Conventional Confocal Laser Scanning Microscopy Research Articles

Deep learning enables confocal laser-scanning microscopy with enhanced resolution.

Theoretical resolution enhancement of confocal laser-scanning microscopy (CLSM) is sacrificed for the best compromise between optical sectioning and the signal-to-noise ratio (SNR). The pixel reassignment reconstruction algorithm can improve the effective spatial resolution of CLSM to its theoretical limit. However, current implementations are not versatile and are time-consuming or technically complex. Here we present a parameter-free post-processing strategy for laser-scanning microscopy based on deep learning, which enables a spatial resolution enhancement by a factor of ∼1.3, compared to conventional CLSM. To speed up the training process for experimental data, transfer learning, combined with a hybrid dataset consisting of simulated synthetic and experimental images, is employed. The overall resolution and SNR improvement, validated by quantitative evaluation metrics, allowed us to correctly infer the fine structures of real experimental images.

The Expandables: Cracking the Staphylococcal Cell Wall for Expansion Microscopy.

Expansion Microscopy (ExM) is a novel tool improving the resolution of fluorescence microscopy by linking the sample into a hydrogel that gets physically expanded in water. Previously, we have used ExM to visualize the intracellular Gram-negative pathogens Chlamydia trachomatis, Simkania negevensis, and Neisseria gonorrhoeae. Gram-positive bacteria have a rigid and thick cell wall that impedes classic expansion strategies. Here we developed an approach, which included a series of enzymatic treatments resulting in isotropic 4× expansion of the Gram-positive pathogen Staphylococcus aureus. We further demonstrate the suitability of the technique for imaging of planktonic bacteria as well as endocytosed, intracellular bacteria at a spatial resolution of approximately 60 nm with conventional confocal laser scanning microscopy.

Rapid Determination of the Distribution of Cellulose Nanomaterial Aggregates in Composites Enabled by Multi-Channel Spectral Confocal Microscopy.

There is increased interest in the use of cellulose nanomaterials for the mechanical reinforcement of composites due to their high stiffness and strength. However, challenges remain in accurately determining their distribution within composite microstructures. We report the use of a range of techniques used to image aggregates of cellulose nanocrystals (CNCs) greater than 10 µm2 within a model thermoplastic polymer. While Raman imaging accurately determines CNC aggregate size, it requires extended periods of analysis and the limited observable area results in poor reproducibility. In contrast, staining the CNCs with a fluorophore enables rapid acquisition with high reproducibility, but overestimates the aggregate size as CNC content increases. Multi-channel spectral confocal laser scanning microscopy is presented as an alternative technique that combines the accuracy of Raman imaging with the speed and reproducibility of conventional confocal laser scanning microscopy, enabling the rapid determination of CNC aggregate distribution within composites.

High-Resolution 3D Imaging of Rabies Virus Infection in Solvent-Cleared Brain Tissue.

The visualization of infection processes in tissues and organs by immunolabeling is a key method in modern infection biology. The ability to observe and study the distribution, tropism, and abundance of pathogens inside of organ tissues provides pivotal data on disease development and progression. Using conventional microscopy methods, immunolabeling is mostly restricted to thin sections obtained from paraffin-embedded or frozen samples. However, the limited 2D image plane of these thin sections may lead to the loss of crucial information on the complex structure of an infected organ and the cellular context of the infection. Modern multicolor, immunostaining-compatible tissue clearing techniques now provide a relatively fast and inexpensive way to study high-volume 3D image stacks of virus-infected organ tissue. By exposing the tissue to organic solvents, it becomes optically transparent. This matches the sample's refractive indices and eventually leads to a significant reduction of light scattering. Thus, in combination with long free working distance objectives, large tissue sections up to 1 mm in size can be imaged by conventional confocal laser scanning microscopy (CLSM) at high resolution. Here, we describe a protocol to apply deep-tissue imaging after tissue clearing to visualize rabies virus distribution in infected brains in order to study topics like virus pathogenesis, spread, tropism, and neuroinvasion.

Measuring Hindered Diffusion Dynamics in Live Cell Plasma Membranes with Confocal and Super-Resolution Imaging

The cellular plasma membrane is a highly heterogeneous structure organised on nano-scales and displays a crucial interaction platform for proteins, lipids and soluble ligands. Investigating the molecular membrane organisation by measuring diffusion dynamics offers a better understanding of its biological function. Fluorescence correlation spectroscopy (FCS) is one of the prominent tools to elucidate these dynamics in living cells but can only report on the dynamics at one given spatial position at a time. Using scanning fluorescence correlation spectroscopy (sFCS), we obtain a multitude of FCS measurements at different spatial locations. Here, we present a statistical analysis pipeline for sFCS data which allows for the accurate determination of the diffusion dynamics and the differentiation of free (Brownian) from hindered (non-Brownian) diffusion modes. We show free diffusion for phospholipids in model membranes and cells but reveal hindered diffusion of sphingolipids and GPI-anchored proteins in cells. Notably, these measurements can be performed using standard fluorescent dyes or proteins on a conventional confocal laser scanning microscope. To further investigate the dynamics on single cell level, we combine sFCS with stimulated emission depletion (STED) microscopy and by alternating conventional and super-resolved excitation we introduce line interleaved excitation scanning STED-FCS (LIESS-FCS). With LIESS-FCS the diffusion modes can be directly determined at multiple spots within the cellular plasma membrane providing detailed insights into organisation and function. Overall we are presenting a novel toolkit to investigate nano-scale molecular diffusion dynamics for shedding a new light on membrane organisation and heterogeneity.

Axially-confined invivo single-cell labeling by primed conversion using blue and red lasers with conventional confocal microscopes.

Green-to-red photoconvertible fluorescent proteins have been found to undergo efficient photoconversion by a new method termed primed conversion that uses dual wave-length illumination with blue and red/near-infrared light. By modifying a confocal laser-scanning microscope (CLSM) such that two laser beams only meet at the focal plane, confined photoconversion at the axial dimension has been achieved. The necessity of this custom modification to the CLSM, however, has precluded the wide-spread use of this method. Here, we investigated whether spatially-restricted primed conversion could be achieved with CLSM without any hardware modification. We found that the primed conversion of Dendra2 using a conventional CLSM with two visible lasers (473nm and 635nm) and a high NA objective lens (NA, 1.30) resulted in dramatic restriction of photoconversion volume: half-width half-maximum for the axial dimension was below 5μm, which is comparable to the outcome of the original method that used the microscope modification. As a proof of this method's effectiveness, we used this technique in living zebrafish embryos and succeeded in revealing the complex anatomy of individual neurons packed between neighboring cells. Because unmodified CLSMs are widely available, this method can be widely applicable for labeling cells with single-cell resolution.

Super-resolved linear fluorescence localization microscopy using photostable fluorophores: A virtual microscopy study

Current approaches to overcome the conventional limit of the resolution potential of light microscopy (of about 200 nm for visible light), often suffer from non-linear effects, which render the quantification of the image intensities in the reconstructions difficult, and also affect the quantification of the biological structure under investigation. As an attempt to face these difficulties, we discuss a particular method of localization microscopy which is based on photostable fluorescent dyes. The proposed method can potentially be implemented as a fast alternative for quantitative localization microscopy, circumventing the need for the acquisition of thousands of image frames and complex, highly dye-specific imaging buffers. Although the need for calibration remains in order to extract quantitative data (such as the number of emitters), multispectral approaches are largely facilitated due to the much less stringent requirements on imaging buffers. Furthermore, multispectral acquisitions can be readily obtained using commercial instrumentation such as e.g. the conventional confocal laser scanning microscope.

Quantitative Analysis of Nanoscale Step Dynamics in High-Temperature Solution-Grown Single Crystal 4H-SiC via In Situ Confocal Laser Scanning Microscope

Nanoscale understanding of high-temperature crystal growth dynamics in solution has been a challenge to be tackled by many researchers engaged in investigating solution processes for bulk single crystal growth. Here we propose a new approach to in situ observation at a buried solid/liquid interface in high-temperature solution using a conventional confocal laser scanning microscope. In the solution growth of 4H-SiC with Si–Ni based alloy flux as a model system, we show the ability to quantitatively analyze step motions at the growing SiC crystal on the nanoscale at high temperatures up to 1700 °C in a vacuum. The temperature-dependent step-advance rates for various steps with different step heights demonstrated the advantageous effect of adding Al to the flux on the step-flow growth of SiC: addition of just 4 at% Al effectively suppressed step-bunching. These experiments point to the importance of in situ nanoscale observation in understanding solution growth mechanisms, and hence the potential to acceler...

Plasmon-Resonant Gold Nanostars With Variable Size as Contrast Agents for Imaging Applications

Plasmon-resonant nanostars (NSts) have recently found applications in biophotonics due to their unique optical and chemical characteristics, showing comparable or superior properties than other anisotropic plasmon-resonant nanoparticles. In this paper, we synthesized gold NSts by the seed-mediated surfactant-free method. By varying the diameters and amount of spherical seeds we tuned the final NSts tip-to-tip sizes to 50, 82, 100, and 120 nm ensuring the plasmon-resonant peak location between 710 and 830 nm, and the scattering/absorption ratio at the plasmon-resonant wavelengths being 0.12, 0.25, 0.30, 0.35 correspondingly. We investigated the application of the NSts as contrast agents for imaging techniques operating at visible and infrared wavelengths: optical coherence tomography (OCT) and Doppler OCT with the spectrum centered at 930-nm wavelength, as well as for conventional confocal laser scanning microscopy (CLSM) working at 633 nm. The most intense OCT signal was registered from the largest NSts, in correspondence with spectroscopy measurements at 930-nm wavelength. For imaging of nanoparticles incubated with living cells, we applied CLSM in combined scattering and transmission modes, and observed localization of the NSts on the cell surface. Due to the highest scattering at the CLSM operating wavelength, the strongest signal was obtained from the 82-nm particles; the lowest intensity of the CLSM backscattered signal was detected from the cells labeled with the smallest NSts. Thus, by tuning the initial concentration of seeds, it is possible to adjust the size (and scattering properties) of the nanostars to the operating wavelength of the optical device to achieve the best performance.

Local Variability of Parameters for Characterization of the Corneal Subbasal Nerve Plexus

Purpose: The corneal subbasal nerve plexus (SNP) offers high potential for early diagnosis of diabetic peripheral neuropathy. Changes in subbasal nerve fibers can be assessed in vivo by confocal laser scanning microscopy (CLSM) and quantified using specific parameters. While current study results agree regarding parameter tendency, there are considerable differences in terms of absolute values. The present study set out to identify factors that might account for this high parameter variability.Materials and methods: In three healthy subjects, we used a novel method of software-based large-scale reconstruction that provided SNP images of the central cornea, decomposed the image areas into all possible image sections corresponding to the size of a single conventional CLSM image (0.16 mm2), and calculated a set of parameters for each image section. In order to carry out a large number of virtual examinations within the reconstructed image areas, an extensive simulation procedure (10,000 runs per image) was implemented.Results: The three analyzed images ranged in size from 3.75 mm2 to 4.27 mm2. The spatial configuration of the subbasal nerve fiber networks varied greatly across the cornea and thus caused heavily location-dependent results as well as wide value ranges for the parameters assessed. Distributions of SNP parameter values varied greatly between the three images and showed significant differences between all images for every parameter calculated (p < 0.001 in each case).Conclusions: The relatively small size of the conventionally evaluated SNP area is a contributory factor in high SNP parameter variability. Averaging of parameter values based on multiple CLSM frames does not necessarily result in good approximations of the respective reference values of the whole image area. This illustrates the potential for examiner bias when selecting SNP images in the central corneal area.

A Single-Photon Avalanche Camera for Fluorescence Lifetime Imaging Microscopy and Correlation Spectroscopy

Confocal laser scanning microscopy (CLSM) is commonly used to observe molecules of biological relevance in their native environment, the live cell, and study their spatial distribution and interactions nondestructively. CLSM can be easily extended to measure the lifetime of the excited state, the concentration and the diffusion properties of fluorescently labeled molecules, using fluorescence lifetime imaging microscopy (FLIM) and fluorescence correlation spectroscopy (FCS), respectively, in order to provide information about the local environment and the kinetics of molecular interaction in live cells. However, these parameters cannot be measured simultaneously using conventional CLSM due to damaging effects that are associated with strong illumination, including phototoxicity, photobleaching, and saturation of the fluorescence signal. To overcome these limitations, we have developed a new camera consisting of 1024 single-photon avalanche diodes that is optimized for multifocal microscopy, FLIM and FCS. We show proof-of-principle measurements of fluorescence intensity distribution and lifetime of the enhanced green fluorescent protein expressed in live cells and measurement of quantum dot diffusion in solution by FCS using the same detector.

Easy performance of 6-color confocal immunofluorescence with 4-laser line microscopes

Confocal laser scanning microscopy is an advanced technique for imaging tissue samples in vitro and in vivo at high optical resolution. The development of new fluorochrome variants do not only make it possible to perform multicolor flow cytometry of single cells, but in combination with high resolution laser scanning systems also to investigate the distribution of cells in lymphoid tissues by confocal immunofluorescence analyses, thus allowing the distinction of various cell populations directly in the tissue. Here, we provide a protocol for the visualization of at least six differently fluorochrome-labeled antibodies at the same time using a conventional confocal laser scanning microscope with four laser lines (405nm, 488nm, 555nm, and 639nm laser wavelength) in both murine and human tissue samples. We further demonstrate that compensation correction algorithms are not necessary to reduce spillover of fluorochromes into other channels when the used fluorochromes are combined according to their specific emission bands and the varying Stokes shift for co-excited fluorochromes with the same laser line.

Triplet–Triplet Annihilation Upconversion Based Nanocapsules for Bioimaging Under Excitation by Red and Deep‐Red Light

Non-toxic and biocompatible triplet-triplet annihilation upconversion based nanocapsules (size less than 225 nm) were successfully fabricated by the combination of miniemulsion and solvent evaporation techniques. A first type of nanocapsules displays an upconversion spectrum characterized by the maximum of emission at λmax = 550 nm under illumination by red light, λexc = 633 nm. The second type of nanocapsules fluoresces at λmax = 555 nm when excited with deep-red light, λexc = 708 nm. Conventional confocal laser scanning microscopy (CLSM) and flow cytometry were applied to determine uptake and toxicity of the nanocapsules for various (mesenchymal stem and HeLa) cells. Red light (λexc = 633 nm) with extremely low optical power (less than 0.3 μW) or deep-red light (λexc = 708 nm) was used in CLSM experiments to generate green upconversion fluorescence. The cell images obtained with upconversion excitation demonstrate order of magnitude better signal to background ratio than the cell images obtained with direct excitation of the same fluorescence marker.

3D Structural Illumination Microscopy of the Skeletal Muscle Excitation-Contraction Coupling Macromolecular Complex

To study the structural organization of protein components associated with the membrane compartments involved in skeletal muscle excitation-contraction coupling, we stained enzymatically dissociated mouse FDB fibers with commercially available specific antibodies. Imaging was based on 3 dimensional structured illumination microscopy (3D-SIM, Zeiss Elyra system using a 63x/1.4 Plan-Apochromat lens and an EMCCD camera) or conventional confocal laser scanning microscopy for comparison (Zeiss LSM700). We investigated the localization pattern and distribution of RyR, Cav1.1 and of other protein components involved in excitation-contraction coupling. As expected, imaging of FBD fibers stained with anti -RyR Ab by conventional confocal microscopy revealed highly ordered band-line structures regularly distributed along the sarcomeres which strongly overlapped with Cav1.1. Analysis of the same FDB preparation at higher resolution (Dx-y 110-130 nm and Dz 280-340 nm) by 3D-SIM revealed a more distinct pattern of distribution. RyRs form 100 nm clusters, which are regularly separated and distributed along the longitudinal axis of the fiber. Anti-Cav 1.1 Ab stained clusters having a sarcomeric distribution co-localizing with RyRs. Cav 1.1 Ab also stained structures adjacent to but not overlapping with RyRs. These results suggest the power of the 3D-SIM approach to gain further insight into the structural organization of sarcotubular membranes in normal and diseased condition.

High-Speed Imaging of Amoeboid Movements Using Light-Sheet Microscopy

Light-sheet microscopy has been developed as a powerful tool for live imaging in biological studies. The efficient illumination of specimens using light-sheet microscopy makes it highly amenable to high-speed imaging. We therefore applied this technology to the observation of amoeboid movements, which are too rapid to capture with conventional microscopy. To simplify the setup of the optical system, we utilized the illumination optics from a conventional confocal laser scanning microscope. Using this set-up we achieved high-speed imaging of amoeboid movements. Three-dimensional images were captured at the recording rate of 40 frames/s and clearly outlined the fine structures of fluorescent-labeled amoeboid cellular membranes. The quality of images obtained by our system was sufficient for subsequent quantitative analysis for dynamics of amoeboid movements. This study demonstrates the application of light-sheet microscopy for high-speed imaging of biological specimens.

Microscope-Based Imaging Platform for Large-Scale Analysis of Oral Biofilms

A microscopic method for noninvasively monitoring oral biofilms at the macroscale was developed to describe the spatial distribution of biofilms of different bacterial composition on bovine enamel surfaces (BES). For this purpose, oral biofilm was grown in situ on BES that were fixed at approximal sites of individual upper jaw acrylic devices worn by a volunteer for 3 or 5 days. Eubacteria, Streptococcus spp., and Fusobacterium nucleatum were stained using specific fluorescence in situ hybridization (FISH) probes. The resulting fluorescence signals were subsequently tested by confocal laser scanning microscopy (CLSM) and monitored by an automated wide-field microscope-based imaging platform (Scan∧R). Automated image processing and data analysis were conducted by microscope-associated software and followed by statistical evaluation of the results. The full segmentation of biofilm images revealed a random distribution of bacteria across the entire area of the enamel surfaces examined. Significant differences in the composition of the microflora were recorded across individual as well as between different enamel surfaces varying from sparsely colonized (47.26%) after 3 days to almost full surface coverage (84.45%) after 5 days. The enamel plates that were positioned at the back or in the middle of the oral cavity were found to be more suitable for the examination of biofilms up to 3 days old. In conclusion, automated microscopy combined with the use of FISH can enable the efficient visualization and meaningful quantification of bacterial composition over the entire sample surface. Due to the possibility of automation, Scan∧R overcomes the technical limitations of conventional CLSM.

Zeeman laser scanning confocal microscope and its ability on reduction of specimen-induced spherical aberration

The spherical aberration induced by refractive-index mismatch results in the degradation on the quality of sectioning images in conventional confocal laser scanning microscope (CLSM). In this research, we have derived the theory of image formation in a Zeeman laser scanning confocal microscope (ZLSCM) and conducted experiments in order to verify the ability of reducing spherical aberration in ZLSCM. A Zeeman laser is used as the light source and produces the linearly polarized photon-pairs (LPPP) laser beam. With the features of common-path propagation of LPPP and optical heterodyne detection, ZLSCM shows the ability of reducing the specimen-induced spherical aberration and improving the axial resolution simultaneously.

Can scanning near‐field optical microscopy be compared with confocal laser scanning microscopy? A preliminary study on α‐sarcoglycan and β1D‐integrin in human skeletal muscle

The dystrophin-glycoprotein complex and the vinculin-talin-integrin system constitute, together a protein machinery, called costameres. The dystrophin-glycoprotein complex contains, among other proteins, also dystrophin and the sarcoglycans subcomplex, proteins playing a key role in the pathogenesis of many muscular dystrophies and linking the cytoplasmic myofibrillar contractile elements to the signal transducing molecules of the extracellular matrix, also providing structural support to the sarcolemma. The vinculin-talin-integrin system connects some components of the extracellular matrix with intermediate filaments of desmin, forming transverse bridges between Z and M lines. In our previous reports we always studied these systems by confocal laser scanning microscopy (CLSM). In this paper we report on the first applications of optical near-field fluorescence microscopy to the spatial localization of alpha-sarcoglycan and beta1D-integrin in human skeletal muscle fibres in order to better compare and test the images obtained with conventional CLSM and with scanning near-field optical microscopy (SNOM). In addition, the analysis of the surface morphology, and the comparison with the fluorescence map is put forward and analyzed for the first time on human muscle fibres. In aperture-SNOM the sample is excited through the nanometre-scale aperture produced at the apex of an optical fibre after tapering and subsequent metal coating. The acquisition of the topography map, simultaneously to the optical signal, by SNOM, permits to exactly overlap the fluorescence images obtained from the two consecutive scans needed for the double localization. Besides, the differences between the topography and the optical spatial patterns permit to assess the absence of artefacts in the fluorescence maps. Although the SNOM represented a good method of analysis, this technique remains a complementary method to the CLSM and it can be accepted in order to confirm the hypothesis advanced by CLSM.

FRET–CLSM and double-labeling indirect immunofluorescence to detect close association of proteins in tissue sections

It is pivotal to identify protein–protein interaction in situ to understand protein function. Conventional methods to determine the interaction of proteins destruct tissue or are applicable to cell culture only. To identify association of proteins in cells in tissue, we adapted indirect double-labeling immunofluorescence and combined it with conventional confocal laser scanning microscopy (CLSM) to measure fluorescence resonance energy transfer (FRET). As a model system, we chose caveolin-1α and caveolin-2, two major components of endothelial caveolae, and examined their interaction in the endothelium of vessels in fixed tissues of laboratory animals and human glomus tumors. Several methodological aspects were examined. Measuring the absolute increase in fluorescence (ΔIF) was superior compared to determining the relative FRET efficiency, because it is more robust against small increases of fluorescence during measurements that results from unavoidable minimal crossreactivity of the secondary antibodies. Both, sequential and simultaneous incubation of secondary antibodies result in robust and reliable increases in ΔIF. If incubated sequentially, however, the acceptor-labeled secondary antibody should be applied first. The size of the secondary reagent (F(ab′)2vs whole antibody) has no major influence. In conclusion, CLSM–FRET can measure close spatial association of proteins in situ and can be applied to human surgical material.

Superresolution size determination in fluorescence microscopy: A comparison between spatially modulated illumination and confocal laser scanning microscopy

Recently developed far field light optical methods are a powerful tool to analyze biological nanostructures and their dynamics, in particular including the interior of three-dimensionally conserved cells. In this article, the recently described method of spatially modulated illumination (SMI) microscopy has been further extended to the online determination of the extension of small, subwavelength sized, fluorescent objects (nanosizing). Using fluorescence excitation with 488 nm, the determination of fluorescent labeled object diameters down to 40 nm corresponding to about 1/12th of the wavelength used for one-photon excitation could be shown. The results of the SMI nanosizing procedure for a detailed, systematic variation of the object diameter are presented together with a fast algorithm for online size evaluation. In addition, we show a direct comparison of the diameter of “colocalization volumes” between SMI nanosizing and conventional confocal laser scanning microscopy.