Measure and model a 3-D space-variant PSF for fluorescence microscopy image deblurring

Evaluating the resolution of conventional optical microscopes through point spread function measurement

In the imaging process of conventional optical microscopy, the primary factor hindering microscope resolution is the energy diffusion of incident light, most directly described by the point spread function (PSF). Therefore, accurate calculation and measurement of PSF are essential for evaluating and enhancing imaging resolution. Currently, there are various methods to obtain PSFs, each with different advantages and disadvantages suitable for different scenarios. To provide a comprehensive analysis of PSF-obtaining methods, this study classifies them into four categories based on different acquisition principles and analyzes their advantages and disadvantages, starting from the propagation property of light in optical physics. Finally, two PSF-obtaining methods are proposed based on mathematical modeling and deep learning, demonstrating their effectiveness through experimental results. This study compares and analyzes these results, highlighting the practical applications of image deblurring.

Three-dimensional point spread function estimation method for mid-wave infrared microscope imaging

A three-dimensional point spread function experimental estimation method based on the system's focal plane array spatial local impulse response of a mid-wave infrared microscope is presented. The method uses several out-of-focus two-dimensional point spread function planes to achieve a single three-dimensional point spread function of the whole microscope's optical spreading, expanding the limits of infrared optical technology by one dimension. This technique includes stages of image acquisition, nonuniformity correction, filtering, and multi-planar reconstruction steps, and its effectiveness is demonstrated on biological sample image restoration by means of a multi-planar refocusing application.

Development of Planar Illumination Strategies for Solving Mysteries in the Sub-Cellular Realm

Optical microscopy has vastly expanded the frontiers of structural and functional biology, due to the non-invasive probing of dynamic volumes in vivo. However, traditional widefield microscopy illuminating the entire field of view (FOV) is adversely affected by out-of-focus light scatter. Consequently, standard upright or inverted microscopes are inept in sampling diffraction-limited volumes smaller than the optical system's point spread function (PSF). Over the last few decades, several planar and structured (sinusoidal) illumination modalities have offered unprecedented access to sub-cellular organelles and 4D (3D + time) image acquisition. Furthermore, these optical sectioning systems remain unaffected by the size of biological samples, providing high signal-to-noise (SNR) ratios for objective lenses (OLs) with long working distances (WDs). This review aims to guide biologists regarding planar illumination strategies, capable of harnessing sub-micron spatial resolution with a millimeter depth of penetration.

Navigating the Light-Sheet Image Analysis Software Landscape: Concepts for Driving Cohesion From Data Acquisition to Analysis

From the combined perspective of biologists, microscope instrumentation developers, imaging core facility scientists, and high performance computing experts, we discuss the challenges faced when selecting imaging and analysis tools in the field of light-sheet microscopy. Our goal is to provide a contextual framework of basic computing concepts that cell and developmental biologists can refer to when mapping the peculiarities of different light-sheet data to specific existing computing environments and image analysis pipelines. We provide our perspective on efficient processes for tool selection and review current hardware and software commonly used in light-sheet image analysis, as well as discuss what ideal tools for the future may look like.

Global deblurring for continuous out-of-focus images using a depth-varying diffusion model

The phenomenon of continuous out-of-focus imaging often occurs in high-magnification optical microscopy when observing large-scale targets. Lacking of accurate depth-varying point spread functions (DVPSFs) for blurred regions at different depths, it is difficult to locally reconstruct the clear images of these blurred regions using traditional deblurring methods, making it unreasonable to globally observe the optical features of large-scale targets in high-magnification optical microscopy. This paper proposes a global deblurring method for continuous out-of-focus images of large-scale sphere samples. In this study, first we analyze the energy diffusion characteristics of the optical imaging process, integrating the relationship between high-frequency energy parameters, optical range distance, and depth of field, and we propose a three-dimensional continuous energy diffusion model for optical imaging. Next, we propose an adaptive weight depth calculation method for a continuously changing surface based on the depth varying diffusion model by introducing the sample surface curvature variation and light direction. Finally, we propose a universal method for deblurring continuous out-of-focus images of large-scale sphere samples for the purpose of observing the global optical features in high-magnification optical microscopy. Moreover, we use dynamic microspheres of different sizes to verify the effectiveness of our proposed method. The results prove that our proposed method can accurately calculate the depth of the sample surface and the energy diffusion parameters at each depth, and it can achieve the image deblurring of a continuously changing surface and the global deblurring of multiple samples in a wide field of view.

3D test sample for the calibration and quality control of stimulated emission depletion (STED) and confocal microscopes

Multiple samples are required to monitor and optimize the quality and reliability of quantitative measurements of stimulated emission depletion (STED) and confocal microscopes. Here, we present a single sample to calibrate these microscopes, align their laser beams and measure their point spread function (PSF) in 3D. The sample is composed of a refractive index matched colloidal crystal of silica beads with fluorescent and gold cores. The microscopes can be calibrated in three dimensions using the periodicity of the crystal; the alignment of the laser beams can be checked using the reflection of the gold cores; and the PSF can be measured at multiple positions and depths using the fluorescent cores. It is demonstrated how this sample can be used to visualize and improve the quality of STED and confocal microscopy images. The sample is adjustable to meet the requirements of different NA objectives and microscopy techniques and additionally can be used to evaluate refractive index mismatches as a function of depth quantitatively.

DVDeconv: An Open-Source MATLAB Toolbox for Depth-Variant Asymmetric Deconvolution of Fluorescence Micrographs

To investigate the cellular structure, biomedical researchers often obtain three-dimensional images by combining two-dimensional images taken along the z axis. However, these images are blurry in all directions due to diffraction limitations. This blur becomes more severe when focusing further inside the specimen as photons in deeper focus must traverse a longer distance within the specimen. This type of blur is called depth-variance. Moreover, due to lens imperfection, the blur has asymmetric shape. Most deconvolution solutions for removing blur assume depth-invariant or x-y symmetric blur, and presently, there is no open-source for depth-variant asymmetric deconvolution. In addition, existing datasets for deconvolution microscopy also assume invariant or x-y symmetric blur, which are insufficient to reflect actual imaging conditions. DVDeconv, that is a set of MATLAB functions with a user-friendly graphical interface, has been developed to address depth-variant asymmetric blur. DVDeconv includes dataset, depth-variant asymmetric point spread function generator, and deconvolution algorithms. Experimental results using DVDeconv reveal that depth-variant asymmetric deconvolution using DVDeconv removes blurs accurately. Furthermore, the dataset in DVDeconv constructed can be used to evaluate the performance of microscopy deconvolution to be developed in the future.

Point spread function degradation model of a polarization imaging system for wide-field subwavelength nanoparticles

We propose a comprehensive point spread function (PSF) degradation model, which considers multiple factors consisting of degradation of specimen retardant sampling and polarization angularly anamorphic sampling, to indicate the image degradation characteristics of polarization imaging systems. First, a one-layer optical coherence tomography (OCT) model was established to express the retardancy of medium-loading specimens. Then, a PSF degradation model of angularly anamorphic polarization sampling was deduced through the retrieval of Stokes parameters. Finally, maximum a posteriori probability (MAP) was adopted to assess the distribution of the proposed model. Hypothesis testing using actual data and numerical simulations demonstrated that the error of the system followed an asymmetric generalized Gaussian distribution (AGGD). Finite-difference time-domain (FDTD) simulation results and an actual imaging experiment demonstrate the consistency of the proposed model and the degradation characteristics of the PSF, which provide support for the improved accuracy and enhanced image quality of the optical field retrieval of nanoparticles.

Deconvolution of light sheet microscopy recordings

We developed a deconvolution software for light sheet microscopy that uses a theoretical point spread function, which we derived from a model of image formation in a light sheet microscope. We show that this approach provides excellent blur reduction and enhancement of fine image details for image stacks recorded with low magnification objectives of relatively high NA and high field numbers as e.g. 2x NA 0.14 FN 22, or 4x NA 0.28 FN 22. For these objectives, which are widely used in light sheet microscopy, sufficiently resolved point spread functions that are suitable for deconvolution are difficult to measure and the results obtained by common deconvolution software developed for confocal microscopy are usually poor. We demonstrate that the deconvolutions computed using our point spread function model are equivalent to those obtained using a measured point spread function for a 10x objective with NA 0.3 and for a 20x objective with NA 0.45.