Super-resolution microscopy: a brief history and new avenues

Nanosecond Transient IR Spectroscopy of Halorhodopsin in Living Cells

The ability to track minute changes of a single amino acid residue in a cellular environment is causing a paradigm shift in the attempt to fully understand the responses of biomolecules that are highly sensitive to their environment. Detecting early protein dynamics in living cells is crucial to understanding their mechanisms, such as those of photosynthetic proteins. Here, we elucidate the light response of the microbial chloride pump NmHR from the marine bacterium Nonlabens marinus, located in the membrane of living Escherichia coli cells, using nanosecond time-resolved UV/vis and IR absorption spectroscopy over the time range from nanoseconds to seconds. Transient structural changes of the retinal cofactor and the surrounding apoprotein are recorded using light-induced time-resolved UV/vis and IR difference spectroscopy. Of particular note, we have resolved the kinetics of the transient deprotonation of a single cysteine residue during the photocycle of NmHR out of the manifold of molecular vibrations of the cells. These findings are of high general relevance, given the successful development of optogenetic tools from photoreceptors to interfere with enzymatic and neuronal pathways in living organisms using light pulses as a noninvasive trigger.

Surpassing light inhomogeneities in structured-illumination microscopy with FlexSIM

Super-resolution structured-illumination microscopy (SIM) is a powerful technique that allows one to surpass the diffraction limit by up to a factor two. Yet, its practical use is hampered by its sensitivity to imaging conditions which makes it prone to reconstruction artefacts. In this work, we present FlexSIM, a flexible SIM reconstruction method capable to handle highly challenging data. Specifically, we demonstrate the ability of FlexSIM to deal with the distortion of patterns, the high level of noise encountered in live imaging, as well as out-of-focus fluorescence. Moreover, we show that FlexSIM achieves state-of-the-art performance over a variety of open SIM datasets.

3D super-resolution optical fluctuation imaging with temporal focusing two-photon excitation

3D super-resolution fluorescence microscopy typically requires sophisticated setups, sample preparation, or long measurements. A notable exception, SOFI, only requires recording a sequence of frames and no hardware modifications whatsoever but being a wide-field method, it faces problems in thick, dense samples. We combine SOFI with temporal focusing two-photon excitation - the wide-field method that is capable of exciting a thin slice in 3D volume. Temporal focusing is simple to implement whenever the excitation path of the microscope can be accessed. The implementation of SOFI is straightforward. By merging these two methods, we obtain super-resolved 3D images of neurons stained with quantum dots. Our approach offers reduced bleaching of out-of-focus fluorescent probes and an improved signal-to-background ratio that can be used when robust resolution improvement is required in thick, dense samples.

Nano-organization of synaptic calcium signaling

Recent studies suggest an exquisite structural nano-organization within single synapses, where sites of evoked fusion - marked by clustering of synaptic vesicles, active zone proteins and voltage-gated calcium channels - are directly juxtaposed to postsynaptic receptor clusters within nanocolumns. This direct nanometer scale alignment between presynaptic fusion apparatus and postsynaptic receptors is thought to ensure the fidelity of synaptic signaling and possibly allow multiple distinct signals to occur without interference from each other within a single active zone. The functional specificity of this organization is made possible by the inherent nano-organization of calcium signals, where all the different calcium sources such as voltage-gated calcium channels, intracellular stores and store-operated calcium entry have dedicated local targets within their nanodomain to ensure precision of action. Here, we discuss synaptic nano-organization from the perspective of calcium signals, where some of the principal findings from early work in the 1980s continue to inspire current studies that exploit new genetic tools and super-resolution imaging technologies.

Supramolecular Complex of Cucurbit[7]uril with Diketopyrrolopyrole Dye: Fluorescence Boost, Biolabeling and Optical Microscopy

New photostable and bright supramolecular complexes based on cucurbit[7]uril (CB7) host and diketopyrrolopyrole (DPP) guest dyes having two positively charged 4-(trimethylammonio)phenyl groups were prepared and characterized. The dye core displays large Stokes shift (in H2O, abs./emission max. 480/550 nm; ϵ~19 000, τfl>4 ns), strong binding with the host (~560 nM Kd) and a linker affording fluorescence detection of bioconjugates with antibody and nanobody. Combination of protein-functionalized DPP dye with CB7 improves photostability and affords up to 12-fold emission gain. Two-color confocal and stimulated emission depletion (STED) microscopy with 595 nm or 655 nm STED depletion lasers shows that the presence of CB7 not only leads to improved brightness and image quality, but also results in DPP becoming cell-permeable.

Observing the Dynamics of an Electrochemically Driven Active Material with Liquid Electron Microscopy

Electrochemical liquid electron microscopy has revolutionized our understanding of nanomaterial dynamics by allowing for direct observation of their electrochemical production. This technique, primarily applied to inorganic materials, is now being used to explore the self-assembly dynamics of active molecular materials. Our study examines these dynamics across various scales, from the nanoscale behavior of individual fibers to the micrometer-scale hierarchical evolution of fiber clusters. To isolate the influences of the electron beam and electrical potential on material behavior, we conducted thorough beam-sample interaction analyses. Our findings reveal that the dynamics of these active materials at the nanoscale are shaped by their proximity to the electrode and the applied electrical current. By integrating electron microscopy observations with reaction-diffusion simulations, we uncover that local structures and their formation history play a crucial role in determining assembly rates. This suggests that the emergence of nonequilibrium structures can locally accelerate further structural development, offering insights into the behavior of active materials under electrochemical conditions.

PyrAtes: Modular Organic Salts with Large Stokes Shifts for Fluo-rescence Microscopy

The deployment of small-molecule fluorescent agents plays an ever-growing role in medicine and drug development. Herein, we complement the portfolio of powerful fluorophores, reporting the serendipitous discovery and development of a novel class with an imidazo[1,2-a]pyridinium triflate core, which we term PyrAtes. These fluorophores are synthesized in a single step from readily available materials (>60 examples) and display Stokes shifts as large as 240 nm, while also reaching NIR-I emissions at λmax as long as 720 nm. Computational studies allow the development of a platform for the prediction of λmax and λEm. Furthermore, we demonstrate the compatibility of these novel fluorophores with live cell imaging in HEK293 cells, suggesting PyrAtes as potent intracellular markers.

Super-resolution techniques for biomedical applications and challenges

Super-resolution (SR) techniques have revolutionized the field of biomedical applications by detailing the structures at resolutions beyond the limits of imaging or measuring tools. These techniques have been applied in various biomedical applications, including microscopy, magnetic resonance imaging (MRI), computed tomography (CT), X-ray, electroencephalogram (EEG), ultrasound, etc. SR methods are categorized into two main types: traditional non-learning-based methods and modern learning-based approaches. In both applications, SR methodologies have been effectively utilized on biomedical images, enhancing the visualization of complex biological structures. Additionally, these methods have been employed on biomedical data, leading to improvements in computational precision and efficiency for biomedical simulations. The use of SR techniques has resulted in more detailed and accurate analyses in diagnostics and research, essential for early disease detection and treatment planning. However, challenges such as computational demands, data interpretation complexities, and the lack of unified high-quality data persist. The article emphasizes these issues, underscoring the need for ongoing development in SR technologies to further improve biomedical research and patient care outcomes.

Traceable localization enables accurate integration of quantum emitters and photonic structures with high yield

In a popular integration process for quantum information technologies, localization microscopy of quantum emitters guides lithographic placement of photonic structures. However, a complex coupling of microscopy and lithography errors degrades registration accuracy, severely limiting device performance and process yield. We introduce a methodology to solve this widespread but poorly understood problem. A new foundation of traceable localization enables rapid characterization of lithographic standards and comprehensive calibration of cryogenic microscopes, revealing and correcting latent systematic effects. Of particular concern, we discover that scale factor deviation and complex optical distortion couple to dominate registration errors. These novel results parameterize a process model for integrating quantum dots and bullseye resonators, predicting higher yield by orders of magnitude, depending on the Purcell factor threshold as a quantum performance metric. Our foundational methodology is a key enabler of the lab-to-fab transition of quantum information technologies and has broader implications to cryogenic and correlative microscopy.

"Covalent-Disassembly"-Based Approaches For Sensing Applications

The detection of analytes with small molecular probes is crucial for the analysis and understanding of chemical, medicinal, environmental and biological situations as well as processes. Classic detection approaches rely on the concept of molecular recognition and bond formation reactions. Bond breakage reactions have been less explored in similar contexts. This concept article introduces metal-salen and metal-imine complexes as "covalent-disassembly"-based (DB)-probes for detecting polyoxophosphates, thiols, amino acids, HCN and changes in pH. It discusses the roles, importance and combinations of structurally functionalized molecular building blocks in the construction of DB-probes. Applications of optimized DB-probes for analyte detection in live cells and foodstuff are also discussed. Furthermore, the mechanism of the disassembly of a Fe(III)-salen probe upon pyrophosphate binding is presented. Extraordinary selectivity for this analyte was achieved by a multistep disassembly sequence including an unprecedented structural change of the metal complex (i. e. "induced-fit" principle). Design principles of probes for sensing applications following the "covalent-disassembly" approach are summarized, which will help improving current systems, but will also facilitate the development of new DB-probes for challenging analytic targets.

Label-free mapping of cetuximab in multi-layered tumor oral mucosa models by atomic force-microscopy-based infrared spectroscopy

Sensitive mapping of drugs and drug delivery systems is pivotal for the understanding and improvement of treatment options. Since labeling alters the physicochemical and potentially the pharmacological properties of the molecule of interest, its label-free detection by photothermal expansion is investigated. We report on a proof-of-concept study to map the cetuximab distribution by atomic-force microscopy-based infrared spectroscopy (AFM-IR). The monoclonal antibody cetuximab was applied to a human tumor oral mucosa model, consisting of a tumor epithelium on a lamina propria equivalent. Hyperspectral imaging in the wavenumber regime between 903 cm-1 and 1312 cm-1 and a probing distance between the data points down to 10 × 10 nm are used for determining the local drug distribution. The local distinction of cetuximab from the tissue background is gained by linear combination modeling making use of reference spectra of the drug and untreated models. The results from this approach are compared to principal component analyses, yielding comparable results. Even single molecule detection appears feasible. The results indicate that cetuximab penetrates the cytosol of tumor cells but does not bind to structures in the cell membrane. In conclusion, AFM-IR mapping of cetuximab proved to sensitively determine drug concentrations at an unprecedented spatial resolution without the need for drug labeling.

Expansion and Light-Sheet Microscopy for Nanoscale 3D Imaging

Expansion Microscopy (ExM) and Light-Sheet Fluorescence Microscopy (LSFM) are forefront imaging techniques that enable high-resolution visualization of biological specimens. ExM enhances nanoscale investigation using conventional fluorescence microscopes, while LSFM offers rapid, minimally invasive imaging over large volumes. This review explores the joint advancements of ExM and LSFM, focusing on the excellent performance of the integrated modality obtained from the combination of the two, which is refer to as ExLSFM. In doing so, the chemical processes required for ExM, the tailored optical setup of LSFM for examining expanded samples, and the adjustments in sample preparation for accurate data collection are emphasized. It is delve into various specimen types studied using this integrated method and assess its potential for future applications. The goal of this literature review is to enrich the comprehension of ExM and LSFM, encouraging their wider use and ongoing development, looking forward to the upcoming challenges, and anticipating innovations in these imaging techniques.

Modulation of Point Spread Function for Super-Resolution Imaging

High image resolution is desired in wave-related areas such as ultrasound, acoustics, optics, and electromagnetics. However, the spatial resolution of an imaging system is limited by the spatial frequency of the point spread function (PSF) of the system due to diffraction. In this article, the PSF is modulated in amplitude, phase, or both to increase the spatial frequency to reconstruct super-resolution images of objects or wave sources/fields, where the modulator can be a focused shear wave produced remotely by, for example, a radiation force from a focused Bessel beam or X-wave, or can be a small particle manipulated remotely by a radiation-force (such as acoustic and optical tweezers) or electrical and magnetic forces. A theory of the PSF-modulation method was developed, and computer simulations and experiments were conducted. The result of an ultrasound experiment shows that a pulse-echo (two-way) image reconstructed has a super-resolution (0.65 mm) as compared to the diffraction limit (2.65 mm) using a 0.5-mm-diameter modulator at 1.483-mm wavelength, and the signal-to-noise ratio (SNR) of the image was about 31 dB. If the minimal SNR of a "visible" image is 3, the resolution can be further increased to about 0.19 mm by decreasing the size of the modulator. Another ultrasound experiment shows that a wave source was imaged (one-way) at about 30-dB SNR using the same modulator size and wavelength above. The image clearly separated two 0.5-mm spaced lines, which gives a 7.26-fold higher resolution than that of the diffraction limit (3.63 mm). Although, in theory, the method has no limit on the highest achievable image resolution, in practice, the resolution is limited by noises. Also, a PSF-weighted super-resolution imaging method based on the PSF-modulation method was developed. This method is easier to implement but may have some limitations. Finally, the methods above can be applied to imaging systems of an arbitrary PSF and can produce 4-D super-resolution images. With a proper choice of a modulator (e.g., a quantum dot) and imaging system, nanoscale (a few nanometers) imaging is possible.

Exploring the future of regenerative medicine: Unveiling the potential of optical microscopy for structural and functional imaging of stem cells

Regenerative medicine, which utilizes stem cells for tissue and organ repair, holds immense promise in healthcare. A comprehensive understanding of stem cell characteristics is crucial to unlock their potential. This study explores the pivotal role of optical microscopy in advancing regenerative medicine as a potent tool for stem cell research. Advanced optical microscopy techniques enable an in-depth examination of stem cell behavior, morphology, and functionality. The review encompasses current optical microscopy, elucidating its capabilities and constraints in stem cell imaging, while also shedding light on emerging technologies for improved stem cell visualization. Optical microscopy, complemented by techniques like fluorescence and multiphoton imaging, enhances our comprehension of stem cell dynamics. The introduction of label-free imaging facilitates noninvasive, real-time stem cell monitoring without external dyes or markers. By pushing the boundaries of optical microscopy, researchers reveal the intricate cellular mechanisms underpinning regenerative processes, thereby advancing more effective therapeutic strategies. The current study not only outlines the future of regenerative medicine but also underscores the pivotal role of optical microscopy in both structural and functional stem cell imaging.

Enhancing axial localization with wavefront control

Enhancing the ability to resolve axial details is crucial in three-dimensional optical imaging. We provide experimental evidence showcasing the ultimate precision achievable in axial localization using vortex beams. For Laguerre-Gauss (LG) beams, this remarkable limit can be attained with just a single intensity scan. This proof-of-principle demonstrates that microscopy techniques based on LG vortex beams can potentially benefit from the introduced quantum-inspired superresolution protocol.

Analyzing the cellular plasma membrane by fast and efficient correlative STED and platinum replica EM

The plasma membrane of mammalian cells links transmembrane receptors, various structural components, and membrane-binding proteins to subcellular processes, allowing inter- and intracellular communication. Therefore, membrane-binding proteins, together with structural components such as actin filaments, modulate the cell membrane in their flexibility, stiffness, and curvature. Investigating membrane components and curvature in cells remains challenging due to the diffraction limit in light microscopy. Preparation of 5-15-nm-thin plasma membrane sheets and subsequent inspection by metal replica transmission electron microscopy (TEM) reveal detailed information about the cellular membrane topology, including the structure and curvature. However, electron microscopy cannot identify proteins associated with specific plasma membrane domains. Here, we describe a novel adaptation of correlative super-resolution light microscopy and platinum replica TEM (CLEM-PREM), allowing the analysis of plasma membrane sheets with respect to their structural details, curvature, and associated protein composition. We suggest a number of shortcuts and troubleshooting solutions to contemporary PREM protocols. Thus, implementation of super-resolution stimulated emission depletion (STED) microscopy offers significant reduction in sample preparation time and reduced technical challenges for imaging and analysis. Additionally, highly technical challenges associated with replica preparation and transfer on a TEM grid can be overcome by scanning electron microscopy (SEM) imaging. The combination of STED microscopy and platinum replica SEM or TEM provides the highest spatial resolution of plasma membrane proteins and their underlying membrane and is, therefore, a suitable method to study cellular events like endocytosis, membrane trafficking, or membrane tension adaptations.

Xanthene, cyanine, oxazine and BODIPY: the four pillars of the fluorophore empire for super-resolution bioimaging

In the realm of biological research, the invention of super-resolution microscopy (SRM) has enabled the visualization of ultrafine sub-cellular structures and their functions in live cells at the nano-scale level, beyond the diffraction limit, which has opened up a new window for advanced biomedical studies to unravel the complex unknown details of physiological disorders at the sub-cellular level with unprecedented resolution and clarity. However, most of the SRM techniques are highly reliant on the personalized special photophysical features of the fluorophores. In recent times, there has been an unprecedented surge in the development of robust new fluorophore systems with personalized features for various super-resolution imaging techniques. To date, xanthene, cyanine, oxazine and BODIPY cores have been authoritatively utilized as the basic fluorophore units in most of the small-molecule-based organic fluorescent probe designing strategies for SRM owing to their excellent photophysical characteristics and easy synthetic acquiescence. Since the future of next-generation SRM studies will be decided by the availability of advanced fluorescent probes and these four fluorescent building blocks will play an important role in progressive new fluorophore design, there is an urgent need to review the recent advancements in designing fluorophores for different SRM methods based on these fluorescent dye cores. This review article not only includes a comprehensive discussion about the recent developments in designing fluorescent probes for various SRM techniques based on these four important fluorophore building blocks with special emphasis on their effective integration into live cell super-resolution bio-imaging applications but also critically evaluates the background of each of the fluorescent dye cores to highlight their merits and demerits towards developing newer fluorescent probes for SRM.

A Versatile Synaptotagmin-1 Nanobody Provides Perturbation-Free Live Synaptic Imaging And Low Linkage-Error in Super-Resolution Microscopy

Imaging of living synapses has relied for over two decades on the overexpression of synaptic proteins fused to fluorescent reporters. This strategy alters the stoichiometry of synaptic components and ultimately affects synapse physiology. To overcome these limitations, here a nanobody is presented that binds the calcium sensor synaptotagmin-1 (NbSyt1). This nanobody functions as an intrabody (iNbSyt1) in living neurons and is minimally invasive, leaving synaptic transmission almost unaffected, as suggested by the crystal structure of the NbSyt1 bound to Synaptotagmin-1 and by the physiological data. Its single-domain nature enables the generation of protein-based fluorescent reporters, as showcased here by measuring spatially localized presynaptic Ca2+ with a NbSyt1- jGCaMP8 chimera. Moreover, the small size of NbSyt1 makes it ideal for various super-resolution imaging methods. Overall, NbSyt1 is a versatile binder that will enable imaging in cellular and molecular neuroscience with unprecedented precision across multiple spatiotemporal scales.

Neodymium acetate as a contrast agent for X-ray phase-contrast tomography

Purpose

X-ray phase-contrast tomography (XPCT) is a non-destructive, three-dimensional imaging modality that provides higher contrast in soft tissue than absorption-based CT and allows one to cover the cytoarchitecture from the centi- and millimeter scale down to the nanoscale. To further increase contrast and resolution of XPCT, for example, in view of addressing connectivity issues in the central nervous system (CNS), metal staining is indispensable. However, currently used protocols, for example, based on osmium and/or uranium are less suited for XPCT, due to an excessive β / δ -ratio. In this work, we explore the suitability of different staining agents for XPCT. Particularly, neodymium(III)-acetate (NdAc), which has recently been proposed as a non-toxic, non-radioactive easy to use alternative contrast agent for uranyl acetate (UAc) in electron microscopy, is investigated. Due to its vertical proximity to UAc in the periodic table, similar chemical but better suited optical properties for phase contrast can be expected.

Approach

Differently stained whole eye samples of wild type mouse and tissues of the CNS are embedded into EPON epoxy resin and scanned using synchrotron as well as with laboratory radiation. Phase retrieval is performed on the projection images, followed by tomographic reconstruction, which enables a quantitative analysis based on the reconstructed electron densities. Segmentation techniques and rendering software is used to visualize structures of interest in the sample.

Results

We show that staining neuronal samples with NdAc enhances contrast, in particular for laboratory scans, allowing high-resolution imaging of biological soft tissue in-house. For the example of murine retina, specifically rods and cones as well as the sclera and the Ganglion cell layer seem to be targeted by the stain. A comparison of electron density by the evaluation of histograms allowed to determine quantitative measures to describe the difference between the examined stains.

Conclusion

The results suggest NdAc to be an effective stain for XPCT, with a preferential binding to anionic groups, such as phosphate and carboxyl groups at cell surfaces, targeting certain layers of the retina with a stronger selectivity compared to other staining agents. Due to the advantageous X-ray optical properties, the stain seems particularly well-suited for phase contrast, with a comparably small number density and an overall superior image quality at laboratory sources.

Intelligent nanomaterials for cancer therapy: recent progresses and future possibilities

Intelligent nanomedicine is currently one of the most active frontiers in cancer therapy development. Empowered by the recent progresses of nanobiotechnology, a new generation of multifunctional nanotherapeutics and imaging platforms has remarkably improved our capability to cope with the highly heterogeneous and complicated nature of cancer. With rationally designed multifunctionality and programmable assembly of functional subunits, the in vivo behaviors of intelligent nanosystems have become increasingly tunable, making them more efficient in performing sophisticated actions in physiological and pathological microenvironments. In recent years, intelligent nanomaterial-based theranostic platforms have showed great potential in tumor-targeted delivery, biological barrier circumvention, multi-responsive tumor sensing and drug release, as well as convergence with precise medication approaches such as personalized tumor vaccines. On the other hand, the increasing system complexity of anti-cancer nanomedicines also pose significant challenges in characterization, monitoring and clinical use, requesting a more comprehensive and dynamic understanding of nano-bio interactions. This review aims to briefly summarize the recent progresses achieved by intelligent nanomaterials in tumor-targeted drug delivery, tumor immunotherapy and temporospatially specific tumor imaging, as well as important advances of our knowledge on their interaction with biological systems. In the perspective of clinical translation, we have further discussed the major possibilities provided by disease-oriented development of anti-cancer nanomaterials, highlighting the critical importance clinically-oriented system design.

Mitochondrial networks through the lens of mathematics

Mitochondria serve a wide range of functions within cells, most notably via their production of ATP. Although their morphology is commonly described as bean-like, mitochondria often form interconnected networks within cells that exhibit dynamic restructuring through a variety of physical changes. Further, though relationships between form and function in biology are well established, the extant toolkit for understanding mitochondrial morphology is limited. Here, we emphasize new and established methods for quantitatively describing mitochondrial networks, ranging from unweighted graph-theoretic representations to multi-scale approaches from applied topology, in particular persistent homology. We also show fundamental relationships between mitochondrial networks, mathematics, and physics, using ideas of graph planarity and statistical mechanics to better understand the full possible morphological space of mitochondrial network structures. Lastly, we provide suggestions for how examination of mitochondrial network form through the language of mathematics can inform biological understanding, and vice versa.

Labeling approaches for DNA-PAINT super-resolution imaging

Super-resolution imaging is becoming a commonly employed tool to visualize biological targets in unprecedented detail. DNA-PAINT is one of the single-molecule localization microscopy-based super-resolution imaging modalities allowing the ultra-high-resolution imaging with superior multiplexing capabilities. We discuss the importance of patterned DNA nanostructures in demonstrating the capabilities of DNA-PAINT and the design of various combinations of imager-docking strand pairs for imaging. Central to the implementation of DNA-PAINT imaging in a biological context is the generation of docking strand-conjugated binders against the target molecules. Several researchers have developed a variety of labelling probes for improving resolution while also providing multiplexing capabilities for the broader application of DNA-PAINT. This review provides a comprehensive summary of the repertoire of labelling probes used for DNA-PAINT in cells and the strategies implemented to chemically modify them with a docking strand.

Airy beam light sheet microscopy boosted by deep learning deconvolution

Common light sheet microscopy comes with a trade-off between light sheet width defining the optical sectioning and the usable field of view arising from the divergence of the illuminating Gaussian beam. To overcome this, low-diverging Airy beams have been introduced. Airy beams, however, exhibit side lobes degrading image contrast. Here, we constructed an Airy beam light sheet microscope, and developed a deep learning image deconvolution to remove the effects of the side lobes without knowledge of the point spread function. Using a generative adversarial network and high-quality training data, we significantly enhanced image contrast and improved the performance of a bicubic upscaling. We evaluated the performance with fluorescently labeled neurons in mouse brain tissue samples. We found that deep learning-based deconvolution was about 20-fold faster than the standard approach. The combination of Airy beam light sheet microscopy and deep learning deconvolution allows imaging large volumes rapidly and with high quality.

Small training dataset convolutional neural networks for application-specific super-resolution microscopy

SIGNIFICANCE

Machine learning (ML) models based on deep convolutional neural networks have been used to significantly increase microscopy resolution, speed [signal-to-noise ratio (SNR)], and data interpretation. The bottleneck in developing effective ML systems is often the need to acquire large datasets to train the neural network. We demonstrate how adding a "dense encoder-decoder" (DenseED) block can be used to effectively train a neural network that produces super-resolution (SR) images from conventional microscopy diffraction-limited (DL) images trained using a small dataset [15 fields of view (FOVs)].

AIM

The ML helps to retrieve SR information from a DL image when trained with a massive training dataset. The aim of this work is to demonstrate a neural network that estimates SR images from DL images using modifications that enable training with a small dataset.

APPROACH

We employ "DenseED" blocks in existing SR ML network architectures. DenseED blocks use a dense layer that concatenates features from the previous convolutional layer to the next convolutional layer. DenseED blocks in fully convolutional networks (FCNs) estimate the SR images when trained with a small training dataset (15 FOVs) of human cells from the Widefield2SIM dataset and in fluorescent-labeled fixed bovine pulmonary artery endothelial cells samples.

RESULTS

Conventional ML models without DenseED blocks trained on small datasets fail to accurately estimate SR images while models including the DenseED blocks can. The average peak SNR (PSNR) and resolution improvements achieved by networks containing DenseED blocks are ≈ 3.2    dB and 2 × , respectively. We evaluated various configurations of target image generation methods (e.g., experimentally captured a target and computationally generated target) that are used to train FCNs with and without DenseED blocks and showed that including DenseED blocks in simple FCNs outperforms compared to simple FCNs without DenseED blocks.

CONCLUSIONS

DenseED blocks in neural networks show accurate extraction of SR images even if the ML model is trained with a small training dataset of 15 FOVs. This approach shows that microscopy applications can use DenseED blocks to train on smaller datasets that are application-specific imaging platforms and there is promise for applying this to other imaging modalities, such as MRI/x-ray, etc.

Actin Bundles Dynamics and Architecture

Cells use the actin cytoskeleton for many of their functions, including their division, adhesion, mechanosensing, endo- and phagocytosis, migration, and invasion. Actin bundles are the main constituent of actin-rich structures involved in these processes. An ever-increasing number of proteins that crosslink actin into bundles or regulate their morphology is being identified in cells. With recent advances in high-resolution microscopy and imaging techniques, the complex process of bundles formation and the multiple forms of physiological bundles are beginning to be better understood. Here, we review the physiochemical and biological properties of four families of highly conserved and abundant actin-bundling proteins, namely, α-actinin, fimbrin/plastin, fascin, and espin. We describe the similarities and differences between these proteins, their role in the formation of physiological actin bundles, and their properties-both related and unrelated to their bundling abilities. We also review some aspects of the general mechanism of actin bundles formation, which are known from the available information on the activity of the key actin partners involved in this process.

Super resolution live imaging: The key for unveiling the true dynamics of membrane traffic around the Golgi apparatus in plant cells

In contrast to the relatively static image of the plants, the world inside each cell is surprisingly dynamic. Membrane-bounded organelles move actively on the cytoskeletons and exchange materials by vesicles, tubules, or direct contact between each other. In order to understand what is happening during those events, it is essential to visualize the working components in vivo. After the breakthrough made by the application of fluorescent proteins, the development of light microscopy enabled many discoveries in cell biology, including those about the membrane traffic in plant cells. Especially, super-resolution microscopy, which is becoming more and more accessible, is now one of the most powerful techniques. However, although the spatial resolution has improved a lot, there are still some difficulties in terms of the temporal resolution, which is also a crucial parameter for the visualization of the living nature of the intracellular structures. In this review, we will introduce the super resolution microscopy developed especially for live-cell imaging with high temporal resolution, and show some examples that were made by this tool in plant membrane research.

Structural Investigation of Therapeutic Antibodies Using Hydroxyl Radical Protein Footprinting Methods

Commercial monoclonal antibodies are growing and important components of modern therapies against a multitude of human diseases. Well-known high-resolution structural methods such as protein crystallography are often used to characterize antibody structures and to determine paratope and/or epitope binding regions in order to refine antibody design. However, many standard structural techniques require specialized sample preparation that may perturb antibody structure or require high concentrations or other conditions that are far from the conditions conducive to the accurate determination of antigen binding or kinetics. We describe here in this minireview the relatively new method of hydroxyl radical protein footprinting, a solution-state method that can provide structural and kinetic information on antibodies or antibody-antigen interactions useful for therapeutic antibody design. We provide a brief history of hydroxyl radical footprinting, examples of current implementations, and recent advances in throughput and accessibility.