Optical imaging. Expansion microscopy

Mini Review: Highlight of Recent Advances and Applications of MALDI Mass Spectrometry Imaging in 2024

Matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) is an emerging imaging tool that allows visualisation of hundreds of analytes unbiasedly in a single experiment. This paper highlights the adaptations of MALDI-MSI in different context in 2024, such as clinical diagnostic, pharmacology, forensics applications, plant metabolism and biology. Challenges and advancements were also discussed regarding sample preparation, instrumentations, data analysis, and integration of machine learning in the trend of single cell resolution and multi-omics. There are still rooms for improvements in sensitivity, spatial resolution, acquisition algorithm and data integration across multi-omics data to enable MALDI-MSI at subcellular level.

Optimized expansion microscopy reveals species-specific spindle microtubule organization in Xenopus egg extracts

The spindle is key to cell division, ensuring accurate chromosome segregation. Although its assembly and function are well studied, the mechanisms regulating spindle architecture remain elusive. Here, we investigate spindle organization differences between Xenopus laevis and tropicalis, leveraging expansion microscopy (ExM) to overcome conventional imaging limitations. We optimized an ExM protocol tailored for Xenopus egg extract spindles, refining fixation, denaturation, and gelation to achieve higher resolution while preserving spindle integrity. Our protocol enables preexpansion immunofluorescence and is seamlessly compatible with both species. To quantitatively compare microtubule organization in expanded spindles between the two species, we developed an analysis pipeline that is able to characterize microtubule bundles throughout spindles. We show that X. laevis spindles exhibit overall a broader range of bundle sizes, while X. tropicalis spindles contain mostly smaller bundles. Although both species show larger bundles near the spindle center, X. tropicalis spindles otherwise consist of very small bundles, whereas X. laevis spindles contain more medium-sized bundles. Altogether, our work reveals species-specific spindle architectures and suggests their adaptation to the different spindle size and chromatin amount. By enhancing resolution and minimizing artifacts, our ExM approach provides new insights into spindle morphology and a robust tool for further studying these large cellular assemblies.

Super-resolution imaging in whole cells and tissues via DNA-PAINT on a spinning disk confocal with optical photon reassignment

Single-Molecule Localization Microscopy (SMLM) has traditionally faced challenges to optimize signal-to-noise ratio, penetration depth, field-of-view (FOV), and spatial resolution simultaneously. Here, we show that DNA-PAINT imaging on a Spinning Disk Confocal with Optical Photon Reassignment (SDC-OPR) system overcomes these trade-offs, enabling high-resolution imaging across multiple cellular layers and large FOVs. We demonstrate the system's capability with DNA origami constructs and biological samples, including nuclear pore complexes, mitochondria, and microtubules, achieving a spatial resolution of 6 nm in the basal plane and sub-10 nm localization precision at depths of 9 µm within a 53 × 53 µm² FOV. Additionally, imaging of the developing Drosophila eye epithelium at depths up to 9 µm with sub-13 nm average localization precision, reveals distinct E-cadherin populations in adherens junctions. Quantitative analysis of Collagen IV deposition in this epithelium indicated an average of 46 ± 27 molecules per secretory vesicle. These results underscore the versatility of DNA-PAINT on an SDC-OPR for advancing super-resolution imaging in complex biological systems.

DNA-PAINT Imaging with Hydrogel Imprinting and Clearing

Hydrogel-embedding is a versatile technique in fluorescence microscopy, offering stabilization, optical clearing, and the physical expansion of biological specimens. DNA-PAINT is a super-resolution microscopy approach based on the diffusion and transient binding of fluorescently labeled oligos, but its feasibility in hydrogels has not yet been explored. In this study, we demonstrate that polyacrylamide hydrogels support sufficient diffusion for effective DNA-PAINT imaging. Using acrydite-anchored oligonucleotides imprinted from patterned DNA origami nanostructures and microtubule filaments in fixed cells, we find that hydrogel embedding preserves docking strand positioning at the nanoscale. Sample clearing via protease treatment had minor structural effects on the microtubule structure and enhanced diffusion and accessibility to hydrogel-imprinted docking strands. Our work demonstrates promising potential for diffusion and binding-based fluorescence imaging applications in hydrogel-embedded samples.

Expansion Microscopy Provides Nanoscale Insight into Nucleolar Reorganization and Nuclear Foci Formation during Nucleolar Stress

The nucleolus, a membraneless organelle crucial for ribosome production, has a unique nanoscale structure whose organization is responsive to cell signals and disease progression. Here, we highlight the potential of Expansion Microscopy (ExM) for capturing intricate spatial and functional information about membraneless organelles such as the nucleolus and nuclear foci. We apply dual protein Expansion Microscopy (dual-proExM) in combination with click Expansion Microscopy (click-ExM) to capture images at the highest resolution reported for the nucleolus of ∼45 ± 2 nm. Inhibition of nucleolar processes triggers a nucleolar stress response, causing distinct structural rearrangements whose molecular basis is an area of active investigation. We investigate time-dependent changes in nucleolar structure and function under nucleolar stress induced by oxaliplatin, actinomycin D, and other platinum-based compounds. Our findings reveal new stages that occur prior to the complete sequestration of RNA Pol I into nucleolar caps, shedding light on the early mechanisms of the nucleolar stress response. RNA transcription is linked to nanoscale protein rearrangements using a combination of click-ExM and pro-ExM, revealing locations of active transcripts during the early stages of nucleolar stress reorganization. With prolonged stress, fibrillarin and NPM1 segregate from the nucleolus into nucleoplasmic foci that are for the first time imaged at nanometer resolution. In addition to revealing new morphological information about the nucleolus, this study demonstrates the potential of ExM for imaging membraneless organelles with nanometer-scale precision.

A novel optimized silver nitrate staining method for visualizing the osteocyte lacuno-canalicular system

A 50% (w/v, equivalent to 2.943 mol/L) silver nitrate solution is commonly used to stain and characterize the osteocyte lacuno-canalicular system (LCS) in bone biology research. However, variability in reagent concentrations and types, along with inconsistent staining procedures, have limited the broader application of this method in osteocyte research. In this study, we present a novel optimized silver nitrate staining technique aimed at addressing these limitations. This new method utilizes a 1 mol/L (equivalent to 16.987%, w/v) silver nitrate solution in combination with a type-B gelatin-formic acid solution at various concentrations (0.05%-0.5% gelatin and 0.05%-5% formic acid, or 1%-2% gelatin and 0.1%-2% formic acid) in volume ratios of 4:1, 2:1, or 1:1, or a 0.5 mol/L silver nitrate solution at a 4:1 ratio. The staining process is carried out for 1 hour under ultraviolet light or 90 minutes under regular room light (or dark), followed by washing with Milli-Q water to terminate the reaction. We applied this new method to stain the osteocyte LCS in bone samples from different species and pathological bone models. The technique consistently produced clear, distinct staining patterns across all samples. Moreover, our novel method revealed a greater number of LCS compared to the traditional 50% silver nitrate solution. This suggests that the commonly used 50% silver nitrate method may disrupt or inadequately reveal the LCS in bones, potentially leading to an underestimation of LCS density and number. In conclusion, our novel silver nitrate staining method provides a simpler and more cost-effective alternative to the traditional technique. By offering a more accurate and comprehensive analysis of the LCS across species, this approach has the potential to advance research on osteocyte morphogenesis, as well as the functional and evolutionary adaptations of the osteocyte LCS across different taxa.

Cryptosporidium modifies intestinal microvilli through an exported virulence factor

Cryptosporidium is a common intestinal infection of vertebrates and a significant threat to public health. Within the epithelial layer of the intestine, the parasite invades and replicates. Infected cells are readily detected under a microscope by the presence of elongated microvilli, particularly around the vacuole where the parasite resides. Here, we identify a family of Cryptosporidium virulence factors that are exported into the host cell during infection and localize to the microvilli. We examine the trafficking and function of the most highly expressed family member, Microvilli protein 1 (MVP1), which appears to control the elongation of microvilli through engagement of host EBP50 and CDC42. Remarkably, this mechanism closely mirrors that of an enteropathogenic Escherichia coli virulence factor, MAP, which is also known to drive host microvilli elongation during infection. This highlights a unique instance where eukaryotic and prokaryotic virulence factors have convergently evolved to modulate host actin structures through a similar mechanism.

Light-microscopy-based connectomic reconstruction of mammalian brain tissue

The information-processing capability of the brain's cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution1,2 with dense cellular labelling. Light microscopy is uniquely positioned to visualize specific molecules, but dense, synapse-level circuit reconstruction by light microscopy has been out of reach, owing to limitations in resolution, contrast and volumetric imaging capability. Here we describe light-microscopy-based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning-based segmentation and analysis of connectivity, thereby directly incorporating molecular information into synapse-level reconstructions of brain tissue. LICONN will allow synapse-level phenotyping of brain tissue in biological experiments in a readily adoptable manner.

A novel workflow for multi-modal imaging of musculoskeletal tissues

According to the World Health Organization (WHO) musculoskeletal conditions are a leading contributor to disability worldwide. This fact is often somewhat overlooked, since musculoskeletal conditions are less likely to be associated with mortality. Nonetheless, treatments, therapies and management of these conditions are extremely costly to national healthcare systems. As with all systemic conditions, biomedical imaging of relevant tissues plays a major role in understanding the fundamental biological processes involved in musculoskeletal health. However, the skeletal system with its relatively large proportion of dense, opaque (often mineralised) tissues can often be more challenging to image, and recently important advances have been made in imaging these complex musculoskeletal tissues. Thus, we here describe a novel workflow in which recent advanced imaging techniques have been modified and optimised for use in musculoskeletal tissues (specifically bone and cartilage). This will allow for investigations, of different phases of these tissues, at new and higher resolutions. Furthermore, the process has been designed to fit with the existing and standard processes which are typically used with these samples (i.e. μCT imaging and standard histology). The additional modalities which have been included here are second harmonic generation (SHG) imaging, tissue clearing, specifically the Passive Clear Lipid-exchanged Acrylamide-hybridised Rigid Imaging Tissue hYdrogel (CLARITY) method known as PACT, and then imaging of these tissues with confocal, multiphoton and light-sheet microscopy. This paper serves to introduce a combination of existing new methods and improvements in imaging of musculoskeletal tissues.

Advances in Spatial Omics Technologies

Rapidly developing spatial omics technologies provide us with new approaches to deeply understanding the diversity and functions of cell types within organisms. Unlike traditional approaches, spatial omics technologies enable researchers to dissect the complex relationships between tissue structure and function at the cellular or even subcellular level. The application of spatial omics technologies provides new perspectives on key biological processes such as nervous system development, organ development, and tumor microenvironment. This review focuses on the advancements and strategies of spatial omics technologies, summarizes their applications in biomedical research, and highlights the power of spatial omics technologies in advancing the understanding of life sciences related to development and disease.

Molecular Level Super-Resolution Fluorescence Imaging

Over the last 30 years, fluorescence microscopy, renowned for its sensitivity and specificity, has undergone a revolution in resolving ever-smaller details. This advancement began with stimulated emission depletion (STED) microscopy and progressed with techniques such as photoactivatable localization microscopy and stochastic optical reconstruction microscopy (STORM). Single-molecule localization microscopy (SMLM), which encompasses methods like direct STORM, has significantly enhanced image resolution. Even though its speed is slower than that of STED, SMLM achieves higher resolution by overcoming photobleaching limitations, particularly through DNA point accumulation for imaging in nanoscale topography (DNA-PAINT), which continuously renews fluorescent labels. Additionally, cryo-fluorescence microscopy and advanced techniques like minimal photon fluxes imaging (MINFLUX) have pushed the boundaries toward molecular resolution SMLM. This review discusses the latest developments in SMLM, highlighting methods like resolution enhancement by sequential imaging (RESI) and PAINT-MINFLUX and exploring axial localization techniques such as supercritical angle fluorescence and metal-induced energy transfer. These advancements promise to revolutionize fluorescence microscopy, providing resolution comparable to that of electron microscopy.

Molecule Differentiation Encoding Microscopy to Dissect Dense Biomolecules in Cellular Nanoenvironments below Spatial Resolution

Cellular biomolecules may exhibit dense distribution and organization at the nanoscale to govern vital biological processes. However, it remains a common challenge to digitize the spatially dense biomolecules under the spatial resolution of microscopies. Here, a proof-of-principle method, molecule differentiation encoding microscopy by orthogonal tandem repeat DNA identifiers is reported, to resolve the copy numbers of dense biomolecules in cellular nanoenvironments. The method encodes each copy of the same biomolecules into different types of DNA barcodes based on stochastic multiplexed reactions. It can transform the overlap of the same spectrum into the overlap of different spectra. Furthermore, an algorithm is developed to automatically quantitate overlapping spots and individual spots. Using this method, RNAs in the cytoplasm, DNA epigenetic modifications in the cell nucleus, and glycans and glycoRNAs on the cell surface are dissected, respectively. It is found that all these biomolecules present dense distribution with diverse degrees in crowded cellular nanoenvironments. Especially, an average 17% copies of U1 glycoRNA of single cells are gathered in various nano environments on the cell surface. The strategy provides a powerful tool for digitally quantitative visualization of dense biomolecules below the spatial resolution of microscopies and can provide insights into underlying functions and mechanisms of the dense distribution information.

TEMI: tissue-expansion mass-spectrometry imaging

The spatial distribution of diverse biomolecules in multicellular organisms is essential for their physiological functions. High-throughput in situ mapping of biomolecules is crucial for both basic and medical research, and requires high scanning speed, spatial resolution, and chemical sensitivity. Here we developed a tissue-expansion method compatible with matrix-assisted laser desorption/ionization mass-spectrometry imaging (TEMI). TEMI reaches single-cell spatial resolution without sacrificing voxel throughput and enables the profiling of hundreds of biomolecules, including lipids, metabolites, peptides (proteins), and N-glycans. Using TEMI, we mapped the spatial distribution of biomolecules across various mammalian tissues and uncovered metabolic heterogeneity in tumors. TEMI can be easily adapted and broadly applied in biological and medical research, to advance spatial multi-omics profiling.

Extracellular polymeric substances in indigenous microalgal-bacterial consortia: advances in characterization techniques and emerging applications

Extracellular polymeric substances (EPS) synthesized by indigenous microalgal-bacterial consortia (IMBC) play multifunctional roles in enhancing wastewater treatment efficiency, nutrient sequestration, and ecological system stability. This comprehensive review critically evaluates state-of-the-art analytical methods for characterizing EPS composition, physicochemical properties, and functional dynamics, including colorimetry, Fourier-transform infrared (FTIR) spectroscopy, X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and confocal laser scanning microscopy (CLSM). While these methods provide critical insights into EPS structure-function relationships, challenges persist in resolving spatial heterogeneity, real-time secretion dynamics, and molecular-scale interactions within complex IMBC systems. Emerging technologies such as expansion microscopy (ExM), electrochemical impedance spectroscopy (EIS), and integrated multi-omics approaches are highlighted as transformative tools for in situ EPS profiling, offering nanoscale resolution and temporal precision. By synthesizing these innovations, this review proposes a multidisciplinary framework to decode EPS-mediated microbial symbiosis, optimize IMBC performance, and advance applications in sustainable bioremediation, bioenergy, and circular resource recovery.

High-Resolution Lensless Microscopy Imaging Based on Fluorescence Intermittency

Lensless imaging microscopy has gained extensive application with the merits of system compactness and cost efficiency; however, its spatial resolution is usually compromised compared to conventional lens-based microscopes. To further enhance the spatial resolution, we built a lensless imaging system integrating a phase mask and a CMOS image sensor, and employed fluorescence fluctuation super-resolution microscopy (FF-SRM) algorithms to fully exploit the fluorescence intermittency (FI) characteristics of fluorescent molecules for high-resolution lensless image reconstruction. The study demonstrates that lensless image sequences processed by the Wiener deconvolution method can effectively retain the original fluorescence intermittency information, allowing for high-resolution reconstruction using FF-SRM algorithms. Furthermore, by combining expansion microscopy (ExM) and leveraging multi-algorithm synergy, we obtained additional improvements in spatial resolution and image quality for lensless imaging, facilitating clear visualization of biological subcellular organelles. This scheme offers a new pathway to achieve high spatial resolution imaging with practical advantages in simplicity and affordability.

Visualization of F-Actin Through Expansion Microscopy (ExM) with Trifunctional Linker-Conjugated Phalloidin

Expansion microscopy (ExM) is an imaging technique that enables super-resolution imaging of biological specimens using conventional confocal microscopy. This process entails the isotropic physical expansion of a (biomolecular) sample that has been cross-linked to a swellable polymer. The grafting of biomolecules (and the subsequent fluorescent readout) is accomplished by introducing an acryloyl group to the amine groups of lysine residues within the proteins, enabling subsequent imaging. However, visualizing actin filaments with high spatial resolution using ExM remains challenging. Herein, we report the construction of a phalloidin conjugate containing actin stains and their application in ExM. This protocol highlights the efficacy of trifunctional linker (TRITON/Actin-ExM) for F-actin imaging, demonstrating that TRITON-labeled actin allows for efficient anchoring and signal retention, enabling robust visualization of actin filaments in expansion microscopy. Key features • Engineered linker (TRITON) design ensures efficient fluorophore attachment, resulting in bright, stable signals during imaging. • Performed pre-expansion and antibody-free labeling. • Detailed and specific visualization of actin filaments in ExM experiments (4-fold expansion).

Deep-tissue transcriptomics and subcellular imaging at high spatial resolution

Limited color channels in fluorescence microscopy have long constrained spatial analysis in biological specimens. We introduce cycle hybridization chain reaction (cycleHCR), a method that integrates multicycle DNA barcoding with HCR to overcome this limitation. cycleHCR enables highly multiplexed imaging of RNA and proteins using a unified barcode system. Whole-embryo transcriptomics imaging achieved precise three-dimensional gene expression and cell fate mapping across a specimen depth of ~310 μm. When combined with expansion microscopy, cycleHCR revealed an intricate network of 10 subcellular structures in mouse embryonic fibroblasts. In mouse hippocampal slices, multiplex RNA and protein imaging uncovered complex gene expression gradients and cell-type-specific nuclear structural variations. cycleHCR provides a quantitative framework for elucidating spatial regulation in deep tissue contexts for research and has potential diagnostic applications.

An Improved SHANEL Procedure for Clearing and Staining Brain Tissue from Multiple Species

Recent advances in tissue clearing chemistry have revolutionized three-dimensional imaging by enabling whole-organ antibody labeling, even in thick human tissue samples. However, these techniques face limitations, including reduced clearance efficiency in thick tissue blocks, prolonged processing times, and other challenges specific to formalin-fixed human brain tissue, such as autofluorescence due to the presence of lipofuscin, neuromelanin pigments, and residual blood. To address these challenges, we have developed an improved SHANEL procedure, iSHANEL, which is compatible with brain tissue from multiple species, including nonrodents. iSHANEL significantly enhances the tissue transparency. It effectively removes lipids, particularly sphingolipids, from brain tissue across different species. For brain vasculature imaging, it offers the better visualization of vascular structures at high magnification, reducing light scattering and background noise. Moreover, iSHANEL can be effectively applied to large tissue from pigs and cynomolgus monkeys, and it preserves protein immunogenicity well, as evidenced by immunostaining with the microglia-specific marker IBA-1. We also investigated methods to reduce blood vessel autofluorescence. Overall, iSHANEL provides an improved procedure for the high-resolution 3D imaging of brain tissue across multiple species.

High-Throughput Volumetric Mapping Facilitated by Active Tissue SHRINK

Comprehensive visualization of tissue architecture in large organs such as the brain is crucial for understanding functional relationships across key tissue regions. However, the large size of whole organs makes it challenging to image their entirety with subcellular resolution, often requiring prolonged imaging sessions, volume reconstruction, and compromises in spatial coverage. Here, Scalable Hydrogel-embedded Rapid Imaging of tissue NetworK (SHRINK) is reported to address this challenge through active tissue shrinkage and clearing. Utilizing the identified hydrogel network to preserve the spatial pattern of proteins in situ and remove the uncrosslinked biomolecules to create space, it is shown that SHRINK isotropically drives the reduction of sample sizes down to 16% of their original volume while maintaining high cellular and tissue-level integrity in a reversible manner. The size reduction and the corresponding 3D concentrating of the biomolecules render a more than sixfold enhancement for throughput and signal respectively, which addresses a key bottleneck for the stimulated Raman scattering (SRS) microscopy, ideal for 3D, label-free and super-multiplex tissue mapping. It is further demonstrated that SHRINK-SRS achieves organ-scale mapping of brain, intestine, heart, and kidney tissues. SHRINK offers a powerful approach to overcome traditional imaging barriers, enabling rapid and detailed visualization of large organs.

PIP2 promotes the incorporation of CD43, PSGL-1, and CD44 into nascent HIV-1 particles

Determinants regulating sorting of host transmembrane proteins at sites of enveloped virus assembly on the plasma membrane (PM) remain poorly understood. Here, we demonstrate that the PM acidic phospholipid phosphatidylinositol 4,5-bisphosphate (PIP2) regulates this sorting into an enveloped virus, HIV-1. Incorporation of CD43, PSGL-1, and CD44 into HIV-1 particles has profound effects on viral spread; however, the mechanisms promoting their incorporation were unknown. We found that depletion of cellular PIP2 blocks incorporation of CD43, PSGL-1, and CD44 into HIV-1 particles. Expansion microscopy revealed that PIP2 depletion diminishes nanoscale coclustering between viral structural protein Gag and the three transmembrane proteins at the PM and that Gag induces PIP2 enrichment at its vicinity. CD43, PSGL-1, and CD44 also increased local PIP2 density, revealing their PIP2 affinity. Together, these results support a previously unknown mechanism where local enrichment of an acidic phospholipid drives coclustering between viral structural and cellular transmembrane proteins, thereby modulating the content, and hence the fate, of progeny virus particles.

Super-resolution expansion microscopy in plant roots

Super-resolution methods provide far better spatial resolution than the optical diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless, they have yet to attain widespread use in plants, largely due to plants' challenging optical properties. Expansion microscopy (ExM) improves effective resolution by isotropically increasing the physical distances between sample structures while preserving relative spatial arrangements and clearing the sample. However, its application to plants has been hindered by the rigid, mechanically cohesive structure of plant tissues. Here, we report on whole-mount ExM of thale cress (Arabidopsis thaliana) root tissues (PlantEx), achieving a 4-fold resolution increase over conventional microscopy. Our results highlight the microtubule cytoskeleton organization and interaction between molecularly defined cellular constituents. Combining PlantEx with stimulated emission depletion microscopy, we increase nanoscale resolution and visualize the complex organization of subcellular organelles from intact tissues by example of the densely packed COPI-coated vesicles associated with the Golgi apparatus and put these into a cellular structural context. Our results show that ExM can be applied to increase effective imaging resolution in Arabidopsis root specimens.

Visualisation of Euglena gracilis organelles and cytoskeleton using expansion microscopy

This article explores the use of expansion microscopy, a technique that enhances resolution in fluorescence microscopy, on the autotrophic protist Euglena gracilis A modified protocol was developed to preserve the cell structures during fixation. Using antibodies against key cytoskeletal and organelle markers, α-tubulin, β-ATPase, and Rubisco activase, the microtubular structures, mitochondria, and chloroplasts were visualised. The organisation of the cytoskeleton corresponded to the findings from electron microscopy while allowing for the visualisation of the flagellar pocket in its entirety and revealing previously unnoticed details. This study offered insights into the shape and development of mitochondria and chloroplasts under varying conditions, such as culture ages and light cycles. This work demonstrated that expansion microscopy is a robust tool for visualising cellular structures in E. gracilis, an organism whose internal structures cannot be stained using standard immunofluorescence because of its complex pellicle. This technique also serves as a complement to electron microscopy, facilitating tomographic reconstructions in a routine fashion.

3D reconstruction of neuronal allometry and neuromuscular projections in asexual planarians using expansion tiling light sheet microscopy

The intricate coordination of the neural network in planarian growth and regeneration has remained largely unrevealed, partly due to the challenges of imaging the CNS in three dimensions (3D) with high resolution and within a reasonable timeframe. To address this gap in systematic imaging of the CNS in planarians, we adopted high-resolution, nanoscale imaging by combining tissue expansion and tiling light-sheet microscopy, achieving up to fourfold linear expansion. Using an automatic 3D cell segmentation pipeline, we quantitatively profiled neurons and muscle fibers at the single-cell level in over 400 wild-type planarians during homeostasis and regeneration. We validated previous observations of neuronal cell number changes and muscle fiber distribution. We found that the increase in neuron cell number tends to lag behind the rapid expansion of somatic cells during the later phase of homeostasis. By imaging the planarian with up to 120 nm resolution, we also observed distinct muscle distribution patterns at the anterior and posterior poles. Furthermore, we investigated the effects of β-catenin-1 RNAi on muscle fiber distribution at the posterior pole, consistent with changes in anterior-posterior polarity. The glial cells were observed to be close in contact with dorsal-ventral muscle fibers. Finally, we observed disruptions in neural-muscular networks in inr-1 RNAi planarians. These findings provide insights into the detailed structure and potential functions of the neural-muscular system in planarians and highlight the accessibility of our imaging tool in unraveling the biological functions underlying their diverse phenotypes and behaviors.

Microtubules as a versatile reference standard for expansion microscopy

Expansion microscopy (ExM) is continually improving, and new ExM variants need to be validated on well-defined biological structures. There is no consensus on validation structures for ExM, especially as nuclear pore complexes or DNA nanorulers are not popular for ExM studies. Here we propose that microtubules should be used for ExM validation. The diameter of microtubules immunostained using primary and secondary antibodies is sufficiently large for the validation of techniques with resolutions better than 50 nm. For techniques with higher precision (up to ~10 nm), microtubules can be assembled and imaged in vitro, using a protocol that we introduce here. Alternatively, a cellular extraction procedure can be employed, followed by labeling the peptide chains of the tubulin molecules with NHS-ester fluorophores. Finally, for nanometer-scale techniques, single tubulin molecules can be analyzed. We conclude that microtubules are valuable structures for the validation of ExM and related technologies.

mSphere of Influence: The ever-expanding universe of parasite cell biology

Ben Liffner studies the cell biology of apicomplexan parasites. In this mSphere of Influence article, he reflects on two key papers: "Three-dimensional ultrastructure of Plasmodium falciparum throughout cytokinesis" by R. M. Rudlaff, S. Kraemer, J. Marshman, J. D. Dvorin, et al. (PLoS Pathog 16:e1008587, 2020, https://doi.org/10.1371/journal.ppat.1008587) and "Expansion microscopy provides new insights into the cytoskeleton of malaria parasites including the conservation of a conoid" by E. Bertiaux, A. C. Balestra, L. Bournonville, V. Louvel, et al. (PLoS Biol 19:e3001020, 2021, https://doi.org/10.1371/journal.pbio.3001020). These two studies provided Ben with the conceptual framework to understand how parasites are organized in three dimensions, and the technique of ultrastructure expansion microscopy that he has since used to investigate this intriguing area of biology.

A key role for hepatitis C virus NS5A serine 225 phosphorylation revealed by super-resolution microscopy

NS5A is a multi-functional phosphoprotein that plays a key role in hepatitis C virus (HCV) genome replication and assembly. The consequences of NS5A phosphorylation for HCV biology remain largely undefined. We previously identified serine 225 (S225) as a major phosphorylation site within the low complexity sequence 1 (LCSI) of NS5A and used a phosphoablatant mutant (S225A) to define the role of this phosphorylation event in genome replication, NS5A-host interactions and sub-cellular localisation. In this study, we investigate this further by raising an antiserum to S225 phosphorylated NS5A (pS225). Western blot analysis revealed that pS225 was predominantly in the hyper-phosphorylated NS5A species. Using a panel of phosphoablatant mutants of other phosphorylation sites in LCSI, we obtained evidence that is consistent with bidirectional hierarchical phosphorylation initiated by phosphorylation at S225. Using super-resolution microscopy (Airyscan and Expansion), we revealed a unique architecture of NS5A-positive punctae in HCV-infected cells; pS225 was present on the surface of these punctae, close to lipid droplets. Although S225 phosphorylation was not specifically affected by treatment with the NS5A-targeting direct acting antiviral agent daclatasvir, this resulted in the condensation of NS5A-positive punctae into larger structures, recapitulating the S225A phenotype. These data are consistent with a key role for S225 phosphorylation in the regulation of NS5A function.

Expansion microscopy reveals thylakoid organisation alterations due to genetic mutations and far-red light acclimation

The thylakoid membrane is the site of the light-dependent reactions of photosynthesis. It is a continuous membrane, folded into grana stacks and the interconnecting stroma lamellae. The CURVATURE THYLAKOID1 (CURT1) protein family is involved in the folding of the membrane into the grana stacks. The thylakoid membrane remodels its architecture in response to light conditions, but its 3D organisation and dynamics remain incompletely understood. To resolve these details, an imaging technique is needed that provides high-resolution 3D images in a high-throughput manner. Recently, we have used expansion microscopy, a technique that meets these criteria, to visualise the thylakoid membrane isolated from spinach. Here, we show that this protocol can also be used to visualise enveloped spinach chloroplasts. Additionally, we present an improved protocol for resolving the thylakoid structure of Arabidopsis thaliana. Using this protocol, we show the changes in thylakoid architecture in response to long-term far-red light acclimation and due to knocking out CURT1A. We show that far-red light acclimation results in higher grana stacks that are packed closer together. In addition, the distance between stroma lamellae, which are wrapped around the grana, decreases. In the curt1a mutant, grana have an increased diameter and height, and the distance between grana is increased. Interestingly, in this mutant, the stroma lamellae occasionally approach the grana stacks from the top. These observations show the potential of expansion microscopy to study the thylakoid membrane architecture.

Fluorescent labeling strategies for molecular bioimaging

Super-resolution microscopy (SRM) has transformed biological imaging by circumventing the diffraction limit of light and enabling the visualization of cellular structures and processes at the molecular level. Central to the capabilities of SRM is fluorescent labeling, which ensures the precise attachment of fluorophores to biomolecules and has direct impact on the accuracy and resolution of imaging. Continuous innovation and optimization in fluorescent labeling are essential for the successful application of SRM in cutting-edge biological research. In this review, we discuss recent advances in fluorescent labeling strategies for molecular bioimaging, with a special focus on protein labeling. We compare different approaches, highlight technological breakthroughs, and address challenges such as linkage error and labeling density. By evaluating both established and emerging methods, we aim to guide researchers through all aspects that should be considered before opting for any labeling technique.

Genetically-encoded markers for confocal visualization of single dense core vesicles

Neuronal dense core vesicles (DCVs) store and release a diverse array of neuromodulators, trophic factors, and bioamines. The analysis of single DCVs has largely been possible only using electron microscopy, which makes understanding cargo segregation and DCV heterogeneity difficult. To address these limitations, we develop genetically encoded markers for DCVs that can be used in combination with standard immunohistochemistry and expansion microscopy to enable single-vesicle resolution with confocal microscopy in Drosophila.

Nanoscale Resolution Imaging of Whole Mouse Embryos Using Expansion Microscopy

Nanoscale imaging of whole vertebrates is essential for the systematic understanding of human diseases, yet this goal has not yet been achieved. Expansion microscopy (ExM) is an attractive option for accomplishing this aim; however, the expansion of even mouse embryos at mid- and late-developmental stages, which have fewer calcified body parts than adult mice, is yet to be demonstrated due to the challenges of expanding calcified tissues. Here, we introduce a state-of-the-art ExM technique, termed whole-body ExM, that utilizes cyclic digestion. This technique allows for the super-resolution, volumetric imaging of anatomical structures, proteins, and endogenous fluorescent proteins (FPs) within embryonic and neonatal mice by expanding them 4-fold. The key feature of whole-body ExM is the alternating application of two enzyme compositions repeated multiple times. Through the simple repetition of this digestion process with an increasing number of cycles, mouse embryos of various stages up to E18.5, and even neonatal mice, which display a dramatic difference in the content of calcified tissues compared to embryos, are expanded without further laborious optimization. Furthermore, the whole-body ExM's ability to retain FP signals allows the visualization of various neuronal structures in transgenic mice. Whole-body ExM could facilitate studies of molecular changes in various vertebrates.

From morphology to single-cell molecules: high-resolution 3D histology in biomedicine

High-resolution three-dimensional (3D) tissue analysis has emerged as a transformative innovation in the life sciences, providing detailed insights into the spatial organization and molecular composition of biological tissues. This review begins by tracing the historical milestones that have shaped the development of high-resolution 3D histology, highlighting key breakthroughs that have facilitated the advancement of current technologies. We then systematically categorize the various families of high-resolution 3D histology techniques, discussing their core principles, capabilities, and inherent limitations. These 3D histology techniques include microscopy imaging, tomographic approaches, single-cell and spatial omics, computational methods and 3D tissue reconstruction (e.g. 3D cultures and spheroids). Additionally, we explore a wide range of applications for single-cell 3D histology, demonstrating how single-cell and spatial technologies are being utilized in the fields such as oncology, cardiology, neuroscience, immunology, developmental biology and regenerative medicine. Despite the remarkable progress made in recent years, the field still faces significant challenges, including high barriers to entry, issues with data robustness, ambiguous best practices for experimental design, and a lack of standardization across methodologies. This review offers a thorough analysis of these challenges and presents recommendations to surmount them, with the overarching goal of nurturing ongoing innovation and broader integration of cellular 3D tissue analysis in both biology research and clinical practice.

BOOST: a robust ten-fold expansion method on hour-scale

Expansion microscopy enhances the microscopy resolution by physically expanding biological specimens and improves the visualization of structural and molecular details. Numerous expansion microscopy techniques and labeling methods have been developed over the past decade to cater to specific research needs. Nonetheless, a shared limitation among current protocols is the extensive sample processing time, particularly for challenging-to-expand biological specimens (e.g., formalin-fixed paraffin-embedded (FFPE) sections and large three-dimensional specimens). Here we present BOOST, a rapid and robust expansion microscopy workflow that leverages a series of microwave-accelerated expansion microscopy chemistry. Specifically, BOOST enables a single-step 10-fold expansion of cultured cells, tissue sections, and even the challenging-to-expand FFPE sections under 90 minutes. Notably, BOOST pioneers a 10-fold expansion of large millimeter-sized three-dimensional specimens, previously unattainable to the best of our knowledge. The workflow is also easily adaptable based on stable and common reagents, thus boosting the potential adoption of expansion microscopy for applications.

ExPOSE: a comprehensive toolkit to perform expansion microscopy in plant protoplast systems

Expansion microscopy (ExM) achieves nanoscale imaging by physical expansion of fixed biological tissues embedded in a swellable hydrogel, enhancing the resolution of any optical microscope several-fold. While ExM is commonly used in animal cells and tissues, there are few plant-specific protocols. Protoplasts are a widely used cell system across plant species, especially in studying biomolecule localization. Here, we present an approach to achieve robust expansion of plant protoplasts, termed Expansion microscopy in plant PrOtoplast SystEms (ExPOSE). We demonstrate that coupling ExPOSE with other imaging techniques, immunofluorescence and in situ hybridization chain reaction to visualize proteins and mRNAs, respectively, greatly enhances the spatial resolution of endogenous biomolecules. Additionally, in this study, we tested the effectiveness and versatility of this technique to observe biomolecular condensates in Arabidopsis protoplasts and transcription factors in maize protoplasts at increased resolution. ExPOSE can be relatively inexpensive, fast, and simple to implement.

TEMI: Tissue Expansion Mass Spectrometry Imaging

The spatial distribution of diverse biomolecules in multicellular organisms is essential for their physiological functions. High-throughput in situ mapping of biomolecules is crucial for both basic and medical research, and requires high scanning speed, spatial resolution, and chemical sensitivity. Here, we developed a Tissue Expansion method compatible with matrix-assisted laser desorption/ionization Mass spectrometry Imaging (TEMI). TEMI reaches single-cell spatial resolution without sacrificing voxel throughput and enables the profiling of hundreds of biomolecules, including lipids, metabolites, peptides (proteins), and N-glycans. Using TEMI, we mapped the spatial distribution of biomolecules across various mammalian tissues and uncovered metabolic heterogeneity in tumors. TEMI can be easily adapted and broadly applied in biological and medical research, to advance spatial multi-omics profiling.

Bio-orthogonal Glycan Imaging of Cultured Cells and Whole Animal C. elegans with Expansion Microscopy

Complex carbohydrates called glycans play crucial roles in regulating cell and tissue physiology, but how they map to nanoscale anatomical features must still be resolved. Here, we present the first nanoscale map of mucin-type O-glycans throughout the entirety of the Caenorhabditis elegans model organism. We constructed a library of multifunctional linkers to probe and anchor metabolically labeled glycans in expansion microscopy (ExM). A flexible strategy was demonstrated for the chemical synthesis of linkers with a broad inventory of bio-orthogonal functional groups, fluorophores, anchorage chemistries, and linker arms. Employing C. elegans as a test bed, metabolically labeled O-glycans were resolved on the gut microvilli and other nanoscale anatomical features. Transmission electron microscopy images of C. elegans nanoanatomy validated the fidelity and isotropy of gel expansion. Whole organism maps of C. elegans O-glycosylation in the first larval stage revealed O-glycan "hotspots" in unexpected anatomical locations, including the body wall furrows. Beyond C. elegans, we validated ExM protocols for nanoscale imaging of metabolically labeled glycans on cultured mammalian cells. Together, our results suggest the broad applicability of the multifunctional reagents for imaging glycans and other metabolically labeled biomolecules at enhanced resolutions with ExM.

Synthetic Lipid Biology

Cells contain thousands of different lipids. Their rapid and redundant metabolism, dynamic movement, and many interactions with other biomolecules have justly earned lipids a reputation as a vexing class of molecules to understand. Further, as the cell's hydrophobic metabolites, lipids assemble into supramolecular structures─most commonly bilayers, or membranes─from which they carry out myriad biological functions. Motivated by this daunting complexity, researchers across disciplines are bringing order to the seeming chaos of biological lipids and membranes. Here, we formalize these efforts as "synthetic lipid biology". Inspired by the idea, central to synthetic biology, that our abilities to understand and build biological systems are intimately connected, we organize studies and approaches across numerous fields to create, manipulate, and analyze lipids and biomembranes. These include construction of lipids and membranes from scratch using chemical and chemoenzymatic synthesis, editing of pre-existing membranes using optogenetics and protein engineering, detection of lipid metabolism and transport using bioorthogonal chemistry, and probing of lipid-protein interactions and membrane biophysical properties. What emerges is a portrait of an incipient field where chemists, biologists, physicists, and engineers work together in proximity─like lipids themselves─to build a clearer description of the properties, behaviors, and functions of lipids and membranes.

Functionalized Docetaxel Probes for Refined Visualization of Mitotic Spindles by Expansion Microscopy

Visualizing the ultrastructure of mitotic spindles, the macromolecular machines that segregate chromosomes during mitosis, by fluorescence imaging remains challenging. Here we introduce an azido- and amino-functionalized docetaxel probe, which upon labeling of microtubules can be fixed, click-labeled and linked into hydrogels. The new probe is particularly useful for super-resolution imaging of dense microtubule structures in mitotic spindles. Multicolor expansion microscopy of mitotic cells allowed us to visualize the different phases of mitosis with unprecedented spatial resolution.

Lipid-Directed Covalent Labeling of Plasma Membranes for Long-Term Imaging, Barcoding and Manipulation of Cells

Fluorescent probes for cell plasma membranes (PM) generally exploit a noncovalent labeling mechanism, which constitutes a fundamental limitation in multiple bioimaging applications. Here, we report a concept of lipid-directed covalent labeling of PM, which exploits transient binding to the lipid membrane surface generating a high local dye concentration, thus favoring covalent ligation to random proximal membrane proteins. This concept yielded fluorescent probes for PM called MemGraft, which are built of a dye (cyanine Cy3 or Cy5) bearing a low-affinity membrane anchor and a reactive group: an activated ester or a maleimide. In contrast to specially designed control dyes and commercial Cy3-based labels of amino or thiol groups, MemGraft probes stain efficiently PM, revealing the crucial role of the membrane anchor combined with optimal reactivity of the activated ester or the maleimide. MemGraft probes overcome existing limitations of noncovalent probes, which makes them compatible with cell fixation, permeabilization, trypsinization, and the presence of serum. The latter allows long-term cell tracking and video imaging of cell PM dynamics without the signs of phototoxicity. The covalent strategy also enables staining and long-term tracking of cocultured cells labeled in different colors without exchange of probes. Moreover, the combination of MemGraft-Cy3 and MemGraft-Cy5 probes at different ratios enabled long-term cell barcoding in at least 5 color codes, important for tracking and visualizing multiple populations of cells. Ultimately, we found that the MemGraft strategy enables efficient biotinylation of the cell surface, opening the path to cell surface engineering and cell manipulation.

Derivative Technologies of Expansion Microscopy and Applications in Biomedicine

Expansion microscopy (ExM) is an innovative super-resolution imaging technique that utilizes physical expansion to magnify biological samples, facilitating the visualization of cellular structures that are challenging to observe using traditional optical microscopes. The fundamental principle of ExM revolves around employing a specialized hydrogel to uniformly expand biological samples, thereby achieving super-resolution imaging under conventional optical imaging conditions. This technology finds application not only in various biological samples such as cells and tissue sections, but also enables super-resolution imaging of large biological molecules including proteins, nucleic acids, and metabolite molecules. In recent years, numerous researchers have delved into ExM, resulting in the continuous development of a range of derivative technologies that optimize experimental protocols and broaden practical application fields. This article presents a comprehensive review of these derivative technologies, highlighting the utilization of ExM for anchoring nucleic acids, proteins, and other biological molecules, as well as its applications in biomedicine. Furthermore, this review offers insights into the future development prospects of ExM technology.

3D imaging and pathological analysis of microglia in LPS-treated mice with light-sheet fluorescence microscopy

Although two-dimensional (2D) histology and immunohistochemistry techniques have long been established and successfully applied to obtain structural information from tissues, recent advances in tissue clearing and expansion approaches combined with light sheet microscopy have led to the realization of three-dimensional (3D) nondestructive pathology, which may revolutionize our knowledge of the morphology of an organ or the whole body in its true state. Employing these 3D technologies, we obtained imaging data of microglia in whole hippocampus of mice. We established a simple procedure to analyze the 3D structures of microglia using the commercial software Amira. Major 3D structural parameters, including the volume of the whole cell, volume of the cell body, Feret's maximum/minimum diameter, number of total branches, fractal dimension, convex hull, and number of intersections,were measured. We found that lipopolysaccharide administration markedly changed multiple 3D morphological parameters of microglia. 3D analysis of microglial structures provides a more comprehensive evaluation than 2D analysis, which can be applied in future neuroscience research.

Dense, continuous membrane labeling and expansion microscopy visualization of ultrastructure in tissues

Lipid membranes are key to the nanoscale compartmentalization of biological systems, but fluorescent visualization of them in intact tissues, with nanoscale precision, is challenging to do with high labeling density. Here, we report ultrastructural membrane expansion microscopy (umExM), which combines an innovative membrane label and optimized expansion microscopy protocol, to support dense labeling of membranes in tissues for nanoscale visualization. We validate the high signal-to-background ratio, and uniformity and continuity, of umExM membrane labeling in brain slices, which supports the imaging of membranes and proteins at a resolution of ~60 nm on a confocal microscope. We demonstrate the utility of umExM for the segmentation and tracing of neuronal processes, such as axons, in mouse brain tissue. Combining umExM with optical fluctuation imaging, or iterating the expansion process, yields ~35 nm resolution imaging, pointing towards the potential for electron microscopy resolution visualization of brain membranes on ordinary light microscopes.

Seq-Scope-eXpanded: Spatial Omics Beyond Optical Resolution

Sequencing-based spatial transcriptomics (sST) enables transcriptome-wide gene expression mapping but falls short of reaching the optical resolution (200-300 nm) of imaging-based methods. Here, we present Seq-Scope-X (Seq-Scope-eXpanded), which empowers submicrometer-resolution Seq-Scope with tissue expansion to surpass this limitation. By physically enlarging tissues, Seq-Scope-X minimizes transcript diffusion effects and increases spatial feature density by an additional order of magnitude. In liver tissue, this approach resolves nuclear and cytoplasmic compartments in nearly every single cell, uncovering widespread differences between nuclear and cytoplasmic transcriptome patterns. Independently confirmed by imaging-based methods, these results suggest that individual hepatocytes can dynamically switch their metabolic roles. Seq-Scope-X is also applicable to non-hepatic tissues such as brain and colon, and can be modified to perform spatial proteomic analysis, simultaneously profiling hundreds of barcode-tagged antibody stains at microscopic resolutions in mouse spleens and human tonsils. These findings establish Seq-Scope-X as a transformative tool for ultra-high-resolution whole-transcriptome and proteome profiling, offering unparalleled spatial precision and advancing our understanding of cellular architecture, function, and disease mechanisms.

Mapping Protein Distribution in the Canine Photoreceptor Sensory Cilium and Calyceal Processes by Ultrastructure Expansion Microscopy

Purpose

Photoreceptors are highly polarized sensory neurons, possessing a unique ciliary structure known as the photoreceptor sensory cilium (PSC). Vertebrates have two subtypes of photoreceptors: rods, which are responsible for night vision, and cones, which enable daylight vision and color perception. Despite the identification of functional and morphological differences between these subtypes, ultrastructural analysis of the PSC molecular architecture between rods and cones is still lacking. This study employed ultrastructure expansion microscopy (U-ExM) to characterize the PSC molecular architecture in canine retina.

Methods

Canine neuroretinas (5-mm punches) were fixed in paraformaldehyde solution for either short or long durations. Additionally, 20-µm-thick cryosections from frozen archival retinal tissues fixed using the longer protocol were analyzed. A U-ExM protocol previously developed for mouse retina was adapted to these canine tissues with a battery of specific antibodies that label the various compartments of the PSC.

Results

We demonstrated that U-ExM is applicable to both non-frozen and cryopreserved retinal tissues processed with standard paraformaldehyde fixation. Using this validated U-ExM protocol, we revealed the molecular localization of numerous ciliopathy-related proteins in canine photoreceptors. Furthermore, we identified significant architectural differences in the PSC, ciliary rootlet, and calyceal processes between canine rods and cones.

Conclusions

U-ExM is a powerful tool for studying the PSC molecular architecture using frozen archival retinas that are processed following standard paraformaldehyde fixation and embedding protocols. The findings gained from this study pave the way for a better understanding of alterations in the molecular architecture of the PSC in canine models of retinal ciliopathies.

One step 4× and 12× 3D-ExM enables robust super-resolution microscopy of nanoscale cellular structures

Super-resolution microscopy has become an indispensable tool across diverse research fields, offering unprecedented insights into biological architectures with nanometer scale resolution. Compared with traditional nanometer-scale imaging methods such as electron microscopy, super-resolution microscopy offers several advantages, including the simultaneous labeling of multiple target biomolecules with high specificity and simpler sample preparation, making it accessible to most researchers. In this study, we introduce two optimized methods of super-resolution imaging: 4-fold and 12-fold 3D-isotropic and preserved Expansion Microscopy (4× and 12× 3D-ExM). 3D-ExM is a straightforward expansion microscopy technique featuring a single-step process, providing robust and reproducible 3D isotropic expansion for both 2D and 3D cell culture models. With standard confocal microscopy, 12× 3D-ExM achieves a lateral resolution of <30 nm, enabling the visualization of nanoscale structures, including chromosomes, kinetochores, nuclear pore complexes, and Epstein-Barr virus particles. These results demonstrate that 3D-ExM provides cost-effective and user-friendly super-resolution microscopy, making it highly suitable for a wide range of cell biology research, including studies on cellular and chromatin architectures.