Bending the rules: widefield microscopy and the Abbe limit of resolution

A method for reproducible high-resolution imaging of 3D cancer cell spheroids

Multicellular tumour cell spheroids embedded within three-dimensional (3D) hydrogels or extracellular matrices (ECM) are widely used as models to study cancer growth and invasion. Standard methods to embed spheroids in 3D matrices result in random placement in space which limits the use of inverted fluorescence microscopy techniques, and thus the resolution that can be achieved to image molecular detail within the intact spheroid. Here, we leverage UV photolithography to microfabricate PDMS (polydimethylsiloxane) stamps that allow for generation of high-content, reproducible well-like structures in multiple different imaging chambers. Addition of multicellular tumour spheroids into stamped collagen structures allows for precise positioning of spheroids in 3D space for reproducible high-/super-resolution imaging. Embedded spheroids can be imaged live or fixed and are amenable to immunostaining, allowing for greater flexibility of experimental approaches. We describe the use of these spheroid imaging chambers to analyse cell invasion, cell-ECM interaction, ECM alignment, force-dependent intracellular protein dynamics and extension of fine actin-based protrusions with a variety of commonly used inverted microscope platforms. This method enables reproducible, high-/super-resolution live imaging of multiple tumour spheroids, that can be potentially extended to visualise organoids and other more complex 3D in vitro systems.

MicroLED/LED electro-optical integration techniques for non-display applications

MicroLEDs offer an extraordinary combination of high luminance, high energy efficiency, low cost, and long lifetime. These characteristics are highly desirable in various applications, but their usage has, to date, been primarily focused toward next-generation display technologies. Applications of microLEDs in other technologies, such as projector systems, computational imaging, communication systems, or neural stimulation, have been limited. In non-display applications which use microLEDs as light sources, modifications in key electrical and optical characteristics such as external efficiency, output beam shape, modulation bandwidth, light output power, and emission wavelengths are often needed for optimum performance. A number of advanced fabrication and processing techniques have been used to achieve these electro-optical characteristics in microLEDs. In this article, we review the non-display application areas of the microLEDs, the distinct opto-electrical characteristics required for these applications, and techniques that integrate the optical and electrical components on the microLEDs to improve system-level efficacy and performance.

A biologist's guide to planning and performing quantitative bioimaging experiments

Technological advancements in biology and microscopy have empowered a transition from bioimaging as an observational method to a quantitative one. However, as biologists are adopting quantitative bioimaging and these experiments become more complex, researchers need additional expertise to carry out this work in a rigorous and reproducible manner. This Essay provides a navigational guide for experimental biologists to aid understanding of quantitative bioimaging from sample preparation through to image acquisition, image analysis, and data interpretation. We discuss the interconnectedness of these steps, and for each, we provide general recommendations, key questions to consider, and links to high-quality open-access resources for further learning. This synthesis of information will empower biologists to plan and execute rigorous quantitative bioimaging experiments efficiently.

[Closer to the native architecture of the cell using Cryo-ExM]

Most cellular imaging techniques, such as light or electron microscopy, require that the biological sample is first fixed by chemical cross-linking agents. This necessary step is also known to damage molecular nanostructures or even sub-cellular organization. To overcome this problem, another fixation approach was invented more than 40 years ago, which consists in cryo-fixing biological samples, thus allowing to preserve their native state. However, this method has been scarcely used in light microscopy due to the complexity of its implementation. In this review, we present a recently developed super-resolution method called expansion microscopy, which, when coupled with cryo-fixation, allows to visualize at a nanometric resolution the cell architecture as close as possible to its native state.

What Is Motion? Recent Advances in the Study of Molecular Movement Patterns of the Peptidoglycan Synthesis Machines

How proteins move through space and time is a fundamental question in biology. While great strides have been made toward a mechanistic understanding of protein movement, many questions remain. We discuss the biological implications of motion in the context of the peptidoglycan (PG) synthesis machines. We reviewed systems in several bacteria, including Escherichia coli, Bacillus subtilis, and Streptococcus pneumoniae, and present a comprehensive view of our current knowledge regarding movement dynamics. Discrepancies are also addressed because "one size does not fit all". For bacteria to divide, new PG is synthesized and incorporated into the growing cell wall by complex multiprotein nanomachines consisting of PG synthases (transglycosylases [TG] and/or transpeptidases [TP]) as well as a variety of regulators and cytoskeletal factors. Advances in imaging capabilities and labeling methods have revealed that these machines are not static but rather circumferentially transit the cell via directed motion perpendicular to the long axis of model rod-shaped bacteria such as E. coli and B. subtilis. The enzymatic activity of the TG:TPs drives motion in some species while motion is mediated by FtsZ treadmilling in others. In addition, both directed and diffusive motion of the PG synthases have been observed using single-particle tracking technology. Here, we examined the biological role of diffusion regarding transit. Lastly, findings regarding the monofunctional transglycosylases (RodA and FtsW) as well as the Class A PG synthases are discussed. This minireview serves to showcase recent advances, broach mechanistic unknowns, and stimulate future areas of study.

A Layered View on Focal Adhesions

Simple Summary

The cytoskeleton is a network of protein fibres within cells that provide structure and support intracellular transport. Focal adhesions are protein complexes associated with the outer cell membrane that are found at the ends of specialised actin fibres of this cytoskeleton. They mediate cell adhesion by connecting the cytoskeleton to the extracellular matrix, a protein and sugar network that surrounds cells in tissues. Focal adhesions also translate forces on actin fibres into forces contributing to cell migration. Cell adhesion and migration are crucial to diverse biological processes such as embryonic development, proper functioning of the immune system or the metastasis of cancer cells. Advances in fluorescence microscopy and data analysis methods provided a more detailed understanding of the dynamic ways in which proteins bind and dissociate from focal adhesions and how they are organised within these protein complexes. In this review, we provide an overview of the advances in the current scientific understanding of focal adhesions and summarize relevant imaging techniques. One of the key insights is that focal adhesion proteins are organised into three layers parallel to the cell membrane. We discuss the relevance of this layered nature for the functioning of focal adhesion.

Abstract

The cytoskeleton provides structure to cells and supports intracellular transport. Actin fibres are crucial to both functions. Focal Adhesions (FAs) are large macromolecular multiprotein assemblies at the ends of specialised actin fibres linking these to the extracellular matrix. FAs translate forces on actin fibres into forces contributing to cell migration. This review will discuss recent insights into FA protein dynamics and their organisation within FAs, made possible by advances in fluorescence imaging techniques and data analysis methods. Over the last decade, evidence has accumulated that FAs are composed of three layers parallel to the plasma membrane. We focus on some of the most frequently investigated proteins, two from each layer, paxillin and FAK (bottom, integrin signalling layer), vinculin and talin (middle, force transduction layer) and zyxin and VASP (top, actin regulatory layer). Finally, we discuss the potential impact of this layered nature on different aspects of FA behaviour.

Compartmentalization of Sphingolipid metabolism: Implications for signaling and therapy

Sphingolipids (SLs) are a family of bioactive lipids implicated in a variety of cellular processes, and whose levels are controlled by an interlinked network of enzymes. While the spatial distribution of SL metabolism throughout the cell has been understood for some time, the implications of this for SL signaling and biological outcomes have only recently begun to be fully explored. In this review, we outline the compartmentalization of SL metabolism and describe advances in tools for investigating and probing compartment-specific SL functions. We also briefly discuss the implications of SL compartmentalization for cell signaling and therapeutic approaches to targeting the SL network.

Super-Resolution Fluorescence Microscopy Methods for Assessing Mouse Biology

Super-resolution (diffraction unlimited) microscopy was developed 15 years ago; the developers were awarded the Nobel Prize in Chemistry in recognition of their work in 2014. Super-resolution microscopy is increasingly being applied to diverse scientific fields, from single molecules to cell organelles, viruses, bacteria, plants, and animals, especially the mammalian model organism Mus musculus. In this review, we explain how super-resolution microscopy, along with fluorescence microscopy from which it grew, has aided the renaissance of the light microscope. We cover experiment planning and specimen preparation and explain structured illumination microscopy, super-resolution radial fluctuations, stimulated emission depletion microscopy, single-molecule localization microscopy, and super-resolution imaging by pixel reassignment. The final section of this review discusses the strengths and weaknesses of each super-resolution technique and how to choose the best approach for your research. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.

Probing Small Distances in Live Cell Imaging

For probing small distances in living cells, methods of super-resolution microscopy and molecular sensing are reported. A main requirement is low light exposure to maintain cell viability and to avoid photobleaching of relevant fluorophores. From this point of view, Structured Illumination Microscopy (SIM), Axial Tomography, Total Internal Reflection Fluorescence Microscopy (TIRFM) and often a combination of these methods are used. To show the high potential of these techniques, measurements on cell-substrate topology as well as on intracellular translocation of the glucose transporter GLUT4 are described. In addition, molecular parameters can be deduced from spectral data, fluorescence lifetimes or non-radiative energy transfer (FRET) between a donor and an acceptor molecule. As an example, FRET between the epidermal growth factor receptor (EGFR) and the growth factor receptor-bound protein 2 (Grb2) is described. Since this interaction, as well as further processes of cellular signaling (e.g., translocation of GLUT4) are sensitive to stimulation by pharmaceutical agents, methods (e.g., TIRFM) are transferred from a fluorescence microscope to a multi-well reader system for simultaneous detection of large cell populations.

From Microscopy to Nanoscopy: Defining an Arabidopsis thaliana Meiotic Atlas at the Nanometer Scale

Visualization of meiotic chromosomes and the proteins involved in meiotic recombination have become essential to study meiosis in many systems including the model plant Arabidopsis thaliana. Recent advances in super-resolution technologies changed how microscopic images are acquired and analyzed. New technologies enable observation of cells and nuclei at a nanometer scale and hold great promise to the field since they allow observing complex meiotic molecular processes with unprecedented detail. Here, we provide an overview of classical and advanced sample preparation and microscopy techniques with an updated Arabidopsis meiotic atlas based on super-resolution microscopy. We review different techniques, focusing on stimulated emission depletion (STED) nanoscopy, to offer researchers guidance for selecting the optimal protocol and equipment to address their scientific question.

The frontier of live tissue imaging across space and time

What you see is what you get-imaging techniques have long been essential for visualization and understanding of tissue development, homeostasis, and regeneration, which are driven by stem cell self-renewal and differentiation. Advances in molecular and tissue modeling techniques in the last decade are providing new imaging modalities to explore tissue heterogeneity and plasticity. Here we describe current state-of-the-art imaging modalities for tissue research at multiple scales, with a focus on explaining key tradeoffs such as spatial resolution, penetration depth, capture time/frequency, and moieties. We explore emerging tissue modeling and molecular tools that improve resolution, specificity, and throughput.

The construction of high-magnification homemade lenses for a simple microscope: an easy "DIY" tool for biological and interdisciplinary education

The rise of microscopy in the seventeenth century allowed scientists to discover a new world of microorganisms and achieve great physiological advances. One of the first microscopes of the epoch was Antonie van Leeuwenhoek's microscope, a deceptively simple device that contains a single ball lens housed in a metal plate allowing the observation of samples at up to ×250 magnification. Such magnification was much greater than that achieved by rudimentary compound microscopes of the era, allowing for the discovery of microscopic, single-celled life, an achievement that marked the study of biology up to the nineteenth century. Since Leeuwenhoek's design uses a single ball lens, it is possible to fabricate variations for educational activities in physics and biology university and high school classrooms. A fundamental problem, however, with home-built microscopes is that it is difficult to work with glass. We developed a simple protocol to make ball lenses of glass and gelatin with high magnification that can be done in a university/high school classroom, and we designed an optimized support for focusing and taking photographs with a smartphone. The protocol details a simple, easily accessible, low-cost, and effective tool for the observation of microscopic samples, possible to perform anywhere without the need for a laboratory or complex tools. Our protocol has been implemented in classrooms in Chile to a favorable reception.

A comparative study on the use of microscopy in pharmacology and cell biology research

Microscopy is the main technique to visualize and study the structure and function of cells. The impact of optical and electron microscopy techniques is enormous in all fields of biomedical research. It is possible that different research areas rely on microscopy in diverse ways. Here, we analyzed comparatively the use of microscopy in pharmacology and cell biology, among other biomedical sciences fields. We collected data from articles published in several major journals in these fields. We analyzed the frequency of use of different optical and electron microscopy techniques: bright field, phase contrast, differential interference contrast, polarization, conventional fluorescence, confocal, live cell imaging, super resolution, transmission and scanning electron microscopy, and cryoelectron microscopy. Our analysis showed that the use of microscopy has a distinctive pattern in each research area, and that nearly half of the articles from pharmacology journals did not use any microscopy method, compared to the use of microscopy in almost all the articles from cell biology journals. The most frequent microscopy methods in all the journals in all areas were bright field and fluorescence (conventional and confocal). Again, the pattern of use was different: while the most used microscopy methods in pharmacology were bright field and conventional fluorescence, in cell biology the most used methods were conventional and confocal fluorescence, and live cell imaging. We observed that the combination of different microscopy techniques was more frequent in cell biology, with up to 6 methods in the same article. To correlate the use of microscopy with the research theme of each article, we analyzed the proportion of microscopy figures with the use of cell culture. We analyzed comparatively the vocabulary of each biomedical sciences field, by the identification of the most frequent words in the articles. The collection of data described here shows a vast difference in the use of microscopy among different fields of biomedical sciences. The data presented here could be valuable in other scientific and educational contexts.

Translocation of (ultra)fine particles and nanoparticles across the placenta; a systematic review on the evidence of in vitro, ex vivo, and in vivo studies

Fetal development is a crucial window of susceptibility in which exposure may lead to detrimental health outcomes at birth and later in life. The placenta serves as a gatekeeper between mother and fetus. Knowledge regarding the barrier capacity of the placenta for nanoparticles is limited, mostly due to technical obstacles and ethical issues. We systematically summarize and discuss the current evidence and define knowledge gaps concerning the maternal-fetal transport and fetoplacental accumulation of (ultra)fine particles and nanoparticles. We included 73 studies on placental translocation of particles, of which 21 in vitro/ex vivo studies, 50 animal studies, and 2 human studies on transplacental particle transfer. This systematic review shows that (i) (ultra)fine particles and engineered nanoparticles can bypass the placenta and reach fetal units as observed for all the applied models irrespective of the species origin (i.e., rodent, rabbit, or human) or the complexity (i.e., in vitro, ex vivo, or in vivo), (ii) particle size, particle material, dose, particle dissolution, gestational stage of the model, and surface composition influence maternal-fetal translocation, and (iii) no simple, standardized method for nanoparticle detection and/or quantification in biological matrices is available to date. Existing evidence, research gaps, and perspectives of maternal-fetal particle transfer are highlighted.

Deep learning-enhanced fluorescence microscopy via degeneration decoupling

Deep learning-based reconstruction has emerged as an effective tool in fluorescence microscopy, with the potential to resolve diffraction-limited structures. However, most deep-learning reconstruction methods employed an end-to-end strategy, which ignored physical laws in the imaging process and made the preparation of training data highly challenging as well. In this study, we have proposed a novel deconvolution algorithm based on an imaging model, deep-learning priors and the alternating direction method of multipliers. This scheme decouples the reconstruction into two separate sub-problems, one for deblurring and one for restraining noise and artifacts. As a result of the decoupling, we are able to introduce deep-learning image priors and a variance stabilizing transform against targeted image degeneration due to the low photon budget. Deep-learning priors are learned from the general image dataset, in which biological images do not have to be involved, and are more powerful than hand-designed ones. Moreover, the use of the imaging model ensures high fidelity and generalization. Experiments on various kinds of measurement data show that the proposed algorithm outperforms existing state-of-the-art deconvolution algorithms in resolution enhancement and generalization.

Imaging Flies by Fluorescence Microscopy: Principles, Technologies, and Applications

The development of fluorescent labels and powerful imaging technologies in the last two decades has revolutionized the field of fluorescence microscopy, which is now widely used in diverse scientific fields from biology to biomedical and materials science. Fluorescence microscopy has also become a standard technique in research laboratories working on Drosophila melanogaster as a model organism. Here, we review the principles of fluorescence microscopy technologies from wide-field to Super-resolution microscopy and its application in the Drosophila research field.

Geometric partitioning of cohesin and condensin is a consequence of chromatin loops

SMC (structural maintenance of chromosomes) complexes condensin and cohesin are crucial for proper chromosome organization. Condensin has been reported to be a mechanochemical motor capable of forming chromatin loops, while cohesin passively diffuses along chromatin to tether sister chromatids. In budding yeast, the pericentric region is enriched in both condensin and cohesin. As in higher-eukaryotic chromosomes, condensin is localized to the axial chromatin of the pericentric region, while cohesin is enriched in the radial chromatin. Thus, the pericentric region serves as an ideal model for deducing the role of SMC complexes in chromosome organization. We find condensin-mediated chromatin loops establish a robust chromatin organization, while cohesin limits the area that chromatin loops can explore. Upon biorientation, extensional force from the mitotic spindle aggregates condensin-bound chromatin from its equilibrium position to the axial core of pericentric chromatin, resulting in amplified axial tension. The axial localization of condensin depends on condensin's ability to bind to chromatin to form loops, while the radial localization of cohesin depends on cohesin's ability to diffuse along chromatin. The different chromatin-tethering modalities of condensin and cohesin result in their geometric partitioning in the presence of an extensional force on chromatin.

Methods for imaging mammalian mitochondrial morphology: A prospective on MitoGraph

Mitochondria are found in a variety of shapes, from small round punctate structures to a highly interconnected web. This morphological diversity is important for function, but complicates quantification. Consequently, early quantification efforts relied on various qualitative descriptors that understandably reduce the complexity of the network leading to challenges in consistency across the field. Recent application of state-of-the-art computational tools have resulted in more quantitative approaches. This prospective highlights the implementation of MitoGraph, an open-source image analysis platform for measuring mitochondrial morphology initially optimized for use with Saccharomyces cerevisiae. Here Mitograph was assessed on five different mammalian cells types, all of which were accurately segmented by MitoGraph analysis. MitoGraph also successfully differentiated between distinct mitochondrial morphologies that ranged from entirely fragmented to hyper-elongated. General recommendations are also provided for confocal imaging of labeled mitochondria (using mito-YFP, MitoTracker dyes and immunostaining parameters). Widespread adoption of MitoGraph will help achieve a long-sought goal of consistent and reproducible quantification of mitochondrial morphology.

Angles-centroids fitting calibration and the centroid algorithm applied to reverse Hartmann test

In this paper, we develop an angles-centroids fitting (ACF) system and the centroid algorithm to calibrate the reverse Hartmann test (RHT) with sufficient precision. The essence of ACF calibration is to establish the relationship between ray angles and detector coordinates. Centroids computation is used to find correspondences between the rays of datum marks and detector pixels. Here, the point spread function of RHT is classified as circle of confusion (CoC), and the fitting of a CoC spot with 2D Gaussian profile to identify the centroid forms the basis of the centroid algorithm. Theoretical and experimental results of centroids computation demonstrate that the Gaussian fitting method has a less centroid shift or the shift grows at a slower pace when the quality of the image is reduced. In ACF tests, the optical instrumental alignments reach an overall accuracy of 0.1 pixel with the application of laser spot centroids tracking program. Locating the crystal at different positions, the feasibility and accuracy of ACF calibration are further validated to 10^-6-10^-4 rad root-mean-square error of the calibrations differences.

Navigating challenges in the application of superresolution microscopy

In 2014, the Nobel Prize in Chemistry was awarded to three scientists who have made groundbreaking contributions to the field of superresolution (SR) microscopy (SRM). The first commercial SR microscope came to market a decade earlier, and many other commercial options have followed. As commercialization has lowered the barrier to using SRM and the awarding of the Nobel Prize has drawn attention to these methods, biologists have begun adopting SRM to address a wide range of questions in many types of specimens. There is no shortage of reviews on the fundamental principles of SRM and the remarkable achievements made with these methods. We approach SRM from another direction: we focus on the current practical limitations and compromises that must be made when designing an SRM experiment. We provide information and resources to help biologists navigate through common pitfalls in SRM specimen preparation and optimization of image acquisition as well as errors and artifacts that may compromise the reproducibility of SRM data.

Visualization of the 3D structures of small organisms via LED-SIM

Background

Innovative new techniques that aid in the visualization of microscopic anatomical structures have improved our understanding of organismal biology significantly. It is often challenging to observe internal 3D structures, despite the use of techniques such as confocal laser scanning microscopy (CLSM), micro-computed tomography (Micro-CT), magnetic resonance imaging (MRI), focused ion beam scanning electron microscopy (FIB-SEM) and others. In the current paper, we assess LED-SIM (DMD-based LED-illumination structured illumination microscopy), which facilitates the acquisition of nano- and micro-3D structures of small organisms in a high-resolution format (500 nm in the XY-plane and 930 nm along the Z-axis).

Results

We compare other microstructural imaging techniques (involving conventional optical microscopy, CLSM and Micro-CT) with LED-SIM to assess the quality (e.g. resolution, penetration depth, etc.) of LED-SIM images, as well as to document the potential short-comings of LED-SIM. Based on these results we present an optimized set of protocols to ensure that LED-SIM arthropod and nematode samples with different cuticles or textures are prepared for analysis in an optimal manner. Six arthropod and nematode specimens were tested and shown to be suitable for LED-SIM imaging, which was found to yield high resolution 3D images.

Conclusions

Although LED-SIM still must be thoroughly tested before it is widely accepted and the Z-axis resolution still requires improvement, this technique offers distinct high quality 3D images. LED-SIM can be highly effective and may provide high quality 3D images for zoological studies following the guidelines of sample preparation presented in the current paper.

Electronic supplementary material

The online version of this article (doi:10.1186/s12983-016-0158-9) contains supplementary material, which is available to authorized users.

Clift MJ, Blank F, Petri-Fink A, Rothen-Rutishauser B. Quantification of nanoparticles at the single-cell level: an overview about state-of-the-art techniques and their limitations

With the increasing production and use of engineered nanoparticles it is crucial that their interaction with biological systems is understood. Due to the small size of nanoparticles, their identification and localization within single cells is extremely challenging. Therefore, various cutting-edge techniques are required to detect and to quantify metals, metal oxides, magnetic, fluorescent, as well as electron-dense nanoparticles. Several techniques will be discussed in detail, such as inductively coupled plasma atomic emission spectroscopy, flow cytometry, laser scanning microscopy combined with digital image restoration, as well as quantitative analysis by means of stereology on transmission electron microscopy images. An overview will be given regarding the advantages of those visualization/quantification systems, including a thorough discussion about limitations and pitfalls.

Dynamics and organization of cortical microtubules as revealed by superresolution structured illumination microscopy

Plants employ acentrosomal mechanisms to organize cortical microtubule arrays essential for cell growth and differentiation. Using structured illumination microscopy (SIM) adopted for the optimal documentation of Arabidopsis (Arabidopsis thaliana) hypocotyl epidermal cells, dynamic cortical microtubules labeled with green fluorescent protein fused to the microtubule-binding domain of the mammalian microtubule-associated protein MAP4 and with green fluorescent protein-fused to the alpha tubulin6 were comparatively recorded in wild-type Arabidopsis plants and in the mitogen-activated protein kinase mutant mpk4 possessing the former microtubule marker. The mpk4 mutant exhibits extensive microtubule bundling, due to increased abundance and reduced phosphorylation of the microtubule-associated protein MAP65-1, thus providing a very useful genetic tool to record intrabundle microtubule dynamics at the subdiffraction level. SIM imaging revealed nano-sized defects in microtubule bundling, spatially resolved microtubule branching and release, and finally allowed the quantification of individual microtubules within cortical bundles. Time-lapse SIM imaging allowed the visualization of subdiffraction, short-lived excursions of the microtubule plus end, and dynamic instability behavior of both ends during free, intrabundle, or microtubule-templated microtubule growth and shrinkage. Finally, short, rigid, and nondynamic microtubule bundles in the mpk4 mutant were observed to glide along the parent microtubule in a tip-wise manner. In conclusion, this study demonstrates the potential of SIM for superresolution time-lapse imaging of plant cells, showing unprecedented details accompanying microtubule dynamic organization.