Enhanced fluorescence blinking of AF647 fluorophores in Mowiol via violet and UV light induced recovery for superior localization microscopy

Blinking of fluorophores is essential in the context of single molecule localization-based optical super-resolution microscopy methods. To make the fluorescence molecule undergo blinking specific complex chemical mounting buffer systems, combined with suitable oxygen scavengers, and reducing agents are required. For instance to realise blinking in widely used fluorescence tags, like Alexa Fluor 647 (AF647), they are to be mounted on anti-fading buffer such as Mowiol and reducing agent such as Beta (β) - ME. However, the quality of the super-resolved images is decided by the total number of blinking events or in other words net duration for which the fluorescence blinking persists. In this paper we investigate how a violet and UV light induced fluorescence recovery mechanism can enhance the duration of fluorescence blinking. Our study uses AF647 dye conjugated with Phalloidin antibody in U87MG cell line mounted on Mowiol andβ- ME. On the basis of the investigation we optimize the intensity, at the sample plane, of fluorescence excitation laser at 638 nm and fluorescence recovery beam at 405 nm or in the UV giving the maximum possible fluorescence blinking duration. We observe that the longer blinking duration, using the optimized illumination scheme, has brought down the resolution in the super-resolved image, as given by Fourier Ring Correlation method, from 168 nm to 112 nm, while the separation between two nearby resolvable filaments has been brought down to ≤ 60 nm.

Study on the orthogonality property of Zernike modes in light beams undergoing free space propagation

This paper presents a study to investigate how the orthogonality property of Zernike modes gets modified as a light beam carrying the mode in its phase propagates through free space. We use a numerical simulation using scalar diffraction theory to generate propagated light beams carrying the commonly encountered Zernike modes. We present our results in terms of the inner product and orthogonality contrast matrix at propagation distances ranging from near field to far field regions. Our study will help in the understanding of how far the Zernike modes describing the phase profile of a light beam in a given plane remain approximately orthogonal to one another on propagation.

Synchronization and clock recovery in a ferroelectric liquid crystal spatial light modulator based free-space optical communication link

Synchronization of the transmitter and receiver is crucial in a free-space optical communication system for the proper transfer and retrieval of user information. In this work, we propose a method for the synchronization and recovery of the clock signal at the receiver from the optical signal modulated by a ferroelectric liquid crystal spatial light modulator (FLCSLM) in the transmitter. We have demonstrated our scheme by building an experimental arrangement that comprises an FLCSLM based computer generated holography assembly for modulating the laser beam in the transmitter and a photodiode cum micro-controller circuit in the receiver to generate the synchronized clock. We present the experimental results to demonstrate the accuracy of the recovered clock and the successful retrieval of the transmitted user information. The scheme can work for amplitude modulated, phase modulated, or complex amplitude modulated information transfer based on the FLCSLM.

Experimental demonstration of in situ surface and thickness profile measurements of thin film during deposition using a grating array based wavefront sensor

Here we introduce an in situ and non-intrusive surface and thickness profile monitoring scheme of thin-film growth during deposition. The scheme is implemented using a programmable grating array based zonal wavefront sensor integrated with a thin-film deposition unit. It provides both 2D surface and thickness profiles of any reflecting thin film during deposition without requiring the properties of the thin-film material. The proposed scheme comprises a mechanism to nullify the effect of vibrations which is normally built in with the vacuum pumps of thin-film deposition systems and is largely immune to the fluctuations in the probe beam intensity. The final thickness profile obtained is compared with independent off-line measurement and the two results are observed to be in agreement.

Diffraction-induced divergence of propagating Zernike mode aberrations

In this paper, we study how a propagating laser beam carrying Zernike mode aberrations in its phase profile undergoes divergence due to diffraction. We first numerically simulate the propagation of Zernike modes through different distances using the Fresnel diffraction integral. We observe that a light beam carrying different Zernike modes results in irradiance patterns of various shapes and sizes. We introduce a new parameter to quantify the divergence experienced by different modes. Based on our numerical simulation study, we then construct a functional form to quantify the divergence of different Zernike modes while propagating different distances. The results using the functional form agree very well with the numerical simulation results. The proposed functional form can be employed even for a beam carrying a combination of Zernike modes.

Improved linear response in a modal wavefront sensor

The modal wavefront sensor provides a direct and less computationally intensive way, relative to a zonal wavefront sensor, of estimating the various aberration modes present in a beam of light. Such wavefront sensors are particularly useful when the optical system concerned is affected by a limited number of aberration modes. Unfortunately, the basic design of the modal wavefront sensor suffers from reduced linear response and intermodal crosstalk. As a result of the reduced linear response, the magnitude of an aberration mode estimated by a modal wavefront sensor may differ from the actual strength of the aberration mode. This difference is even more if other aberration modes, in addition to the aberration mode to be detected, also referred to as the sensor mode, are present in the beam. In this paper we propose a modal wavefront sensing scheme where the sensor output has a significantly enhanced linear response. The proposed scheme also provides superior intermodal crosstalk immunity, especially for a few selected aberration modes. We first show theoretically how by incorporating a variable magnitude of the sensor mode into the beam the precise strength of the same mode can be estimated. Results from numerical simulation and an experiment using a proof of principle setup demonstrate the improved performance by the proposed scheme.

A laser scanning microscope executing intraframe polarization switching of the illumination beam

The polarization of the illumination beam in a beam scanning microscope such as the confocal microscope plays an important role in extracting the orientational information of the molecules in the specimen. In this paper, we present the development of a beam scanning microscope comprising a custom designed optical arrangement to obtain images of the same target with different polarizations of the illumination beam. The optical arrangement, based on a ferroelectric liquid crystal spatial light modulator (FELCSLM), can generate homogeneous as well as non-homogeneous user defined polarization profiles over the cross-sectional area of the illumination beam. Here, we employ a computer generated holography technique and exploit the programmability of the FELCSLM display to considerably reduce the time gap between two successive illuminations of each location of the specimen with two different polarizations. We demonstrate the working of the beam scanning microscope where the polarization profile of the illumination beam is switched at the end of every line scanned, in contrast to a conventional beam scanning microscope where the polarization can be switched at the end of every frame scanned. Preliminary experimental results obtained using a polarization sensitive target confirm the feasibility of the proposed scheme.

Improvement in error propagation in the Shack-Hartmann-type zonal wavefront sensors

Estimation of the wavefront from measured slope values is an essential step in a Shack-Hartmann-type wavefront sensor. Using an appropriate estimation algorithm, these measured slopes are converted into wavefront phase values. Hence, accuracy in wavefront estimation lies in proper interpretation of these measured slope values using the chosen estimation algorithm. There are two important sources of errors associated with the wavefront estimation process, namely, the slope measurement error and the algorithm discretization error. The former type is due to the noise in the slope measurements or to the detector centroiding error, and the latter is a consequence of solving equations of a basic estimation algorithm adopted onto a discrete geometry. These errors deserve particular attention, because they decide the preference of a specific estimation algorithm for wavefront estimation. In this paper, we investigate these two important sources of errors associated with the wavefront estimation algorithms of Shack-Hartmann-type wavefront sensors. We consider the widely used Southwell algorithm and the recently proposed Pathak-Boruah algorithm [J. Opt.16, 055403 (2014)JOOPDB0150-536X10.1088/2040-8978/16/5/055403] and perform a comparative study between the two. We find that the latter algorithm is inherently superior to the Southwell algorithm in terms of the error propagation performance. We also conduct experiments that further establish the correctness of the comparative study between the said two estimation algorithms.

Note: Current induced fluctuations in the orientation of the beam diffracted by a liquid crystal spatial light modulator

In this paper, we report a peculiar movement of the beam cross sections associated with both the diffracted and undiffracted laser beams from a liquid crystal spatial light modulator (LCSLM). The beam movement becomes noticeable when the beam position is monitored continuously for several hours. We perform experiments to show that the beam movement is non-mechanical in nature and is connected with the power on/off instants of the LCSLM as well as the heat conductivity of the mounting slab which acts as the rigid support to the LCSLM panel. We also present a detailed analysis of the experimental findings to ascertain the possible cause of the beam fluctuations.

Zonal wavefront sensing with enhanced spatial resolution

In this Letter, we introduce a scheme to enhance the spatial resolution of a zonal wavefront sensor. The zonal wavefront sensor comprises an array of binary gratings implemented by a ferroelectric spatial light modulator (FLCSLM) followed by a lens, in lieu of the array of lenses in the Shack-Hartmann wavefront sensor. We show that the fast response of the FLCSLM device facilitates quick display of several laterally shifted binary grating patterns, and the programmability of the device enables simultaneous capturing of each focal spot array. This eventually leads to a wavefront estimation with an enhanced spatial resolution without much sacrifice on the sensor frame rate, thus making the scheme suitable for high spatial resolution measurement of transient wavefronts. We present experimental and numerical simulation results to demonstrate the importance of the proposed wavefront sensing scheme.

Experimental observation of the aberration effects on a radially polarized beam

In the last couple of decades the radially polarized beam has been gaining a lot of importance in diverse areas owing to its unique properties, especially near the focus of a lens. For instance, when focused tightly, the radially polarized beam produces a strong axially polarized field on the optical axis near the focus. Some of the areas where the radially polarized beam is found to be useful are optical trapping, laser machining, optical data storage, optical superresolution, and so on. Considering the fact that there is not any optical system that can be treated as perfectly aberration free, the applications of the radially polarized beam can, in practice, more or less be affected by the presence of aberrations. Indeed, there have been studies to understand the properties of the radially polarized beam in the presence of various aberrations. However, most such studies have been purely theoretical without being complimented by experimental results. In this paper, we present a comprehensive experimental investigation on the effect of aberrations on a focused radially polarized beam. The accuracy of our experimental results is confirmed by comparing them with the equivalent numerical simulation results.

Experimental demonstration of a light beam with superior aberration resilience

In this Letter, we present the experimental results of a focused light beam that exhibits superior resilience to various common monochromatic aberrations. The light beam, obtained by applying a helical phase mask on an azimuthally polarized beam, has an Airy pattern that is like a circularly symmetric focal spot. Our results show that the beam in the presence of aberrations has better performance in terms of the Strehl ratio and the effect on the radius of the encircled energy relative to a normal linearly polarized or circularly polarized beam. Our experimental results agree well with the corresponding theoretical results.

Zonal wavefront sensing using a grating array printed on a polyester film

In this paper, we describe the development of a zonal wavefront sensor that comprises an array of binary diffraction gratings realized on a transparent sheet (i.e., polyester film) followed by a focusing lens and a camera. The sensor works in a manner similar to that of a Shack-Hartmann wavefront sensor. The fabrication of the array of gratings is immune to certain issues associated with the fabrication of the lenslet array which is commonly used in zonal wavefront sensing. Besides the sensing method offers several important advantages such as flexible dynamic range, easy configurability, and option to enhance the sensing frame rate. Here, we have demonstrated the working of the proposed sensor using a proof-of-principle experimental arrangement.

Poynting vector profile of a tightly focused radially polarized beam in the presence of primary aberrations

The Poynting vector profile of a tightly focused radially polarized beam has some unique and interesting properties. For instance the light on the optical axis in the focal volume corresponds to a null Poynting vector, indicating the light there to be nonpropagating. However, the beam here is considered to be an unaberrated one. Thus it will be important to know whether the commonly occurring monochromatic aberrations can have any effect on the ideal Poynting vector profile of a radially polarized beam. In this paper we make use of the Fourier transform form of the vectorial diffraction theory to investigate the effect of primary aberrations on the Poynting vector profile of a radially polarized beam under tight focusing conditions. We present here the results from our study on the behavior of both the time averaged and time dependent Poynting vector profiles in the focal volume.

Note: laser beam scanning using a ferroelectric liquid crystal spatial light modulator

In this work we describe laser beam scanning using a ferroelectric liquid crystal spatial light modulator. Commercially available ferroelectric liquid crystal spatial light modulators are capable of displaying 85 colored images in 1 s using a time dithering technique. Each colored image, in fact, comprises 24 single bit (black and white) images displayed sequentially. We have used each single bit image to write a binary phase hologram. For a collimated laser beam incident on the hologram, one of the diffracted beams can be made to travel along a user defined direction. We have constructed a beam scanner employing the above arrangement and demonstrated its use to scan a single laser beam in a laser scanning optical sectioning microscope setup.

Note: a simple experimental arrangement to generate optical vortex beams

In this Note, we present a simple experimental arrangement to generate optical vortex beams. We have demonstrated how by taking print of an interferogram on a transparent sheet, vortex beams with various topological charges can be generated. Experimental results show that the vortex beam indeed carries the topological charge that is used to compute the interferograms. In addition to being simple and inexpensive, one major advantage of the arrangement is that it makes it possible to generate different vortex beams quickly, unlike using the photographic process to create the holograms.

Axial separation of orthogonally polarized focal field components due to a radially polarized beam

In this paper, we investigate the field distribution in the focal volume of an aberrated radially polarized beam. Using two different forms of the vectorial diffraction theory, we show that the presence of defocus in the beam displaces both the axially and the radially polarized fields parallel to the optical axis of the focusing lens, while the presence of spherical aberration primarily shifts the longitudinally polarized field only. This facilitates axial separation of the two orthogonally polarized field components, resulting in a significant boost to the ratio of the peak longitudinally polarized field to the peak laterally polarized field in the focal plane. We further show that with an appropriate combination of oppositely signed defocus and spherical aberration, the energy density in the focal volume due to the longitudinally polarized field can be caused to peak at the focal plane. The results obtained are expected to be beneficial to the applications requiring a stronger longitudinally polarized focal field relative to the laterally polarized focal field component.

Zonal wavefront sensor with reduced number of rows in the detector array

In this paper, we describe a zonal wavefront sensor in which the photodetector array can have a smaller number of rows. The test wavefront is incident on a two-dimensional array of diffraction gratings followed by a single focusing lens. The periodicity and the orientation of the grating rulings of each grating can be chosen such that the +1 order beam from the gratings forms an array of focal spots in the detector plane. We show that by using a square array of zones, it is possible to generate an array of +1 order focal spots having a smaller number of rows, thus reducing the height of the required detector array. The phase profile of the test wavefront can be estimated by measuring the displacements of the +1 order focal spots for the test wavefront relative to the +1 order focal spots for a plane reference wavefront. The narrower width of the photodetector array can offer several advantages, such as a faster frame rate of the wavefront sensor, a reduced amount of cross talk between the nearby detector zones, and a decrease in the maximum thermal noise. We also present experimental results of a proof-of-concept experimental arrangement using the proposed wavefront sensing scheme.

Interferometry using binary holograms without high order diffraction effects

We describe a technique for a phase-stepping interferometer based on programmable binary phase holograms, particularly useful for optical testing of aspheric or free-form surfaces. It is well-known that binary holograms can be used to generate reference surfaces for interferometry, but a major problem is that cross talk from higher diffraction orders and aliasing can reduce the fidelity of the system. Here, we propose a new encoding technique which improves the accuracy of the technique and demonstrate its implementation using a binary liquid crystal spatial light modulator.

Optical sectioning microscope with a binary hologram based beam scanning

We describe the development of a beam scanning microscope that can perform optical sectioning based on the principle of confocal microscopy. The scanning is performed by a laser beam diffracted from a dynamic binary hologram implemented using a liquid crystal spatial light modulator. Using the proposed scanning mechanism, unlike the conventional confocal microscopes, scanning over a two-dimensional area of the sample can be obtained without the use of a pair of galvo mirror scanners. The proposed microscope has a number of advantages, such as superior frame to frame repeatability, simpler optical arrangement, increased pixel dwell time relative to the time between two pixels, illumination of only the sample points without pulsing the laser, and absolute control over the amplitude and phase of the illumination beam on a pixel to pixel basis. The proposed microscope can be particularly useful for applications requiring very long exposure time or very large working distance objective lenses. In this paper we present experimental implementation of the setup using a nematic liquid crystal spatial light modulator and proof-of-concept experimental results.

Lateral resolution enhancement in confocal microscopy by vectorial aperture engineering

This article reports the design and implementation of a lateral resolution-enhancement technique in confocal microscopy that can work, in principle, either in the reflection mode or in the fluorescence mode. Taking the difference between two images corresponding to two different vectorially (involving amplitude, phase, and polarization of light) engineered illumination pupils or apertures of a confocal microscope, high spatial frequency contents in the resultant image can be significantly enhanced. This can be realized by incorporating an extra vectorial beam-forming element into the illumination beam path of a conventional confocal microscope. The method of the proposed technique has been explained by giving it an analytical treatment supported by numerical simulation results. The technique has been implemented in a reflection mode confocal microscope and results obtained are presented.

Zonal wavefront sensing using an array of gratings

We describe a zonal-wavefront-sensing technique using an array of plane diffraction gratings. A spatially coherent beam, whose wavefront is to be measured, is incident on the array of gratings. The direction of a diffracted beam of a certain diffraction order is a function of the orientation and periodicity of the corresponding grating. Thus, by choosing the orientation and periodicity of each grating appropriately and by having a lens immediately behind the grating array, it is possible to get an array of focal spots. The profile of the incident wavefront can be estimated from the displacements of these focal spots relative to those due to an unaberrated beam. The arrangement makes it possible to increase the separation between two adjacent focal spots corresponding to two nearby gratings without effecting the areas of the gratings. Consequently, a relatively large dynamic range in wavefront measurement can be achieved without compromising the accuracy. With the arrangement it is also possible to use a photodetector array whose outline is independent of the grating array outline. The proposed wavefront-sensing technique is implemented experimentally using a liquid-crystal spatial-light modulator in conjunction with a CCD camera, and the obtained results are presented.

Minerals and functional groups present in the jackfruit seed: a spectroscopic investigation

In this work, emission and Fourier transform infrared spectra of the jackfruit seed, in powdered form, are recorded. Analysis of the emission spectrum confirms the presence of two hitherto undetected elements, manganese and magnesium. The Fourier transform infrared spectrum reveals the presence of some specific functional groups, attributed to the different bands present in the spectrum.

Laser scanning confocal microscope with programmable amplitude, phase, and polarization of the illumination beam

We describe the design and construction of a laser scanning confocal microscope with programmable beam forming optics. The amplitude, phase, and polarization of the laser beam used in the microscope can be controlled in real time with the help of a liquid crystal spatial light modulator, acting as a computer generated hologram, in conjunction with a polarizing beam splitter and two right angled prisms assembly. Two scan mirrors, comprising an on-axis fast moving scan mirror for line scanning and an off-axis slow moving scan mirror for frame scanning, configured in a way to minimize the movement of the scanned beam over the pupil plane of the microscope objective, form the XY scan unit. The confocal system, that incorporates the programmable beam forming unit and the scan unit, has been implemented to image in both reflected and fluorescence light from the specimen. Efficiency of the system to programmably generate custom defined vector beams has been demonstrated by generating a bottle structured focal volume, which in fact is the overlap of two cross polarized beams, that can simultaneously improve both the lateral and axial resolutions if used as the de-excitation beam in a stimulated emission depletion confocal microscope.

Stimulated emission depletion microscopy with a supercontinuum source and fluorescence lifetime imaging

We demonstrate stimulated emission depletion (STED) microscopy implemented in a laser scanning confocal microscope using excitation light derived from supercontinuum generation in a microstructured optical fiber. Images with resolution improvement beyond the far-field diffraction limit in both the lateral and axial directions were acquired by scanning overlapped excitation and depletion beams in two dimensions using the flying spot scanner of a commercially available laser scanning confocal microscope. The spatial properties of the depletion beam were controlled holographically using a programmable spatial light modulator, which can rapidly change between different STED imaging modes and also compensate for aberrations in the optical path. STED fluorescence lifetime imaging microscopy is demonstrated through the use of time-correlated single photon counting.

Susceptibility to and correction of azimuthal aberrations in singular light beams

We show how the effects of azimuthal optical aberrations on singular light beams can result in an intensity modulation in the beam waist or focal point spread function (PSF) that is directly proportional to the amplitude of the applied phase aberration. The resulting distortions are enough to significantly degrade the utility of the singular beams even in well corrected optical systems. However we show that pattern of these intensity modulations is related to the azimuthal order of the applied aberration and we suggest how this can be used to measure those aberrations. We demonstrate a closed loop system using a liquid crystal spatial light modulator as a programmable diffractive optical element to both generate the beam and correct for the sensed aberrations based on feed back from a CCD detected intensity image of the focal point spread function.