Multiplexed PSF Engineering for Three-Dimensional Multicolor Particle Tracking

Depth-enhanced high-throughput microscopy by compact PSF engineering

High-throughput microscopy is vital for screening applications, where three-dimensional (3D) cellular models play a key role. However, due to defocus susceptibility, current 3D high-throughput microscopes require axial scanning, which lowers throughput and increases photobleaching and photodamage. Point spread function (PSF) engineering is an optical method that enables various 3D imaging capabilities, yet it has not been implemented in high-throughput microscopy due to the cumbersome optical extension it typically requires. Here we demonstrate compact PSF engineering in the objective lens, which allows us to enhance the imaging depth of field and, combined with deep learning, recover 3D information using single snapshots. Beyond the applications shown here, this work showcases the usefulness of high-throughput microscopy in obtaining training data for deep learning-based algorithms, applicable to a variety of microscopy modalities.

Simultaneous spectral differentiation of multiple fluorophores in super-resolution imaging using a glass phase plate

By engineering the point-spread function (PSF) of single molecules, different fluorophore species can be imaged simultaneously and distinguished by their unique PSF patterns. Here, we insert a silicon-dioxide phase plate at the Fourier plane of the detection path of a wide-field fluorescence microscope to produce distinguishable PSFs (X-PSFs) at different wavelengths. We demonstrate that the resulting PSFs can be localized spatially and spectrally using a maximum-likelihood estimation algorithm and can be utilized for hyper-spectral super-resolution microscopy of biological samples. We produced superresolution images of fixed U2OS cells using X-PSFs for dSTORM imaging with simultaneous illumination of up to three fluorophore species. The species were distinguished only by the PSF pattern. We achieved ∼21-nm lateral localization precision (FWHM) and ∼17-nm axial precision (FWHM) with an average of 1,800 - 3,500 photons per PSF and a background as high as 130 - 400 photons per pixel. The modified PSF distinguished fluorescent probes with ∼80 nm separation between spectral peaks.

Near index matching enables solid diffractive optical element fabrication via additive manufacturing

Diffractive optical elements (DOEs) have a wide range of applications in optics and photonics, thanks to their capability to perform complex wavefront shaping in a compact form. However, widespread applicability of DOEs is still limited, because existing fabrication methods are cumbersome and expensive. Here, we present a simple and cost-effective fabrication approach for solid, high-performance DOEs. The method is based on conjugating two nearly refractive index-matched solidifiable transparent materials. The index matching allows for extreme scaling up of the elements in the axial dimension, which enables simple fabrication of a template using commercially available 3D printing at tens-of-micrometer resolution. We demonstrated the approach by fabricating and using DOEs serving as microlens arrays, vortex plates, including for highly sensitive applications such as vector beam generation and super-resolution microscopy using MINSTED, and phase-masks for three-dimensional single-molecule localization microscopy. Beyond the advantage of making DOEs widely accessible by drastically simplifying their production, the method also overcomes difficulties faced by existing methods in fabricating highly complex elements, such as high-order vortex plates, and spectrum-encoding phase masks for microscopy.

Single-molecule imaging in the primary cilium

The primary cilium is an important signaling organelle critical for normal development and tissue homeostasis. Its small dimensions and complexity necessitate advanced imaging approaches to uncover the molecular mechanisms behind its function. Here, we outline how single-molecule fluorescence microscopy can be used for tracking molecular dynamics and interactions and for super-resolution imaging of nanoscale structures in the primary cilium. Specifically, we describe in detail how to capture and quantify the 2D dynamics of individual transmembrane proteins PTCH1 and SMO and how to map the 3D nanoscale distributions of the inversin compartment proteins INVS, ANKS6, and NPHP3. This protocol can, with minor modifications, be adapted for studies of other proteins and cell lines to further elucidate the structure and function of the primary cilium at the molecular level.

Impact of Saccharomyces cerevisiae on the Field of Single-Molecule Biophysics

Cellular functions depend on the dynamic assembly of protein regulator complexes at specific cellular locations. Single Molecule Tracking (SMT) is a method of choice for the biochemical characterization of protein dynamics in vitro and in vivo. SMT follows individual molecules in live cells and provides direct information about their behavior. SMT was successfully applied to mammalian models. However, mammalian cells provide a complex environment where protein mobility depends on numerous factors that are difficult to control experimentally. Therefore, yeast cells, which are unicellular and well-studied with a small and completely sequenced genome, provide an attractive alternative for SMT. The simplicity of organization, ease of genetic manipulation, and tolerance to gene fusions all make yeast a great model for quantifying the kinetics of major enzymes, membrane proteins, and nuclear and cellular bodies. However, very few researchers apply SMT techniques to yeast. Our goal is to promote SMT in yeast to a wider research community. Our review serves a dual purpose. We explain how SMT is conducted in yeast cells, and we discuss the latest insights from yeast SMT while putting them in perspective with SMT of higher eukaryotes.

Monocular kilometer-scale passive ranging by point-spread function engineering

Standard imaging systems are designed for 2D representation of objects, while information about the third dimension remains implicit, as imaging-based distance estimation is a difficult challenge. Existing long-range distance estimation technologies mostly rely on active emission of signal, which as a subsystem, constitutes a significant portion of the complexity, size and cost of the active-ranging apparatus. Despite the appeal of alleviating the requirement for signal-emission, passive distance estimation methods are essentially nonexistent for ranges greater than a few hundreds of meters. Here, we present monocular long-range, telescope-based passive ranging, realized by integration of point-spread-function engineering into a telescope, extending the scale of point-spread-function engineering-based ranging to distances where it has never been tested before. We provide experimental demonstrations of the optical system in a variety of challenging imaging scenarios, including adversarial weather conditions, dynamic targets and scenes of diversified textures, at distances extending beyond 1.7 km. We conclude with brief quantification of the effect of atmospheric turbulence on estimation precision, which becomes a significant error source in long-range optical imaging.

Optimization of Spot Efficiency of Double-Helix Point Spread Function and Its Application in Intracellular Imaging

The nano-scale spatial positioning of nanoparticles in tumor cells can be achieved through the double-helix point spread functions (DH-PSF). Nevertheless, certain issues such as low light intensity concentration of the main lobes, the influence of the side lobes, and the aberrations of the imaging system result in poor image quality and reduce the positioning accuracy of the fluorescent nanoparticles. In this paper, an iterative optimization algorithm that combines Laguerre–Gaussian modes and Zernike polynomials is proposed. The double-helix point spread function, constructed by the linear superposition of the Laguerre–Gaussian mode and Zernike polynomials, is used to express aberrations in the imaging system. The simulation results indicated that the light intensity concentration of the main lobes is increased by 45.51% upon the use of the optimization process. Based on the simulation results, the phase modulation plate was designed and processed while a 4f positioning imaging system was built. Human osteosarcoma cells, labeled by CdTe/CdS/ZnS quantum dots, were used as samples, and the position imaging experiment was carried out. The image information entropy was used as the clarity evaluation index. The experimental results showed that the image information entropy of the DH-PSF position imaging was reduced from 4.22 before optimization to 2.65 after optimization, and the image clarity was significantly improved. This result verified the effectiveness of the optimization method that was proposed in this work.

Resolving the Three-Dimensional Rotational and Translational Dynamics of Single Molecules Using Radially and Azimuthally Polarized Fluorescence

We report a radially and azimuthally polarized (raPol) microscope for high detection and estimation performance in single-molecule orientation-localization microscopy (SMOLM). With 5000 photons detected from Nile red (NR) transiently bound within supported lipid bilayers (SLBs), raPol SMOLM achieves 2.9 nm localization precision, 1.5° orientation precision, and 0.17 sr precision in estimating rotational wobble. Within DPPC SLBs, SMOLM imaging reveals the existence of randomly oriented binding pockets that prevent NR from freely exploring all orientations. Treating the SLBs with cholesterol-loaded methyl-β-cyclodextrin (MβCD-chol) causes NR's orientational diffusion to be dramatically reduced, but curiously NR's median lateral displacements drastically increase from 20.8 to 75.5 nm (200 ms time lag). These jump diffusion events overwhelmingly originate from cholesterol-rich nanodomains within the SLB. These detailed measurements of single-molecule rotational and translational dynamics are made possible by raPol's high measurement precision and are not detectable in standard SMLM.