Characterization of flat-fielding systems for quantitative microscopy

A Rapid Nanofocusing Method for a Deep-Sea Gene Sequencing Microscope Based on Critical Illumination

In the deep-sea environment, the volume available for an in-situ gene sequencer is severely limited. In addition, optical imaging systems are subject to real-time, large-scale defocusing problems caused by ambient temperature fluctuations and vibrational perturbations. To address these challenges, we propose an edge detection algorithm for defocused images based on grayscale gradients and establish a defocus state detection model with nanometer resolution capabilities by relying on the inherent critical illumination light field. The model has been applied to a prototype deep-sea gene sequencing microscope with a 20× objective. It has demonstrated the ability to focus within a dynamic range of ±40 μm with an accuracy of 200 nm by a single iteration within 160 ms. By increasing the number of iterations and exposures, the focusing accuracy can be refined to 78 nm within a dynamic range of ±100 μm within 1.2 s. Notably, unlike conventional photoelectric hill-climbing, this method requires no additional hardware and meets the wide dynamic range, speed, and high-accuracy autofocusing requirements of deep-sea gene sequencing in a compact form factor.

Collimated flat-top beam shaper metasurface doublet based on the complex-amplitude constraint Gerchberg-Saxton algorithm

Collimated flat-top beam shapers primarily consisting of freeform lenses have a wide range of applications and pose challenges in terms of processing and integration when the diameter is less than millimeters. Metasurfaces represent a promising solution to planarize optics, can mimic any surface curvature without additional fabrication difficulty, and are suitable for flat-top optics. The conventional metasurface design approach relies on imparting the required phase using meta-atoms and encounters challenges in amplitude modulation due to near-field coupling and varying transmittances among meta-atoms with different phases, making the design of flat-top beam shapers difficult. In this paper, we propose a complex-amplitude constraint Gerchberg-Saxton algorithm for designing a collimated flat-top beam shaper metasurface doublet, which avoids the influence of strong near-field coupling on the amplitude distribution and simultaneously considers the amplitude-phase characteristics of the meta-atoms. A collimated flat-top beam with exceptional homogeneity U p of approximately 0.01, a wavefront error less than 0.1λ, and a transmittance higher than 86 % is experimentally obtained, comparable to commercial products based on freeform lenses. A collimated flat-top beam shaper metasurface doublet for generating flat-top beam is introduced, promoting efficient integration with laser systems.

Freeform surface topology prediction for prescribed illumination via semi-supervised learning

Despite significant advances in the field of freeform optical design, there still remain various unsolved problems. One of these is the design of smooth, shallow freeform topologies, consisting of multiple convex, concave and saddle shaped regions, in order to generate a prescribed illumination pattern. Such freeform topologies are relevant in the context of glare-free illumination and thin, refractive beam shaping elements. Machine learning techniques already proved to be extremely valuable in solving complex inverse problems in optics and photonics, but their application to freeform optical design is mostly limited to imaging optics. This paper presents a rapid, standalone framework for the prediction of freeform surface topologies that generate a prescribed irradiance distribution, from a predefined light source. The framework employs a 2D convolutional neural network to model the relationship between the prescribed target irradiance and required freeform topology. This network is trained on the loss between the obtained irradiance and input irradiance, using a second network that replaces Monte-Carlo raytracing from source to target. This semi-supervised learning approach proves to be superior compared to a supervised learning approach using ground truth freeform topology/irradiance pairs; a fact that is connected to the observation that multiple freeform topologies can yield similar irradiance patterns. The resulting network is able to rapidly predict smooth freeform topologies that generate arbitrary irradiance patterns, and could serve as an inspiration for applying machine learning to other open problems in freeform illumination design.

A spatially uniform illumination source for widefield multi-spectral optical microscopy

Illumination uniformity is a critical parameter for excitation and data extraction quality in widefield biological imaging applications. However, typical imaging systems suffer from spatial and spectral non-uniformity due to non-ideal optical elements, thus require complex solutions for illumination corrections. We present Effective Uniform Color-Light Integration Device (EUCLID), a simple and cost-effective illumination source for uniformity corrections. EUCLID employs a diffuse-reflective, adjustable hollow cavity that allows for uniform mixing of light from discrete light sources and modifies the source field distribution to compensate for spatial non-uniformity introduced by optical components in the imaging system. In this study, we characterize the light coupling efficiency of the proposed design and compare the uniformity performance with the conventional method. EUCLID demonstrates a remarkable illumination improvement for multi-spectral imaging in both Nelsonian and Koehler alignment with a maximum spatial deviation of ≈ 1% across a wide field-of-view.

The K2: Open-source simultaneous triple-color TIRF microscope for live-cell and single-molecule imaging

Imaging the dynamics and interactions of biomolecules at the single-molecule level in live cells and reconstituted systems has generated unprecedented knowledge about the biomolecular processes underlying many cellular functions. To achieve the speed and sensitivity needed to detect and follow individual molecules, these experiments typically require custom-built microscopes or custom modifications of commercial systems. The costs of such single-molecule microscopes, their technical complexity and the lack of open-source documentation on how to build custom setups therefore limit the accessibility of single-molecule imaging techniques. To advance the adaptation of dynamic single-molecule imaging by a wider community, we present the "K2": an open-source, simultaneous triple-color total internal reflection fluorescence (TIRF) microscope specifically designed for live-cell and single-molecule imaging. We explain our design considerations and provide step-by-step building instructions, parts list and full CAD models. The modular design of this TIRF microscope allows users to customize it to their scientific and financial needs, or to re-use parts of our design to improve the capabilities of their existing setups without necessarily having to build a full copy of the K2 microscope.

Quality assessment in light microscopy for routine use through simple tools and robust metrics

Although there is a need to demonstrate reproducibility in light microscopy acquisitions, the lack of standardized guidelines monitoring microscope health status over time has so far impaired the widespread use of quality control (QC) measurements. As scientists from 10 imaging core facilities who encounter various types of projects, we provide affordable hardware and open source software tools, rigorous protocols, and define reference values to assess QC metrics for the most common fluorescence light microscopy modalities. Seven protocols specify metrics on the microscope resolution, field illumination flatness, chromatic aberrations, illumination power stability, stage drift, positioning repeatability, and spatial-temporal noise of camera sensors. We designed the MetroloJ_QC ImageJ/Fiji Java plugin to incorporate the metrics and automate analysis. Measurements allow us to propose an extensive characterization of the QC procedures that can be used by any seasoned microscope user, from research biologists with a specialized interest in fluorescence light microscopy through to core facility staff, to ensure reproducible and quantifiable microscopy results.

Single-molecule counting applied to the study of GPCR oligomerization

Single-molecule counting techniques enable a precise determination of the intracellular abundance and stoichiometry of proteins and macromolecular complexes. These details are often challenging to quantitatively assess yet are essential for our understanding of cellular function. Consider G-protein-coupled receptors-an expansive class of transmembrane signaling proteins that participate in many vital physiological functions making them a popular target for drug development. While early evidence for the role of oligomerization in receptor signaling came from ensemble biochemical and biophysical assays, innovations in single-molecule measurements are now driving a paradigm shift in our understanding of its relevance. Here, we review recent developments in single-molecule counting with a focus on photobleaching step counting and the emerging technique of quantitative single-molecule localization microscopy-with a particular emphasis on the potential for these techniques to advance our understanding of the role of oligomerization in G-protein-coupled receptor signaling.

Tunable Wide-Field Illumination and Single-Molecule Photoswitching with a Single MEMS Mirror

Homogeneous illumination in single-molecule localization microscopy (SMLM) is key for the quantitative analysis of super-resolution images. Therefore, different approaches for flat-field illumination have been introduced as alternative to the conventional Gaussian illumination. Here, we introduce a single microelectromechanical systems (MEMS) mirror as a tunable and cost-effective device for adapting wide-field illumination in SMLM. In flat-field mode the MEMS allowed for consistent SMLM metrics across the entire field of view. Employing single-molecule photoswitching, we developed a simple yet powerful routine to benchmark different illumination schemes on the basis of local emitter brightness and ON-state lifetime. Moreover, we propose that tuning the MEMS beyond optimal flat-field conditions enables to study the kinetics of photoswitchable fluorophores within a single acquisition.

Characterization of a fiber-coupled EvenField illumination system for fluorescence microscopy

Fluorescence microscopy benefits from spatially and temporally homogeneous illumination with the illumination area matched to the shape and size of the camera sensor. Fiber-coupled illumination schemes have the added benefit of straightforward and robust alignment and ease of installation compared to free-space coupled illumination. Commercial and open-source fiber-coupled, homogenized illumination schemes have recently become available to the public; however, there have been no published comparisons of speckle reduction schemes to date. We characterize three different multimode fibers in combination with two laser speckle reduction devices and compare spatial and temporal profiles to a commercial unit. This work yields a new design, the EvenField Illuminator, which is freely available for researchers to integrate into their own imaging systems.