Fast finite difference solver for optical microscopy in deep biological tissue.

Optical scattering poses a significant challenge to high-resolution microscopy within deep tissue. To accurately predict the performance of various microscopy techniques in thick samples, we present a computational model that efficiently solves Maxwell's equation in highly scattering media. This toolkit simulates the deterioration of the laser beam point spread function (PSF) without making a paraxial approximation, enabling accurate modeling of high-numerical-aperture (NA) objective lenses commonly employed in experiments. Moreover, this framework is applicable to a broad range of scanning microscopy techniques including confocal microscopy, stimulated emission depletion (STED) microscopy, and ground-state depletion microscopy. Notably, the proposed method requires only readily obtainable macroscopic tissue parameters. As a practical demonstration, we investigate the performance of Laguerre-Gaussian (LG) versus Hermite-Gaussian (HG) depletion beams in STED microscopy.

OpenSTED: open-source dynamic intensity minimum system for stimulated emission depletion microscopy.

Significance: Stimulated emission depletion (STED) is a powerful super-resolution microscopy technique that can be used for imaging live cells. However, the high STED laser powers can cause significant photobleaching and sample damage in sensitive biological samples. The dynamic intensity minimum (DyMIN) technique turns on the STED laser only in regions of the sample where there is fluorescence signal, thus saving significant sample photobleaching. The reduction in photobleaching allows higher resolution images to be obtained and longer time-lapse imaging of live samples. A stand-alone module to perform DyMIN is not available commercially. Aim: In this work, we developed an open-source design to implement three-step DyMIN on a STED microscope and demonstrated reduced photobleaching for timelapse imaging of beads, cells, and tissue. Approach: The DyMIN system uses a fast multiplexer circuit and inexpensive field-programmable gate array controlled by Labview software that operates as a stand-alone module for a STED microscope. All software and circuit diagrams are freely available. Results: We compared time-lapse images of bead samples using our custom DyMIN system to conventional STED and recorded a ∼ 46 % higher signal when using DyMIN after a 50-image sequence. We further demonstrated the DyMIN system for time-lapse STED imaging of live cells and brain tissue slices. Conclusions: Our open-source DyMIN system is an inexpensive add-on to a conventional STED microscope that can reduce photobleaching. The system can significantly improve signal to noise for dynamic time-lapse STED imaging of live samples.

Experimental measurement of the geometric phase of non-geodesic circles.

We present and implement a method for the experimental measurement of geometric phase of non-geodesic (small) circles on any SU(2) parameter space. This phase is measured by subtracting the dynamic phase contribution from the total phase accumulated. Our design does not require theoretical anticipation of this dynamic phase value and the methods are generally applicable to any system accessible to interferometric and projection measurements. Experimental implementations are presented for two settings: (1) the sphere of modes of orbital angular momentum, and (2) the Poincaré sphere of polarizations of Gaussian beams.

Amplitude structure of optical vortices determines annihilation dynamics.

We show that annihilation dynamics between oppositely charged optical vortex pairs can be manipulated by the initial size of the vortex cores, consistent with hydrodynamics. When sufficiently close together, vortices with strongly overlapped cores annihilate more quickly than vortices with smaller cores that must wait for diffraction to cause meaningful core overlap. Numerical simulations and experimental measurements for vortices with hyperbolic tangent cores of various initial sizes show that hydrodynamics governs their motion, and reveal distinct phases of vortex recombination; decreasing the core size of an annihilating pair can prevent the annihilation event.

Tilted Poincaré sphere geodesics.

We provide the first, to the best of our knowledge, experimental demonstration of a geometric phase generated in association with closed Poincaré sphere trajectories comprising geodesic arcs that do not start, end, or necessarily even include, the north and south poles that represent pure Laguerre-Gaussian modes. Arbitrarily tilted (elliptical) single vortex states are prepared with a spatial light modulator, and Poincaré sphere circuits are driven by beam transit through a series of π-converters and Dove prisms.

Hydrodynamics explanation for the splitting of higher-charge optical vortices.

We show that a two-dimensional hydrodynamics model provides a physical explanation for the splitting of higher-charge optical vortices under elliptical deformations. The model is applicable to laser light and quantum fluids alike. The study delineates vortex breakups from vortex unions under different forms of asymmetry in the beam, and it is also applied to explain the motion of intact higher-charge vortices.

Hidden Silicon-Vacancy Centers in Diamond.

We characterize a high-density sample of negatively charged silicon-vacancy (SiV^{-}) centers in diamond using collinear optical multidimensional coherent spectroscopy. By comparing the results of complementary signal detection schemes, we identify a hidden population of SiV^{-} centers that is not typically observed in photoluminescence and which exhibits significant spectral inhomogeneity and extended electronic T_{2} times. The phenomenon is likely caused by strain, indicating a potential mechanism for controlling electric coherence in color-center-based quantum devices.

Selective excitation of plasmon resonances with single V-point cylindrical vector beams.

We use a rigorous group theoretical method to identify a class of cylindrical vector beams that can selectively excite the plasmon modes of axially symmetric plasmonic structures. Our choice of the single V-point cylindrical vector beams as the basis to decompose cylindrical beams dramatically simplifies the symmetry analysis in the group theory framework. With numerical simulations, we demonstrate that any plasmon eigenmodes, bright or dark, can be selectively excited individually or jointly. A straightforward protocol to get access to the desired plasmon mode using symmetry coupling is presented.

Observation of the rotational Doppler shift with spatially incoherent light.

The rotational Doppler shift (RDS) is typically measured by illuminating a rotating target with a laser prepared in a simple, known orbital angular momentum (OAM) superposition. We establish theoretically and experimentally that detecting the rotational Doppler shift does not require the incident light to have a well-defined OAM spectrum but instead requires well-defined correlations within the OAM spectrum. We demonstrate measurement of the rotational Doppler shift using spatially incoherent light.

Fast phase cycling in non-collinear optical two-dimensional coherent spectroscopy.

As optical two-dimensional coherent spectroscopy (2DCS) is extended to a broader range of applications, it is critical to improve the detection sensitivity of optical 2DCS. We developed a fast phase-cycling scheme in a non-collinear optical 2DCS implementation by using liquid crystal phase retarders to modulate the phases of two excitation pulses. The background in the signal can be eliminated by combining either two or four interferograms measured with a proper phase configuration. The effectiveness of this method was validated in optical 2DCS measurements of an atomic vapor. This fast phase-cycling scheme will enable optical 2DCS in novel emerging applications that require enhanced detection sensitivity.

Detection technique effect on rotational Doppler measurements.

There are two established methods for measuring rotational Doppler shift: (1) heterodyne and (2) fringe. We identify a key distinction, that only the heterodyne method is sensitive to the rotating object's phase, which results in significant differences in the signal-to-noise ratio (SNR) when measuring multiple rotating particles. When used to measure randomly distributed rotating particles, the fringe method produces its strongest SNR when a single particle is present and its SNR tends to zero as the number of particles increases, whereas the heterodyne method's SNR increases proportionally to the number of particles in the beam.

Optical vortex braiding with Bessel beams.

We propose the braiding of optical vortices in a laser beam with more than $ 2\pi $2π rotation by superposing Bessel modes with a plane wave. We experimentally demonstrate this by using a Bessel-Gaussian beam and a coaxial Gaussian, and we present measurements of three complete braids. The amount of braiding is fundamentally limited only by the numerical aperture of the system, and we discuss how braiding can be controlled experimentally for any number of vortices.

The Effect of Cyclic Strain on Human Fibroblasts With Lamin A/C Mutations and Its Relation to Heart Disease.

Although mutations in the Lamin A/C gene (LMNA) cause a variety of devastating diseases, the pathological mechanism is often unknown. Lamin A/C proteins play a crucial role in forming a meshwork under the nuclear membrane, providing the nucleus with mechanical integrity and interacting with other proteins for gene regulation. Most LMNA mutations result in heart diseases, including some types that primarily have heart disease as the main pathology. In this study, we used cells from patients with different LMNA mutations that primarily lead to heart disease. Indeed, it is a mystery why a mutation to the protein in every nucleus of the body manifests as a disease of primarily the heart in these patients. Here, we aimed to investigate if strains mimicking those within the myocardial environment are sufficient to cause differences in cells with and without the LMNA mutation. To test this, a stretcher device was used to induce cyclic strain upon cells, and viability/proliferation, cytoskeleton and extracellular matrix organization, and nuclear morphology were quantified. The properties of cells with Hutchinson-Gilford progeria syndrome (HGPS) were found to be significantly different from all other cell lines and were mostly in line with previous findings. However, the properties of cells from patients who primarily had heart diseases were not drastically different when compared to individuals without the LMNA mutation. Our results indicated that cyclic strain alone was insufficient to cause any significant differences that could explain the mechanisms that lead to heart diseases in these patients with LMNA mutations.

A Fiber-Coupled Stimulated Emission Depletion Microscope for Bend-Insensitive Through-Fiber Imaging.

We present results for a new type of fiber-coupled stimulated emission depletion (STED) microscope which uses a single fiber to transport STED and excitation light, as well as collect the fluorescence signal. Our method utilizes two higher-order eigenmodes of polarization maintaining (PM) fiber to generate the doughnut-shaped STED beam. The modes are excited with separate beams that share no temporal coherence, yielding output that is independent of fiber bending. We measured the resolution using 45 nm fluorescent beads and found a median bead image size of 116 nm. This resolution does not change as function of fiber bending radius, demonstrating robust operation. We report, for the first time, STED images of fixed biological samples collected in the epi-direction through fiber. Our microscope design shows promise for future use in super-resolution micro-endoscopes and in vivo neural imaging in awake and freely-behaving animals.

Absolute phase calibration in phase-modulated multidimensional coherent spectroscopy.

Establishing the correct phase in multidimensional coherent spectroscopy (MDCS) experiments is critical because the interpretation of quantum pathways is based on the phase of their associated spectral features but is not trivial because the phase introduced by experimental conditions can contaminate the signal. Most phase-modulated MDCS (PM-MDCS) experiments study molecular systems for which the spectra can be phased to produce absorptive lineshapes, but this assumption of absorptive lineshapes can break down in more complicated systems. We present a robust technique for correcting the phase in PM-MDCS experiments and demonstrate accurate spectrum phasing for an anharmonic system.

Quantum Turbulent Structure in Light.

The infinite superpositions of random plane waves are known to be threaded with vortex line singularities which form complicated tangles and obey strict topological rules. We observe that within these structures, a timelike axis appears to emerge with which we can define vortex velocities in a useful way: With both numerical simulations and optical experiments, we show that the statistics of these velocities match those of turbulent quantum fluids such as superfluid helium and atomic Bose-Einstein condensates. These statistics are shown to be independent of system scale. These results raise deep questions about the general nature of quantum chaos and the role of nonlinearity in the structure of turbulence.

Modified Coring Tool Designs Reduce Iceberg Lettuce Cross-Contamination.

Contaminated coring tools may transfer bacteria to iceberg lettuce. The efficiency of coring tool design modifications in reducing bacterial transfer to lettuce heads was evaluated under simulated field operations. The standard coring tool consists of a stainless steel cylindrical tube welded to a tab that is inserted into a plastic handle. Design modifications included removal of the welded portion, incorporation of a shorter front straight bottom edge, or an angled bottom edge toward the front. In the first study, coring tools of four different designs were inoculated by dipping in a tryptic soy broth (TSB) suspension that contained 8.85 Log CFU/mL of Escherichia coli K-12 and then were used to core 100 lettuce heads, consecutively. Use of the standard tool resulted in 91% ± 9% positive lettuce heads. Removing the welded surface from the standard tool resulted in the highest reduction of E. coli transfer (44% ± 11.9% positive lettuce heads, P < 0.05), whereas incorporation of a short front straight edge with no welding resulted in 65.6% ± 5.6% of the cored lettuce heads being positive for E. coli. Removal of the welded surface resulted in a 40% decrease in E. coli contamination among the last 20 cored lettuce heads (81 to 100), which indicates that coring tool design modifications resulted in reduced cross-contamination. In the second study, the transfer of Salmonella to coring tools after their immersion in rinsing solutions was evaluated using imaging. The tools were dip inoculated for 2 min in water, water with lettuce extract, or TSB containing 7 Log CFU/mL bioluminescent Salmonella Newport; they were then imaged to observe spatial distribution of bacteria. There was greater retention and spatial distribution of Salmonella on the surface of tools immersed in water containing lettuce extract than in TSB and water. The results of the second study indicate that rinsing solutions that contain lettuce particulate and organic load could facilitate cross-contamination of Salmonella Newport to tool surfaces.

Characterizing vortex beams from a spatial light modulator with collinear phase-shifting holography.

We demonstrate collinear phase-shifting holography for measuring complex optical modes of twisted light beams with orbital angular momentum (OAM) generated by passing a laser through a spatial light modulator (SLM). This technique measures the mode along the direction of propagation from the SLM and requires no additional optics, so it can be used to aid alignment of the SLM, to efficiently check for the effects of beam wander, and to fully characterize generated beams before use in other experiments. Optimized error analysis and careful SLM alignment allow us to generate and measure OAM with purity as high as 99.9%.

Diagonal slice four-wave mixing: natural separation of coherent broadening mechanisms.

We present an ultrafast coherent spectroscopy data acquisition scheme that samples slices of the time domain used in multidimensional coherent spectroscopy to achieve faster data collection than full spectra. We derive analytical expressions for resonance lineshapes using this technique that completely separate homogeneous and inhomogeneous broadening contributions into separate projected lineshapes for arbitrary inhomogeneous broadening. These lineshape expressions are also valid for slices taken from full multidimensional spectra and allow direct measurement of the parameters contributing to the lineshapes in those spectra as well as our own.

Deconvolution of optical multidimensional coherent spectra.

Optical coherent multidimensional spectroscopy is a powerful technique for unraveling complex and congested spectra by spreading them across multiple dimensions, removing the effects of inhomogeneity, and revealing underlying correlations. As the technique matures, the focus is shifting from understanding the technique itself to using it to probe the underlying dynamics in the system being studied. However, these dynamics can be difficult to discern because they are convolved with the nonlinear optical response of the system. Inspired by methods used to deblur images, we present a method for deconvolving the underlying dynamics from the optical response. To demonstrate the method, we extract the many-particle diffusion Green's functions for excitons in a semiconductor quantum well from two-dimensional coherent spectra.