Hasti Shabani

Comparison of two structured illumination techniques based on different 3D illumination patterns

Manipulating the excitation pattern in optical microscopy has led to several super-resolution techniques. Among different patterns, the lateral sinusoidal excitation was used for the first demonstration of structured illumination microscopy (SIM), which provides the fastest SIM acquisition system (based on the number of raw images required) compared to the multi-spot illumination approach. Moreover, 3D patterns that include lateral and axial variations in the illumination have attracted more attention recently as they address resolution enhancement in three dimensions. A threewave (3W) interference technique based on coherent illumination has already been shown to provide super-resolution and optical sectioning in 3D-SIM. In this paper, we investigate a novel tunable technique that creates a 3D pattern from a set of multiple incoherently illuminated parallel slits that act as light sources for a Fresnel biprism. This setup is able to modulate the illumination pattern in the object space both axially and laterally with adjustable modulation frequencies. The 3D forward model for the new system is developed here to consider the effect of the axial modulation due to the 3D patterned illumination. The performance of 3D-SIM based on 3W interference and the tunable system are investigated in simulation and compared based on two different criteria. First, restored images obtained for both 3D-SIM systems using a generalized Wiener filter are compared to determine the effect of the illumination pattern on the reconstruction. Second, the effective frequency response of both systems is studied to determine the axial and lateral resolution enhancement that is obtained in each case.

3D structured illumination microscopy using an incoherent illumination system based on a Fresnel biprism

Three-dimensional (3D) structured illumination (SI) patterns that include lateral and axial variations have attracted more attention recently as their use in fluorescence microscope enhances the 3D resolution of the native imaging system. 3D SI patterns have already been created by interfering three mutually-coherent waves using a diffraction grating or some electro-optical devices such as spatial light modulators. Here, an interesting approach to generate a 3D SI pattern of tunable modulation frequency is shown. Our proposed illumination system is based on the incoherent illumination of a Fresnel biprism using several equidistant linear sources (i.e., slits). Previously, we investigated and compared numerically this tunable SI microscopy (SIM) system with the one achieved with three-wave interference. In this contribution, we implement our proposed incoherent 3D SIM system of tunable-frequency in an open-setup. We evaluate the axial confinement of the illumination pattern obtained with this system by recording the SI pattern using a mirror sample and different number of slits and compare these data with simulation results. Moreover, we verify that with a higher number of slits used, the axial confinement of the pattern increases, and consequently, the system’s optical sectioning capability improves.

Preprocessing method to correct illumination pattern in sinusoidal-based structured illumination microscopy

The restored images in structured illumination microscopy (SIM) can be affected by residual fringes due to a mismatch between the illumination pattern and the sinusoidal model assumed by the restoration method. When a Fresnel biprism is used to generate a structured pattern, this pattern cannot be described by a pure sinusoidal function since it is distorted by an envelope due to the biprism’s edge. In this contribution, we have investigated the effect of the envelope on the restored SIM images and propose a computational method in order to address it. The proposed approach to reduce the effect of the envelope consists of two parts. First, the envelope of the structured pattern, determined through calibration data, is removed from the raw SIM data via a preprocessing step. In the second step, a notch filter is applied to the images, which are restored using the well-known generalized Wiener filter, to filter any residual undesired fringes. The performance of our approach has been evaluated numerically by simulating the effect of the envelope on synthetic forward images of a 6-μm spherical bead generated using the real pattern and then restored using the SIM approach that is based on an ideal pure sinusoidal function before and after our proposed correction method. The simulation result shows 74% reduction in the contrast of the residual pattern when the proposed method is applied. Experimental results from a pollen grain sample also validate the proposed approach.

Improvement of two-dimensional structured illumination microscopy with an incoherent illumination pattern of tunable frequency

In two-dimensional structured illumination microscopy (2D-SIM), high-resolution images with optimal optical sectioning (OS) cannot be obtained simultaneously. This tradeoff can be overcome by using a tunable-frequency 2D-SIM system and a proper reconstruction method. The goal of this work is twofold. First, we present a computational approach to reconstruct optical-sectioned images with super-resolution enhancement (OS-SR) by using a tunable SIM system. Second, we propose an incoherent tunable-frequency 2D-SIM system based on a Fresnel biprism implementation. Integration of the proposed computational method with this tunable structured illumination (SI) system results in a new 2D-SIM system that is advantageous compared to other 2D-SIM systems with comparable complexity, because it provides high-resolution OS images independent of the objective lens used, without the presence of coherent noise and without reducing the contrast of the structured pattern, as in other incoherent implementations. Evaluation of our proposed system is demonstrated with comparative studies of simulated and experimental reconstructed images to validate our theoretical findings. Our experimental results show a simultaneous improvement of the lateral resolution by a factor of 1.8× with the desired OS capability achieved in the resulting OS-SR combination image. Our experimental results also verify that our system can provide better OS capability than the commercial Zeiss ApoTome-SIM system in the investigated study.

Comparison of 3D structured patterns with tunable frequency for use in structured illumination microscopy

Structured illumination microscopy (SIM) doubles the lateral resolution and produces optically-sectioned images. In SIM, the illumination system is modified in order to illuminate the sample by a structured pattern. Previously, axially-localized high-contrast sinusoidal patterns generated using a slit-prism illumination system based on a Fresnel biprism were investigated. In this contribution, we propose a Wollaston prism to replace the Fresnel biprism and produce the corresponding 3D structured illumination pattern. In this study, both optical elements are illuminated by the light emerging from an axial point source. Our results show that the benefits of using a Wollaston prism instead of a Fresnel biprism are twofold: (1) there is no envelope modulation perturbing the sinusoidal patterns and thereby reducing their visibility, and (2) the region of interference fringes is significantly larger than the one created by the Fresnel biprism.

Implementation of an incoherent 3D patterned illumination design in a structured illumination microscope

A novel 3D patterned illumination system using an incoherent light source has potential benefits for structured illumination microscopy (SIM) such as lowered intensity requirements and tunable modulating frequency. The illumination system, based on a coherent source, a set of parallel slits and a beam-splitting Fresnel biprism, generates localized interference fringes with a continuously-tunable range of lateral and axial spatial frequency combinations that are not easily accessible using other existing methods of generating structured illumination. Here we present adaptation of this system to a wide-field fluorescence microscope that tests its suitability for SIM imaging. Numerical simulations and experimental data are used to compare theoretical and practical system properties. Results demonstrate that theoretically predicted illumination properties can be used to select system design parameters and accurately produce specific illumination properties at the microscope sample plane. As part of an imaging system, this illumination approach may improve the applicability of super-resolution SIM to a greater variety of samples.

Experimental Implementation of Wavefront Encoding in 3D Widefield Fluorescence Microscopy Using a Fabricated Phase Mask Designed to Reduce System Depth Variability

Wavefront encoded (WFE) three dimensional fluorescent imaging is studied with a fabricated squared cubic (SQUBIC) phase mask. Experimental results demonstrate that, the WFE system can produce results predicted by simulations, and intermediate WFE images show 3% variability over a 60 µm imaging depth.