Resolution Fluorescence Microscopy Research Articles

Novel druggable space in human KRAS G13D discovered using structural bioinformatics and a P-loop targeting monoclonal antibody

KRAS belongs to a family of small GTPases that act as binary switches upstream of several signalling cascades, controlling proliferation and survival of cells. Mutations in KRAS drive oncogenesis, especially in pancreatic, lung, and colorectal cancers (CRC). Although historic attempts at targeting mutant KRAS with small molecule inhibitors have proven challenging, there are recent successes with the G12C, and G12D mutations. However, clinically important RAS mutations such as G12V, G13D, Q61L, and A146T, remain elusive drug targets, and insights to their structural landscape is of critical importance to develop novel, and effective therapeutic concepts. We present a fully open, P-loop exposing conformer of KRAS G13D by X-ray crystallography at 1.4–2.4 Å resolution in Mg2+-free phosphate and malonate buffers. The G13D conformer has the switch-I region displaced in an upright position leaving the catalytic core fully exposed. To prove that this state is druggable, we developed a P-loop-targeting monoclonal antibody (mAb). The mAb displayed high-affinity binding to G13D and was shown using high resolution fluorescence microscopy to be spontaneously taken up by G13D-mutated HCT 116 cells (human CRC derived) by macropinocytosis. The mAb inhibited KRAS signalling in phosphoproteomic and genomic studies. Taken together, the data propose novel druggable space of G13D that is reachable in the cellular context. It is our hope that these findings will stimulate attempts to drug this fully open state G13D conformer using mAbs or other modalities.

Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopy.

Optical aberrations hinder fluorescence microscopy of thick samples, reducing image signal, contrast, and resolution. Here we introduce a deep learning-based strategy for aberration compensation, improving image quality without slowing image acquisition, applying additional dose, or introducing more optics into the imaging path. Our method (i) introduces synthetic aberrations to images acquired on the shallow side of image stacks, making them resemble those acquired deeper into the volume and (ii) trains neural networks to reverse the effect of these aberrations. We use simulations and experiments to show that applying the trained 'de-aberration' networks outperforms alternative methods, providing restoration on par with adaptive optics techniques; and subsequently apply the networks to diverse datasets captured with confocal, light-sheet, multi-photon, and super-resolution microscopy. In all cases, the improved quality of the restored data facilitates qualitative image inspection and improves downstream image quantitation, including orientational analysis of blood vessels in mouse tissue and improved membrane and nuclear segmentation in C. elegans embryos.

Nanoscale intracellular ultrastructures affected by osmotic pressure using small-angle X-ray scattering

Although intracellular ultrastructures have typically been studied using microscopic techniques, it is difficult to observe ultrastructures at the submicron scale of living cells due to spatial resolution (fluorescence microscopy) or high vacuum environment (electron microscopy). We investigate the nanometer scale intracellular ultrastructures of living CHO cells in various osmolality using small-angle X-ray scattering (SAXS), and especially the structures of ribosomes, DNA double helix, and plasma membranes in-cell environment are observed. Ribosomes expand and contract in response to osmotic pressure, and the inter-ribosomal correlation occurs under isotonic and hyperosmolality. The DNA double helix is not dependent on the osmotic pressure. Under high osmotic pressure, the plasma membrane folds into form a multilamellar structure with a periodic length of about 6 nm. We also study the ultrastructural changes caused by formaldehyde fixation, freezing and heating.

Detailed physicochemical study and thermodynamic aspects of the interaction between nonionic cellulose derivative hydroxyethyl cellulose and anionic surfactant sodium N-dodecanoyl sarcosinate in aqueous media

BackgroundThe scheme of this work was to study the interaction between hydroxyethyl cellulose (HEC), a non-ionic, water soluble biopolymer and sodium N-dodecanoyl sarcosinate (SDDS), a novel, environmentally friendly amino acid-based anionic surfactant in aqueous medium. The study of this type of interaction is relatively less complicated compared to that between a polymer and a surfactant with opposite charges. MethodsThe critical micelle concentration (CMC) of HEC-induced SDDS has been determined by various physicochemical methods such as tensiometry, conductometry, fluorimetry and microcalorimetry. Several thermodynamic and surface parameters related to the binding of SDDS with HEC have been assessed. The aggregation number (Nagg) of SDDS micelles in the presence of non-ionic HEC polymer has been measured by the steady-state fluorescence method. The hydrodynamic diameter (Dh) and zeta potential (ζ) of the polymer-surfactant aggregate have been measured by the dynamic light scattering method. The interaction study has further been amplified by detecting the change in the surface morphology of the polymer due to surfactant binding using Field Emission Scanning Electron Microscopy (FESEM) and high resolution transmission electron microscopy (HR-TEM) imaging in solvent-free state, as well as visualization of the HEC-SDDS micelle in the solution phase using fluorescence microscopy technique. Significant findingsFrom a physicochemical point of view, hydrophobic synergism seems to be important for understanding the interaction pattern of HEC-SDDS combination. In each scenario, the CMC of SDDS decreases with an increase in weight percentage of HEC. The aggregation number (Nagg) of SDDS micelles is also found to decrease with an increase in weight percentage of HEC in the medium. The hydrodynamic diameter (Dh) and zeta potential (ζ) of the polymer-surfactant aggregate, these two parameters have been found to be strongly dependent on the amphiphile concentration. Finally, investigations of the surface morphologies by taking Field Emission Scanning Electron Microscopy (FESEM), high resolution transmission electron microscopy (HR-TEM) and fluorescence microscopy techniques assist the experimental data.

Photoactivated localization microscopy combined with image spatial correlation analysis to study of the distribution and diffusion of Angiotensin II type 1 Receptor in the plasma membrane.

Super resolution fluorescence microscopy, (SRFM) techniques which overcome the spatial diffraction-limit has enabled us to visualize nanoscale cellular events with high temporal and spatial resolution in living cells, but in order to gain reliable mechanistic insights, a quantitative analysis is essential 1–3. In this study we used SRFM combined with novel image analysis as a powerful tool to investigate the mechanisms by which Angiotensin II type 1 Receptors (AT1Rs), are distributed and diffuse in the plasma membrane. This mechanism remains still unclear, despite its crucial role in cardiovascular homeostasis in the cell4,5. The aim of this study is to obtain quantitative information about AT1R dynamics and organization, and their corresponding receptor-ligand complexes in living cells. This was achieved by using photoactivated localization microscopy (PALM) combined with image spatial-temporal correlation analysis. To study nanoscale receptor distribution, a combination of expansion microscopy (ExM) and PALM was used. This study showed that AT1R lateral diffusion increased after binding to the agonist, Angiotensin II (Ang II) while no change for either the biased agonist, SII-Ang II or the antagonist, Losartan, was observed. The receptor diffusion was found to be transiently confined in the PM. In addition, ExM revealed that AT1Rs form nano clusters at the PM, and the cluster size significantly decreased after Ang II treatment. Taking these results together suggests that Ang II binding and activation cause reorganization and changes in the dynamics of AT1Rs at the PM. Our work contributes to a better comprehension of AT1R dynamic in PM and makes for a better understanding of signalling and receptor mechanisms.

“Non-cytotoxic” doses of metal-organic framework nanoparticles increase endothelial permeability by inducing actin reorganization

Cytotoxicity of nanoparticles is routinely characterized by biochemical assays such as cell viability and membrane integrity assays. However, these approaches overlook cellular biophysical properties including changes in the actin cytoskeleton, cell stiffness, and cell morphology, particularly when cells are exposed to “non-cytotoxic” doses of nanoparticles. Zeolitic imidazolate framework-8 nanoparticles (ZIF-8 NPs), a member of metal–organic framework family, has received increasing interest in various fields such as environmental and biomedical sciences. ZIF-8 NPs may enter the blood circulation system after unintended oral and inhalational exposure or intended intravenous injection for diagnostic and therapeutic applications, yet the effect of ZIF-8 NPs on vascular endothelial cells is not well understood. Here, the biophysical impact of “non-cytotoxic” dose ZIF-8 NPs on human aortic endothelial cells (HAECs) is investigated. We demonstrate that “non-cytotoxic” doses of ZIF-8 NPs, pre-defined by a series of biochemical assays, can increase the endothelial permeability of HAEC monolayers by causing cell junction disruption and intercellular gap formation, which can be attributed to actin reorganization within adjacent HAECs. Nanomechanical atomic force microscopy and super resolution fluorescence microscopy further confirm that “non-cytotoxic” doses of ZIF-8 NPs change the actin structure and cell morphology of HAECs at the single cell level. Finally, the underlying mechanism of actin reorganization induced by the “non-cytotoxic” dose ZIF-8 NPs is elucidated. Together, this study indicates that the “non-cytotoxic” doses of ZIF-8 NPs, intentionally or unintentionally introduced into blood circulation, may still pose a threat to human health, considering increased endothelial permeability is essential to the progression of a variety of diseases. From a broad view of cytotoxicity evaluation, it is important to consider the biophysical properties of cells, since they can serve as novel and more sensitive markers to assess nanomaterial’s cytotoxicity.

Spatial quantification of single cell mRNA and ligand binding of the kappa opioid receptor in the rat hypothalamus

Detailed quantification of brain tissue provides a deeper understanding of changes in expression and function. We have created a pipeline to study the detailed expression patterns of the kappa opioid receptor in the rat hypothalamus using high resolution fluorescence microscopy and receptor autoradiography. The workflow involved structured serial sampling of rat hypothalamic nuclei, in situ detection of mRNA and receptor expression, and advanced image analysis. Our results demonstrate how maintaining spatial information can lead to increased understanding of RNA and protein expression. In addition, we show the detailed expression patterns of the kappa opioid receptor in the rat hypothalamus.

Reovirus uses temporospatial compartmentalization to orchestrate core versus outercapsid assembly.

Reoviridae virus family members, such as mammalian orthoreovirus (reovirus), encounter a unique challenge during replication. To hide the dsRNA from host recognition, the genome remains encapsidated in transcriptionally active proteinaceous core capsids that transcribe and release +RNA. De novo +RNAs and core proteins must repeatedly assemble into new progeny cores in order to logarithmically amplify replication. Reoviruses also produce outercapsid (OC) proteins μ1, σ3 and σ1 that assemble onto cores to create highly stable infectious full virions. Current models of reovirus replication position amplification of transcriptionally-active cores and assembly of infectious virions in shared factories, but we hypothesized that since assembly of OC proteins would halt core amplification, OC assembly is somehow regulated. Kinetic analysis of virus +RNA production, core versus OC protein expression, and core particles versus whole virus particle accumulation, indicated that assembly of OC proteins onto core particles was temporally delayed. All viral RNAs and proteins were made simultaneously, eliminating the possibility that delayed OC RNAs or proteins account for delayed OC assembly. High resolution fluorescence and electron microscopy revealed that core amplification occurred early during infection at peripheral core-only factories, while all OC proteins associated with lipid droplets (LDs) that coalesced near the nucleus in a μ1–dependent manner. Core-only factories transitioned towards the nucleus despite cycloheximide-mediated halting of new protein expression, while new core-only factories developed in the periphery. As infection progressed, OC assembly occurred at LD-and nuclear-proximal factories. Silencing of OC μ1 expression with siRNAs led to large factories that remained further from the nucleus, implicating μ1 in the transition to perinuclear factories. Moreover, late during infection, +RNA pools largely contributed to the production of de-novo viral proteins and fully-assembled infectious viruses. Altogether the results suggest an advanced model of reovirus replication with spatiotemporal segregation of core amplification, OC complexes and fully assembled virions.

Structure and principles of self-assembly of giant “sea urchin” type sulfonatophenyl porphine aggregates

Principles of molecular self-assembly into giant hierarchical structures of hundreds of micrometers in size are studied in aggregates of meso-tetra(4-sulfonatophenyl)porphine (TPPS4). The aggregates form a central tubular core, which is covered with radially protruding filamentous non-branching aggregates. The filaments cluster and orient at varying angles from the core surface and some filaments form bundles. Due to shape resemblance, the structures are termed giant sea urchin (GSU) aggregates. Spectrally resolved fluorescence microscopy reveals J- and H-bands of TPPS4 aggregates in both the central core and the filaments. The fluorescence of the core is quenched while filaments exhibit strong fluorescence. Upon drying, the filament fluorescence gets quenched while the core is less affected, showing stronger relative fluorescence. Fluorescence-detected linear dichroism (FDLD) microscopy reveals that absorption dipoles corresponding to J-bands are oriented along the filament axis. The comparison of FDLD with scanning electron microscopy (SEM) reveals the structure of central core comprised of multilayer ribbons, which wind around the core axis forming a tube. Polarimetric second-harmonic generation (SHG) and third-harmonic generation microscopy exhibits strong signal from the filaments with nonlinear dipoles oriented close to the filament axis, while central core displays very low SHG due to close to centrosymmetric organization. Large chiral nonlinear susceptibility points to helical arrangement of the filaments. The investigation shows that TPPS4 molecules form distinct aggregate types, including chiral nanotubes and nanogranular aggregates that associate into the hierarchical GSU structure, prototypical to complex biological structures. The chiral TPPS4 aggregates can serve as harmonophores for nonlinear microscopy.

Another Hilbert inequality and critically separated interpolation nodes

AbstractAbstract: Estimates on the condition number of Vandermonde matrices have implications on several algorithms ranging from polynomial interpolation to sparse super resolution in fluorescence microscopy. Classically, the situation is studied for monomials on real intervals, the complex unit disk, and the complex unit circle. Except for roots of unity and well separated nodes on the unit circle, the condition number grows strongly with increasing polynomial degree. Here, we show that the condition number of the Vandermonde matrix for a particular instance of critically separated nodes on the complex unit circle grows logarithmically with the polynomial degree. The proof is based on a variant of Hilbert's inequality with remainder term.

High-axial-resolution single-molecule localization under dense excitation with a multi-channel deep U-Net.

Single-molecule localization microscopy (SMLM) can bypass the diffraction limit of optical microscopes and greatly improve the resolution in fluorescence microscopy. By introducing the point spread function (PSF) engineering technique, we can customize depth varying PSF to achieve higher axial resolution. However, most existing 3D single-molecule localization algorithms require excited fluorescent molecules to be sparse and captured at high signal-to-noise ratios, which results in a long acquisition time and precludes SMLM's further applications in many potential fields. To address this problem, we propose a novel 3D single-molecular localization method based on a multi-channel neural network based on U-Net. By leveraging the deep network's great advantages in feature extraction, the proposed network can reliably discriminate dense fluorescent molecules with overlapped PSFs and corrupted by sensor noise. Both simulated and real experiments demonstrate its superior performance in PSF engineered microscopes with short exposure and dense excitations, which holds great potential in fast 3D super-resolution microscopy.

Abstract P419: Revealing The Dynamics Of Vesicle Formation During Clathrin-mediated Endocytosis In Living Endothelial Cells

Clathrin-mediated endocytosis (CME) is an essential cellular process for internalizing nutrients and therapeutics at endothelial cell barriers. Studying the formation of cargo containing endocytic vesicles in living cells is challenging due to the limited resolution of fluorescence microscopy and the highly dynamic nature of CME. Moreover, it is currently unknown how the physiological conditions present in vasculature affect CME in endothelial cells. To address this challenge we used a novel microscopy approach, Simultaneous Two-wavelength Axial Ratiometry (STAR), to image vesicle formation dynamics with nanometer axial resolution in living cells. High-throughput analysis revealed that 80% of de novo clathrin accumulations contributed to endocytosis while 20% remained flat, consistent in both human umbilical vein endothelial cells (HUVECs) and our test-bed model green monkey kidney fibroblast-like (Cos-7) cells. We next investigated the interplay between coat curvature and clathrin accumulation in vesicle initiation to identify the mechanism of vesicle formation. Our results support the flexible model of vesicle formation with curvature and clathrin accumulation initiating together at shorter-lived vesicles (<20s) and through a flat-to-curved transition of clathrin lattices at longer-lived vesicles (>20s). Finally, we addressed if physiological conditions present in vasculature alter the dynamics of vesicle formation. We show that increasing osmotic pressure decreased the total number of internalizations but had no impact on the number of flat clathrin accumulations or the mechanism of vesicle formation in Cos-7 cells. In future research, we will test the hypothesis that HUVECs have distinct mechanisms to retain vesicle formation under osmotic pressure or shear stress conditions similar to their native environment. Additionally targeted drug delivery to vascular endothelial cells, for example nanocarriers binding to flat lattices or CCVs leading to different therapeutic outcomes or bioavailability, can potentially be informed by identifying clathrin morphology and dynamics and the mechanisms of endocytosis using STAR microscopy.

Mechanically Triggered Hybridization Chain Reaction.

Cells transmit piconewton forces to receptors to mediate processes such as migration and immune recognition. A major challenge in quantifying such forces is the sparsity of cell mechanical events. Accordingly, molecular tension is typically quantified with high resolution fluorescence microscopy, which hinders widespread adoption and application. Here, we report a mechanically triggered hybridization chain reaction (mechano-HCR) that allows chemical amplification of mechanical events. The amplification is triggered when a cell receptor mechanically denatures a duplex revealing a cryptic initiator to activate the HCR reaction in situ. Importantly, mechano-HCR enables direct readout of pN forces using a plate reader. We leverage this capability and measured mechano-IC50 for aspirin, Y-27632, and eptifibatide. Given that cell mechanical phenotypes are of clinical importance, mechano-HCR may offer a convenient route for drug discovery, personalized medicine, and disease diagnosis.

Mechanically Triggered Hybridization Chain Reaction

AbstractCells transmit piconewton forces to receptors to mediate processes such as migration and immune recognition. A major challenge in quantifying such forces is the sparsity of cell mechanical events. Accordingly, molecular tension is typically quantified with high resolution fluorescence microscopy, which hinders widespread adoption and application. Here, we report a mechanically triggered hybridization chain reaction (mechano‐HCR) that allows chemical amplification of mechanical events. The amplification is triggered when a cell receptor mechanically denatures a duplex revealing a cryptic initiator to activate the HCR reaction in situ. Importantly, mechano‐HCR enables direct readout of pN forces using a plate reader. We leverage this capability and measured mechano‐IC50 for aspirin, Y‐27632, and eptifibatide. Given that cell mechanical phenotypes are of clinical importance, mechano‐HCR may offer a convenient route for drug discovery, personalized medicine, and disease diagnosis.

Targeting cancer cell adhesion molecule, CD146, with low-dose gold nanorods and mild hyperthermia disrupts actin cytoskeleton and cancer cell migration

Cluster of differentiation 146 (CD146), a cancer cell adhesion molecule, is over-expressed on the surfaces of melanoma, breast, ovarian, and prostate cancer cells, and its high expression indicates the migration tendency of these cancer cells and poor patient prognosis. Here, we hypothesize that targeting the CD146 with low-dose gold nanorods combined with mild hyperthermia can stop the migration of these cancer cells. Two metastatic cancer cells including a melanoma and a breast cancer cell line are selected as the model systems. Cell migration assays show that the migration of both cell lines can be completely stopped by the treatment. Atomic force microscopy and super resolution fluorescence microscopy reveal the alterations of actin cytoskeleton and cell morphology correspond to the inhibited cell migration. Further mechanistic analysis indicates the treatment disrupts the actin cytoskeleton by a synergistic mechanism including depleting membrane CD146 and interfering ezrin-radixin-moesin phosphorylation. As a result, we believe targeting CD146 with low-dose gold nanorods and mild hyperthermia could be a versatile, effective, and safe approach for stopping cancer metastasis. More broadly, the concept of targeting cancer cell surface markers that connect the underlying actin cytoskeleton, offers enormous potential in treating cancer metastasis, which accounts for more than 90% of cancer-associated mortality.

Antifungal activity of polymethyl methacrylate/Si3N4 composites against Candida albicans

Previous studies using gram-positive and -negative bacteria demonstrated that hydrolysis of silicon nitride (Si3N4) in aqueous suspensions elutes nitrogen and produces gaseous ammonia while buffering pH. According to immunochemistry assays, fluorescence imaging, and in situ Raman spectroscopy, we demonstrate here that the antipathogenic surface chemistry of Si3N4 can be extended to polymethylmethacrylate (PMMA) by compounding it with a minor fraction (~8 vol.%) of Si3N4 particles without any tangible loss in bulk properties. The hydrolytic products, which were eluted from partly exposed Si3N4 particles at the composite surface, exhibited fungicidal action against Candida albicans. Using a specific nitrative stress sensing dye and highly resolved fluorescence micrographs, we observed in situ congestion of peroxynitrite (ONOO−) radicals in the mitochondria of the Candida cells exposed to the PMMA/Si3N4 composite, while these radicals were absent in the mitochondria of identical cells exposed to monolithic PMMA. These in situ observations suggest that the surface chemistry of Si3N4 mimics the antifungal activity of macrophages, which concurrently produce NO radicals and superoxide anions (O2•−) resulting in the formation of candidacidal ONOO−. The fungicidal properties of PMMA/Si3N4 composites could be used in dental appliances to inhibit the uncontrolled growth of Candida albicans and ensuing candidiasis while being synergic with chemoprophylaxis. Statement of significanceIn a follow-up of previous studies of gram-positive and gram-negative bacteria, we demonstrate here that the antipathogenic surface chemistry of Si3N4 could be extended to polymethylmethacrylate (PMMA) containing a minor fraction (~8 vol.%) of Si3N4 particles without tangible loss in bulk properties. Hydrolytic products eluted from Si3N4 particles at the composite surface exhibited fungicidal action against Candida albicans. Highly resolved fluorescence microscopy revealed congestion of peroxynitrite (ONOO−) radicals in the mitochondria of the Candida cells exposed to the PMMA/Si3N4 composite, while radicals were absent in the mitochondria of identical cells exposed to monolithic PMMA. The fungicidal properties of PMMA/Si3N4 composites could be used in dental appliances to inhibit uncontrolled growth of Candida albicans and ensuing candidiasis in synergy with chemoprophylaxis.

Current challenges and solutions of super-resolution structured illumination microscopy

The resolution of fluorescence microscopy is limited by the diffraction imaging system, and many methods have been proposed to overcome the optical diffraction limit for achieving super-resolution imaging. Structured illumination microscopy (SIM) is one of the most competitive approaches and has demonstrated remarkable achievements. In the last two decades, SIM has been improved in many aspects, such as the enhancement of resolution and imaging depth and virtual modulation-based SIM. In this Perspective, we present an overview of the development of SIM, including the basic theory, application to biomedical studies, and the remarkable progress of SIM. Owing to its flexibility with respect to combination with other methods, SIM can be considered a powerful tool for biomedical study, offering augmented imaging capabilities by exploiting complementary advantages.

Observing Tyrosine Kinase Function by Polarization Resolved Fluorescence Microscopy

Receptor tyrosine kinases are membrane proteins crucial for cell signaling processes. Using techniques of molecular biology, we are trying to develop fluorescently labeled receptor kinases molecules that would allow observations of receptor kinase activation by two-photon polarization microscopy (2PPM). 2PPM is an advanced optical microscopy technique developed by our laboratory that allows observing changes in orientation of fluorescent labels attached to membrane proteins, such as due to conformational changes in the membrane proteins. 2PPM works by analyzing fluorescence images acquired with two perpendicular linear polarizations of the excitation light. Differences between the two images can be used to gain insights into the orientation of the observed fluorescent label, and hence into the conformation of the labeled protein. We have now applied the technique to several tyrosine kinase constructs prepared by other laboratories, as well as to constructs we prepared ourselves. We are now in the process of modifying existing constructs in order to be able to visualize activation of several tyrosine kinase receptors important in disease (such as the insulin receptor in diabetes) and in drug discovery. The poster summarizes our progress and current results.

Adaptive optics in super-resolution microscopy.

Fluorescence microscopy has become a routine tool in biology for interrogating life activities with minimal perturbation. While the resolution of fluorescence microscopy is in theory governed only by the diffraction of light, the resolution obtainable in practice is also constrained by the presence of optical aberrations. The past two decades have witnessed the advent of super-resolution microscopy that overcomes the diffraction barrier, enabling numerous biological investigations at the nanoscale. Adaptive optics, a technique borrowed from astronomical imaging, has been applied to correct for optical aberrations in essentially every microscopy modality, especially in super-resolution microscopy in the last decade, to restore optimal image quality and resolution. In this review, we briefly introduce the fundamental concepts of adaptive optics and the operating principles of the major super-resolution imaging techniques. We highlight some recent implementations and advances in adaptive optics for active and dynamic aberration correction in super-resolution microscopy.

Imaging Microtubules in vitro at High Resolution while Preserving their Structure.

Microtubules (MT) are the most rigid component of the cytoskeleton. Nevertheless, they often appear highly curved in the cellular context and the mechanisms governing their overall shape are poorly understood. Currently, in vitro microtubule analysis relies primarily on electron microscopy for its high resolution and Total Internal Reflection Fluorescence (TIRF) microscopy for its ability to image live fluorescently-labelled microtubules and associated proteins. For three-dimensional analyses of microtubules with micrometer curvatures, we have developed an assay in which MTs are polymerized in vitro from MT seeds adhered to a glass slide in a manner similar to conventional TIRF microscopy protocols. Free fluorescent molecules are removed and the MTs are fixed by perfusion. The MTs can then be observed using a confocal microscope with an Airyscan module for higher resolution. This protocol allows the imaging of microtubules that have retained their original three-dimensional shape and is compatible with high-resolution immunofluorescence detection.