization microscopy or single-molecule
tracking. Here, we introduce BGnet, a deep neural network with a U-net-type
architecture, as a general method to rapidly estimate the background underlying
the image of a point source with excellent accuracy, even when point spread
function (PSF) engineering is in use to create complex PSF shapes. We trained
BGnet to extract the background from images of various PSFs and show that the
identification is accurate for a wide range of different interfering background
structures constructed from many spatial frequencies. Furthermore, we
demonstrate that the obtained background-corrected PSF images, both for
simulated and experimental data, lead to a substantial improvement in
localization precision. Finally, we verify that structured background
estimation with BGnet results in higher quality of super-resolution
reconstructions of biological structures.Comment: 50 pages, 20 figure
Accurate phase retrieval of complex point spread functions with deep residual neural networks
Phase retrieval, i.e. the reconstruction of phase information from intensity
information, is a central problem in many optical systems. Here, we demonstrate
that a deep residual neural net is able to quickly and accurately perform this
task for arbitrary point spread functions (PSFs) formed by Zernike-type phase
modulations. Five slices of the 3D PSF at different focal positions within a
two micron range around the focus are sufficient to retrieve the first six
orders of Zernike coefficients.Comment: 8 pages, 4 figure
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