Tissue clearing technique: Recent progress and biomedical applications

Comprehensive evaluation and application of tissue clearing techniques for 3-D visualization of splenic neural and immune architecture

As the largest secondary lymphoid organ, the spleen plays a crucial role in initiating and sustaining immune responses against blood-borne pathogens through antigen capture and delivery. It is innervated by both autonomic and sensory nerves, which allows for neural modulation of its immune responses. The intricate spatial structure and precise coordination between immune and neural components are essential for proper splenic function, necessitating three-dimensional (3-D) imaging to reveal its architecture. However, the dense fibrous capsule and exceptionally rich vasculature of the spleen pose significant challenges for achieving comprehensive 3-D visualization of the entire organ. Here, we systematically evaluated and compared five cutting-edge tissue clearing approaches-ImmuView, fast light-microscopic analysis of antibody-stained whole organs, small-micelle-mediated human organ efficient clearing and labeling (SHANEL), advanced clear, unobstructed brain imaging cocktails and computational analysis (advanced CUBIC), and clearing-enhanced 3-D microscopy-for their effectiveness in rendering the spleen transparent for multiplexed antibody staining and high-resolution 3-D imaging. Our results indicated that SHANEL provided the clearest visualization of essential splenic neural and immune components. Meanwhile, advanced CUBIC achieved the greatest labeling efficacy for immune cells, albeit with slightly reduced transparency. Importantly, our study marked the first application of these optimized protocols to human spleen tissue, successfully revealing the highly organized immune cell zones and neural networks with enhanced clarity. Notably, we identified the nociceptive sensory innervation within human spleen tissue for the first time. Collectively, these findings establish optimal imaging strategies for visualizing splenic immune cells and neural structure in both murine and human tissues, providing profound insights into the intricate neuroimmune interactions and their pivotal roles in the immune functions of the spleen.NEW & NOTEWORTHY This study systematically assessed five tissue-clearing techniques and optimized the conditions of each protocol to overcome the challenges of splenic 3-D imaging posed by its dense structure and high pigmentation. The results demonstrated SHANEL and advanced CUBIC as the optimal methods for 3-D visualization of diverse splenic immune and neural architecture, with which we successfully mapped splenic neuroimmune landscape and identified nociceptive nerves within the human spleen for the first time.

Three-dimensional imaging and computational quantitation as a novel approach to assess nerve fibers, enteric glial cells, mast cells, and the proximity of mast cells to the nerve fibers in human sigmoid mucosal biopsies from healthy subjects

BACKGROUND

The visualization and quantitation of nerve fibers (NFs), enteric glial cells (EGCs), mast cells (MCs), and their spatial configurations in the human colonic mucosa represent considerable challenges due to the meshed network of these components and the arborizing of NFs in a three-dimensional (3D) structure.

NEW METHOD

We developed a novel approach combining tissue clearing, 3D imaging and computerized quantitation of NFs, EGCs and MCs in sigmoid mucosal biopsies of healthy subjects using a modified CLARITY tissue clearing protocol and adapting Imaris Surfaces Rendering Technology.

RESULTS

The cleared colonic biopsies are compatible with immunostaining using 10 marker antibodies and capable of generating 3D images rendering clear spatial views and computational quantitation of NFs, MCs, EGCs, in particular the proximity of MCs to NFs with Imaris 9.7-9.9.

COMPARISON WITH EXISTING METHODS

Our modified tissue clearing protocol shortened the membrane lipid removal time to 1 day from the original 1-2 weeks and total tissue clearing time to 3-4 days from the original 2-4 weeks. The 3D images displayed a clear spatial landscape of NFs, MCs and EGCs in the biopsies which cannot be portrayed with 2D images acquired from sections. Computerized quantitation is faster than measuring manually, allowing us to quantify a larger number of samples with less bias.

CONCLUSION

The novel approach enables faster tissue clearing/immunolabeling, high-quality 3D imaging and precise computational quantitation of NFs, cells and proximity of MCs to NFs in human sigmoid biopsies which may allow new insight to detect alterations in colonic-related diseases.

An acoustic levitation platform for high-content histological analysis of 3D tissue culture

Miniaturized three-dimensional (3D) cell culture systems, in particular organoids and spheroids, hold great potential for studying morphogenesis, disease modeling, and drug discovery. However, sub-cellular resolution 3D imaging of these biological samples remains a challenge. Histology, the gold standard for ex vivo microscopic interrogation of tissue anatomy, may address this challenge once the associated techniques are adapted. Due to their small size and delicate structure, organoids must be embedded in a supporting hydrogel. The histological sections have low information content because the distribution of the organoids within the gel is not controlled. To address this issue, we introduce an acoustic micromanipulation platform that concentrates and aligns organoids within a histology-compatible hydrogel block. Utilizing an array of micromachined lead zirconate titanate (PZT) transducers, the platform generates localised and precisely controlled acoustic standing waves to levitate organoids to a prescribed plane and fix their positions within a polyethylene glycol diacrylate (PEGDA)-gelatine hydrogel. Organoids from different culture conditions can be co-embedded in a traceable fashion with the use of a custom-design hydrogel grid. Our results demonstrate that more than 70% of spheroids can be positioned within a 150 μm-thick hydrogel block, substantially increasing the information content of histology sections. The platform's versatility, scalability, and ease of use will make histological assessment accessible to every life science laboratory.

Progress on three-dimensional visualizing skin architecture with multiple immunofluorescence staining and tissue-clearing approaches

The skin forms the external covering of the body and is its largest organ, comprising many different cell types. Although the diversity of these cells has been widely studied with various histological methods, our understanding of skin architecture is mainly established on thin tissue sections, which restricted the information available to two dimensions. The development of innovative techniques to induce optical transparency ("clearing") in biological tissues has enabled researchers to visualize the three-dimensional reconstruction of intact organs and thick tissue sections at a cellular resolution. With the aid of tissue-clearing treatment, the labeled cutaneous nerve fibers and blood vessels can be followed for a longer distance on the thicker skin section or the whole mount skin under a fluorescence microscopy or a confocal microscopy. It is beneficial for demonstrating the morphological characteristics of nerve fibers and blood vessels themselves, as well as their spatial interconnection. In this review, we provide a brief summary of the literature on the use of tissue optical clearing methods and describe our experience of multiple fluorescent staining and tissue clearing approaches on thicker skin sections and whole-mount skin in our laboratory. Given the existing conventional methods, we expected to provide a more effective approach to comprehensively study skin architecture.

A highly stable monomeric red fluorescent protein for advanced microscopy

The stability of fluorescent proteins (FPs) is crucial for imaging techniques such as live-cell imaging, super-resolution microscopy and correlative light and electron microscopy. Although stable green and yellow FPs are available, stable monomeric red FPs (RFPs) remain limited. Here we develop an extremely stable monomeric RFP named mScarlet3-H and determine its structure at a 1.5 Å resolution. mScarlet3-H exhibits remarkable resistance to high temperature, chaotropic conditions and oxidative environments, enabling efficient correlative light and electron microscopy imaging and rapid (less than 1 day) whole-organ tissue clearing. In addition, its high photostability allows long-term three-dimensional structured illumination microscopy imaging of mitochondrial dynamics with minimal photobleaching. It also facilitates dual-color live-cell stimulated emission depletion imaging with a high signal-to-noise ratio and strong specificity. Systematic benchmarking against high-performing RFPs established mScarlet3-H as a highly stable RFP for multimodality microscopy in cell cultures and model organisms, complementing green FPs for multiplexed imaging in zebrafish, mice and Nicotiana benthamiana.

Quantifying the relationship between cell proliferation and morphology during development of the face

Morphogenesis requires highly coordinated, complex interactions between cellular processes: proliferation, migration and apoptosis, along with physical tissue interactions. How these cellular and tissue dynamics drive morphogenesis remains elusive. Three dimensional (3D) microscopic imaging holds great promise, and generates elegant images, but generating even moderate throughput for quantified images is challenging for many reasons. As a result, the association between morphogenesis and cellular processes in 3D developing tissues has not been fully explored. To address this gap, we have developed an imaging and image analysis pipeline to enable 3D quantification of cellular dynamics along with 3D morphology for the same individual embryo. Specifically, we focus on how 3D distribution of proliferation relates to morphogenesis during mouse facial development. Our method involves imaging with light-sheet microscopy, automated segmentation of cells and tissues using machine learning-based tools, and quantification of external morphology by geometric morphometrics. Applying this framework, we show that changes in proliferation are tightly correlated with changes in morphology over the course of facial morphogenesis. These analyses illustrate the potential of this pipeline to investigate mechanistic relationships between cellular dynamics and morphogenesis during embryonic development.

Three-dimensional exploration of the chicken embryo, a comparative study of light sheet and histological visualisation

Ultramicroscopy has offered new avenues into the visualisation of tissues within animal models, providing three-dimensional visualisation through the use of light sheet fluorescence microscopy. This study aimed to develop and apply an optical tissue clearing method to investigate the application of light sheet fluorescence microscopy to image late-stage chicken embryos, and compare anatomical visualisation to traditional histological staining. Seventeen-day old specific pathogen free embryos were collected, fixed, and sectioned. Haematoxylin and eosin stained sections were prepared for histology, while light sheet imaging required the tissues to be optically clear. For this, an ethyl cinnamate-based method was utilised, allowing for acquisition of clear, unobstructed three-dimensional images of significant organ structures and systems using only autofluorescence. The use of established histological techniques provided anatomical mapping of structures between familiar histology images and the three-dimensional light sheet images. Rendering of organs using light sheet imaging provided contextual insights into the surrounding tissues and physiological architecture of major organ structures and systems. This was most apparent through the identification of the pulmonary vein and rendering of a volumetric projection of the vasculature branching within the lung and the subsequent merging of vasculature into the left side of the heart. Overall, the visualisation of the chicken embryo was enhanced by combining traditional histology with the information gained by three-dimensional light sheet fluorescence microscopy.

Imaging the enteric nervous system

The enteric nervous system (ENS) has garnered increasing scientific interest due to its pivotal role in digestive processes and its involvement in various gastrointestinal and central nervous system (CNS) disorders, including Crohn's disease, Parkinson's disease, and autism. Despite its significance, the ENS remains relatively underexplored by neurobiologists, primarily because its structure and function are less understood compared to the CNS. This review examines both pioneering methodologies that initially revealed the intricate layered structure of the ENS and recent advancements in studying its three-dimensional (3-D) organization, both in fixed samples and at a functional level, ex-vivo or in-vivo. Traditionally, imaging the ENS relied on histological techniques involving sequential tissue sectioning, staining, and microscopic imaging of single sections. However, this method has limitations representing the full complexity of the ENS's 3-D meshwork, which led to the development of more intact preparations, such as whole-mount preparation, as well as the use of volume imaging techniques. Advancements in 3-D imaging, particularly methods like spinning-disk confocal, 2-photon, and light-sheet microscopies, combined with tissue-clearing techniques, have revolutionized our understanding of the ENS's fine structure. These approaches offer detailed views of its cellular architecture, including interactions among various cell types, blood vessels, and lymphatic vessels. They have also enhanced our comprehension of ENS-related pathologies, such as inflammatory bowel disease, Hirschsprung's disease (HSCR), and the ENS's involvement in neurodegenerative disorders like Parkinson's (PD) and Alzheimer's diseases (AD). More recently, 2-photon or confocal in-vivo imaging, combined with transgenic approaches for calcium imaging, or confocal laser endomicroscopy, have opened new avenues for functional studies of the ENS. These methods enable real-time observation of enteric neuronal and glial activity and their interactions. While routinely used in CNS studies, their application to understanding local circuits and signals in the ENS is relatively recent and presents unique challenges, such as accommodating peristaltic movements. Advancements in 3-D in-vivo functional imaging are expected to significantly deepen our understanding of the ENS and its roles in gastrointestinal and neurological diseases, potentially leading to improved diagnostic and therapeutic strategies.

Unveiling the native architecture of adult cardiac tissue using the 3D-NaissI method

Accurately imaging adult cardiac tissue in its native state is essential for regenerative medicine and understanding heart disease. Current fluorescence methods encounter challenges with tissue fixation. Here, we introduce the 3D-NaissI (3D-Native Tissue Imaging) method, which enables rapid, cost-effective imaging of fresh cardiac tissue samples in their closest native state, and has been extended to other tissues. We validated the efficacy of 3D-NaissI in preserving cardiac tissue integrity using small biopsies under hypothermic conditions in phosphate-buffered saline, offering unparalleled resolution in confocal microscopy for imaging fluorescent small molecules and antibodies. Compared to conventional histology, 3D-NaissI preserves cardiac tissue architecture and native protein epitopes, facilitating the use of a wide range of commercial antibodies without unmasking strategies. We successfully identified specific cardiac protein expression patterns in cardiomyocytes (CMs) from rodents and humans, including for the first time ACE2 localization in the lateral membrane/T-Tubules and SGTL2 in the sarcoplasmic reticulum. These findings shed light on COVID-19-related cardiac complications and suggest novel explanations for therapeutic benefits of iSGLT2 in HFpEF patients. Additionally, we challenge the notion of "connexin-43 lateralization" in heart pathology, suggesting it may be an artifact of cardiac fixation, as 3D-NaissI clearly revealed native connexin-43 expression at the lateral membrane of healthy CMs. We also discovered previously undocumented periodic ring-like 3D structures formed by pericytes that cover the lateral surfaces of CMs. These structures, positive for laminin-2, delineate a specific spatial architecture of laminin-2 receptors on the CM surface, underscoring the pivotal role of pericytes in CM function. Lastly, 3D-NaissI facilitates the mapping of native human protein expression in fresh cardiac autopsies, offering insights into both pathological and non-pathological contexts. Therefore, 3D-NaissI provides unparalleled insights into native cardiac tissue biology and holds the promise of advancing our understanding of physiology and pathophysiology, surpassing standard histology in both resolution and accuracy.

Whole-brain spatial transcriptional analysis at cellular resolution

Recent advances in RNA analysis have deepened our understanding of cellular states in biological tissues. However, a substantial gap remains in integrating RNA expression data with spatial context across organs, primarily owing to the challenges associated with RNA detection within intact tissue volumes. Here, we developed Tris buffer-mediated retention of in situ hybridization chain reaction signal in cleared organs (TRISCO), an effective tissue-clearing method designed for whole-brain spatial three-dimensional (3D) RNA imaging. TRISCO resolved several crucial issues, including the preservation of RNA integrity, achieving uniform RNA labeling, and enhancing tissue transparency. We tested TRISCO using a broad range of cell-identity markers, noncoding and activity-dependent RNAs, within diverse organs of varying sizes and species. TRISCO thus emerges as a powerful tool for single-cell, whole-brain, 3D imaging that enables comprehensive transcriptional spatial analysis across the entire brain.

In situ reprogramming of cardiac fibroblasts into cardiomyocytes in mouse heart with chemicals

Cardiomyocytes are terminal differentiated cells and have limited ability to proliferate or regenerate. Condition like myocardial infarction causes massive death of cardiomyocytes and is the leading cause of death. Previous studies have demonstrated that cardiac fibroblasts can be induced to transdifferentiate into cardiomyocytes in vitro and in vivo by forced expression of cardiac transcription factors and microRNAs. Our previous study have demonstrated that full chemical cocktails could also induce fibroblast to cardiomyocyte transdifferentiation both in vitro and in vivo. With the development of tissue clearing techniques, it is possible to visualize the reprogramming at the whole-organ level. In this study, we investigated the effect of the chemical cocktail CRFVPTM in inducing in situ fibroblast to cardiomyocyte transdifferentiation with two strains of genetic tracing mice, and the reprogramming was observed at whole-heart level with CUBIC tissue clearing technique and 3D imaging. In addition, single-cell RNA sequencing (scRNA-seq) confirmed the generation of cardiomyocytes from cardiac fibroblasts which carries the tracing marker. Our study confirms the use of small molecule cocktails in inducing in situ fibroblast to cardiomyocyte reprogramming at the whole-heart level and proof-of-conceptly providing a new source of naturally incorporated cardiomyocytes to help heart regeneration.

Theoretical framework for calibrating the depth-dependent optical scattering in layered human skin using spatially offset measurements

Spatially offset spectroscopy offers an alternative non-invasive method for enabling deep probing of structures and chemical molecules, which is clinically significant for the characterization of chemical and physical alterations in human skin. However, a more precise depth-resolved quantification using the spatially offset measurements still remains a challenge due to the mixed inhomogeneous scattering. Herein, we report a Monte-Carlo-based quantification modeling platform combined with a novel, to the best of our knowledge, scattering spectrum decomposition method to explore the depth-dependent optical scattering contributions in human skin. In the simplified modeling, human skin was empirically set to be composed of multiple layers, and each layer possessed different photon weights for the spatially offset scattering intensity measurements. The modeling results of photon transportation in-and-out of the layered skin substantially discovered that the layer-dependent scattering contribution was compositely encoded into the spatially offset measurements and varied with the illumination incidence angle. For calibrating the layer-dependent scattering contribution, a modified nonlinear independent component processing algorithm was applied to the spatially offset measurements by decomposing the photon weights of each layer. The calibration results figured out the major scattering contribution of each layer along the offset axis under different incidence angles, which were consistent with previous experimental observations. The proposed theoretical framework establishes a feasible approach for spatially offset optical spectroscopies enabling non-invasive quantitative A-line characterization of the concentrations of skin components.

Fluorescent Water-Soluble Polycationic Chitosan Polymers as Markers for Biological 3D Imaging

Over the last decades, various tissue-clearing techniques have broken the ground for the optical imaging of whole organs and whole-organisms, providing complete representative data sets of three-dimensional biological structures. Along with advancements in this field, the development of fluorescent markers for staining vessels and capillaries has offered insights into the complexity of vascular networks and their impact on disease progression. Here we describe the use of a modified water-soluble chitosan linked to cyanine dyes in combination with ethyl cinnamate-based optical tissue clearing for the 3D visualization of tissue vasculature in depth. The water-soluble fluorescent Chitosans have proven to be an optimal candidate for labeling both vessels and capillaries ex vivo thanks to their increased water solubility, high photostability, and optical properties in the near-infrared window. In addition, the nontoxicity of these markers broadens their applicability to in vitro and in vivo biological applications. Despite the availability of other fluorescent molecules for vascular staining, the present study, for the first time, demonstrates the potential of fluorescent chitosans to depict vessels at the capillary level and opens avenues for advancing the diagnostic field by reducing the complexity and costs of the currently available procedures.

3D visualization of cellular and molecular distributions in human crystalline lenses at different ages

BACKGROUND

The human lens is a highly organized tissue, and it is constructed of delicate inner architectures that ensure its transparency. However, the pattern of cell distribution in the intact lens has rarely been observed or traced in a three-dimensional (3D) perspective.

METHODS

Here, we modified and compared three different kinds of tissue transparency methods to investigate the cellular and molecular changes in the human lens at different ages from a 3D perspective.

RESULTS

First, we analyzed the general 3D parameters of cleared human lenses from 6 months to 72 years of age and found that the equator proportion remained constant with age (23.05% ± 0.36). Next, we visualized the cellular distribution patterns in the anterior capsule and equator, as well as the distribution of cortical fiber cells. Interestingly, we observed the accumulation of equatorial epithelium in adolescents and the asymmetrical denucleation of cortical fiber cells in the elderly. Zonula occludens-1 and tropomyosin receptor kinase A were also identified in the pre-equatorial germinative zone, and its presence decreased when comparing lenses of a 17-year-old to those of a 49-year-old.

CONCLUSION

We present a 3D cellular and molecular reconstruction of the human lens, illustrating the observed alterations in human lens epithelial cells across different ages.

Turning tissues temporarily transparent

A food dye suppresses light scattering in biological tissues to enable deep in vivo imaging.

Far-Red Aggregation-Induced Emission Hydrogel-Reinforced Tissue Clearing for 3D Vasculature Imaging of Whole Lung and Whole Tumor

Understanding the vascular formation and distribution in metastatic lung tumors is a significant challenge due to autofluorescence, antibody/dye diffusion in dense tumor, and fluorophore stability when exposed to solvent-based clearing agents. Here, an approach is presented that redefines 3D vasculature imaging within metastatic tumor, peritumoral lung tissue, and normal lung. Specifically, a far-red aggregation-induced emission nanoparticle with surface amino groups (termed as TSCN nanoparticle, TSCNNP) is designed for in situ formation of hydrogel (TSCNNP@Gel) inside vasculatures to provide structural support and enhance the fluorescence in solvent-based tissue clearing method. Using this TSCNNP@Gel-reinforced tissue clearing imaging approach, the critical challenges are successfully overcome and comprehensive visualization of the whole pulmonary vasculature up to 2 µm resolution is enabled, including its detailed examination in metastatic tumors. Importantly, features of tumor-associated vasculature in 3D panoramic views are unveiled, providing the potential to determine tumor stages, predict tumor progression, and facilitate the histopathological diagnosis of various tumor types.

Advanced Immunolabeling Method for Optical Volumetric Imaging Reveals Dystrophic Neurites of Dopaminergic Neurons in Alzheimer's Disease Mouse Brain

Optical brain clearing combined with immunolabeling is valuable for analyzing molecular tissue structures, including complex synaptic connectivity. However, the presence of aberrant lipid deposition due to aging and brain disorders poses a challenge for achieving antibody penetration throughout the entire brain volume. Herein, we present an efficient brain-wide immunolabeling method, the immuno-active clearing technique (iACT). The treatment of brain tissues with a zwitterionic detergent, specifically SB3-12, significantly enhanced tissue permeability by effectively mitigating lipid barriers. Notably, Quadrol treatment further refines the methodology by effectively eliminating residual detergents from cleared brain tissues, subsequently amplifying volumetric fluorescence signals. Employing iACT, we uncover disrupted axonal projections within the mesolimbic dopaminergic (DA) circuits in 5xFAD mice. Subsequent characterization of DA neural circuits in 5xFAD mice revealed proximal axonal swelling and misrouting of distal axonal compartments in proximity to amyloid-beta plaques. Importantly, these structural anomalies in DA axons correlate with a marked reduction in DA release within the nucleus accumbens. Collectively, our findings highlight the efficacy of optical volumetric imaging with iACT in resolving intricate structural alterations in deep brain neural circuits. Furthermore, we unveil the compromised integrity of DA pathways, contributing to the underlying neuropathology of Alzheimer's disease. The iACT technique thus holds significant promise as a valuable asset for advancing our understanding of complex neurodegenerative disorders and may pave the way for targeted therapeutic interventions.

Edible oil based optical clearing for optical coherence tomography angiography imaging

In optical imaging, optical clearing agents are commonly used to enhance the structural details of a sample. The current study investigates how to use it to improve the data obtained by an optical coherence tomography angiography system. A natural edible oil with no chemical base has been used for optical clearing. In-vivo testing on mice and humans yielded excellent optical clearing. Using computational techniques, the improvement in angiography signal caused by the optical clearing agent is investigated qualitatively and quantitatively. Compared to the control group, applying the edible oil-based optical clearing agent demonstrated improved vessel percentage and refined vascular signal intensity along depth.

Tissue clearing and imaging approaches for in toto analysis of the reproductive system†

New microscopy techniques in combination with tissue clearing protocols and emerging analytical approaches have presented researchers with the tools to understand dynamic biological processes in a three-dimensional context. This paves the road for the exploration of new research questions in reproductive biology, for which previous techniques have provided only approximate resolution. These new methodologies now allow for contextualized analysis of far-larger volumes than was previously possible. Tissue optical clearing and three-dimensional imaging techniques posit the bridging of molecular mechanisms, macroscopic morphogenic development, and maintenance of reproductive function into one cohesive and comprehensive understanding of the biology of the reproductive system. In this review, we present a survey of the various tissue clearing techniques and imaging systems, as they have been applied to the developing and adult reproductive system. We provide an overview of tools available for analysis of experimental data, giving particular attention to the emergence of artificial intelligence-assisted methods and their applicability to image analysis. We conclude with an evaluation of how novel image analysis approaches that have been applied to other organ systems could be incorporated into future experimental evaluation of reproductive biology.

Increased Multiplexity in Optical Tissue Clearing-Based Three-Dimensional Immunofluorescence Microscopy of the Tumor Microenvironment by Light-Emitting Diode Photobleaching

Optical tissue clearing and three-dimensional (3D) immunofluorescence (IF) microscopy is transforming imaging of the complex tumor microenvironment (TME). However, current 3D IF microscopy has restricted multiplexity; only 3 or 4 cellular and noncellular TME components can be localized in cleared tumor tissue. Here we report a light-emitting diode (LED) photobleaching method and its application for 3D multiplexed optical mapping of the TME. We built a high-power LED light irradiation device and temperature-controlled chamber for completely bleaching fluorescent signals throughout optically cleared tumor tissues without compromise of tissue and protein antigen integrity. With newly developed tissue mounting and selected region-tracking methods, we established a cyclic workflow involving IF staining, tissue clearing, 3D confocal microscopy, and LED photobleaching. By registering microscope channel images generated through 3 work cycles, we produced 8-plex image data from individual 400 μm-thick tumor macrosections that visualize various vascular, immune, and cancer cells in the same TME at tissue-wide and cellular levels in 3D. Our method was also validated for quantitative 3D spatial analysis of cellular remodeling in the TME after immunotherapy. These results demonstrate that our LED photobleaching system and its workflow offer a novel approach to increase the multiplexing power of 3D IF microscopy for studying tumor heterogeneity and response to therapy.

Comparison of gut toxicity and microbiome effects in zebrafish exposed to polypropylene microplastics: Interesting effects of UV-weathering on microbiome

Weathered microplastics (MPs) exhibit different physicochemical properties compared to pristine MPs, thus, their effects on the environment and living organisms may also differ. In the present study, we investigated the gut-toxic effects of virgin polypropylene MPs (PP) and UV-weathered PP MPs (UV-PP) on zebrafish. The zebrafish were exposed to the two types of PP MPs at a concentration of 50 mg/L each for 14 days. After exposure, MPs accumulated primarily within the gastrointestinal tract, with UV-PP exhibiting a higher accumulation than PP. The ingestion of PP and UV-PP induced gut damage in zebrafish and increased the gene expression and levels of enzymes related to oxidative stress and inflammation, with no significant differences between the two MPs. Analysis of the microbial community confirmed alterations in the abundance and diversity of zebrafish gut microorganisms in the PP and UV-PP groups, with more pronounced changes in the PP-exposed group. Moreover, the Kyoto Encyclopedia of Genes and Genomes pathway analysis confirmed the association between changes in the gut microorganisms at the phylum and genus levels with cellular responses, such as oxidative stress, inflammation, and tissue damage. This study provides valuable insights regarding the environmental impact of MPs on organisms.

Multiscale and multimodal imaging for three-dimensional vascular and histomorphological organ structure analysis of the pancreas

Exocrine and endocrine pancreas are interconnected anatomically and functionally, with vasculature facilitating bidirectional communication. Our understanding of this network remains limited, largely due to two-dimensional histology and missing combination with three-dimensional imaging. In this study, a multiscale 3D-imaging process was used to analyze a porcine pancreas. Clinical computed tomography, digital volume tomography, micro-computed tomography and Synchrotron-based propagation-based imaging were applied consecutively. Fields of view correlated inversely with attainable resolution from a whole organism level down to capillary structures with a voxel edge length of 2.0 µm. Segmented vascular networks from 3D-imaging data were correlated with tissue sections stained by immunohistochemistry and revealed highly vascularized regions to be intra-islet capillaries of islets of Langerhans. Generated 3D-datasets allowed for three-dimensional qualitative and quantitative organ and vessel structure analysis. Beyond this study, the method shows potential for application across a wide range of patho-morphology analyses and might possibly provide microstructural blueprints for biotissue engineering.

Over 30 Years of DiI Use for Human Neuroanatomical Tract Tracing: A Scoping Review

In the present study, we conducted a scoping review to provide an overview of the existing literature on the carbocyanine dye DiI, in human neuroanatomical tract tracing. The PubMed, Scopus, and Web of Science databases were systematically searched. We identified 61 studies published during the last three decades. While studies incorporated specimens across human life from the embryonic stage onwards, the majority of studies focused on adult human tissue. Studies that utilized peripheral nervous system (PNS) tissue were a minority, with the majority of studies focusing on the central nervous system (CNS). The most common topic of interest in previous tract tracing investigations was the connectivity of the visual pathway. DiI crystals were more commonly applied. Nevertheless, several studies utilized DiI in a paste or dissolved form. The maximum tracing distance and tracing speed achieved was, respectively, 70 mm and 1 mm/h. We identified studies that focused on optimizing tracing efficacy by varying parameters such as fixation, incubation temperature, dye re-application, or the application of electric fields. Additional studies aimed at broadening the scope of DiI use by assessing the utility of archival tissue and compatibility of tissue clearing in DiI applications. A combination of DiI tracing and immunohistochemistry in double-labeling studies have been shown to provide the means for assessing connectivity of phenotypically defined human CNS and PNS neuronal populations.

Rapid clearing and imaging of Mohs and melanoma surgical margins using a low-cost tissue processor

Tissue clearing methods render biological tissues transparent while maintaining tissue structure, enabling visualization of entire tissues. Recent developments in tissue clearing have predominantly emphasized preserving intrinsic fluorescent proteins or aqueous-based tissue clearing and so typically involve complex procedures and long processing times. The utilization of tissue clearing protocols in standard of care histology settings has been less well explored, and protocols for rapid clearing of human tissue specimens are limited. This study presents a novel rapid clearing protocol and demonstrates a low-cost tissue processor for high volume rapid tissue clearing that can be intergraded into standard histology workflow. We demonstrate rapid clearing in dermatological specimens, including both nonmelanoma and melanoma excisions.

Preparation and Characterization of Acrylic and Methacrylic Phospholipid-Mimetic Polymer Hydrogels and Their Applications in Optical Tissue Clearing

The 2-methacryloyloxyethyl phosphorylcholine (MPC) polymers are mimetic to phospholipids, being widely used as biocompatible polymers. In our previous study, MPC polymer hydrogels proved more effective for optical tissue clearing compared to acrylamide (AAm) polymer hydrogels. In the present study, 2-acryloyloxyethyl phosphorylcholine (APC) was synthesized and employed to create hydrogels for a comparative analysis with methacrylic MPC-based hydrogels. APC, an acrylic monomer, was copolymerized with AAm in a similar reactivity. In contrast, MPC, as a methacrylic monomer, demonstrated higher copolymerization reactivity than AAm, leading to a spontaneously delayed two-step polymerization behavior. This suggests that the polymer sequences and network structures became heterogeneous when both methacrylic and acrylic monomers, as well as crosslinkers, were present in the copolymerization system. The molecular weight of the APC polymers was considerably smaller than that of the MPC polymers due to the formation of mid-chain radicals and subsequent β-scission during polymerization. The swelling ratios in water and strain sweep profiles of hydrogels prepared using acrylic and methacrylic compounds differed from those of hydrogels prepared using only acrylic compounds. This implies that copolymerization reactivity influences the polymer network structures and crosslinking density in addition to the copolymer composition. APC-based hydrogels are effective for the optical clearing of tumor tissues and are applicable to both passive and electrophoretic methods.

Using tissue clearing and light sheet fluorescence microscopy for the three-dimensional analysis of sensory and sympathetic nerve endings that innervate bone and dental tissue of mice

Bone and dental tissues are richly innervated by sensory and sympathetic neurons. However, the characterization of the morphology, molecular phenotype, and distribution of nerves that innervate hard tissue has so far mostly been limited to thin histological sections. This approach does not adequately capture dispersed neuronal projections due to the loss of important structural information during three-dimensional (3D) reconstruction. In this study, we modified the immunolabeling-enabled imaging of solvent-cleared organs (iDISCO/iDISCO+) clearing protocol to image high-resolution neuronal structures in whole femurs and mandibles collected from perfused C57Bl/6 mice. Axons and their nerve terminal endings were immunolabeled with antibodies directed against protein gene product 9.5 (pan-neuronal marker), calcitonin gene-related peptide (peptidergic nociceptor marker), or tyrosine hydroxylase (sympathetic neuron marker). Volume imaging was performed using light sheet fluorescence microscopy. We report high-quality immunolabeling of the axons and nerve terminal endings for both sensory and sympathetic neurons that innervate the mouse femur and mandible. Importantly, we are able to follow their projections through full 3D volumes, highlight how extensive their distribution is, and show regional differences in innervation patterns for different parts of each bone (and surrounding tissues). Mapping the distribution of sensory and sympathetic axons, and their nerve terminal endings, in different bony compartments may be important in further elucidating their roles in health and disease.

Efficient 3D imaging and pathological analysis of the human lymphoma tumor microenvironment using light-sheet immunofluorescence microscopy

Rationale: The composition and spatial structure of the lymphoma tumor microenvironment (TME) provide key pathological insights for tumor survival and growth, invasion and metastasis, and resistance to immunotherapy. However, the 3D lymphoma TME has not been well studied owing to the limitations of current imaging techniques. In this work, we take full advantage of a series of new techniques to enable the first 3D TME study in intact lymphoma tissue. Methods: Diverse cell subtypes in lymphoma tissues were tagged using a multiplex immunofluorescence labeling technique. To optically clarify the entire tissue, immunolabeling-enabled three-dimensional imaging of solvent-cleared organs (iDISCO+), clear, unobstructed brain imaging cocktails and computational analysis (CUBIC) and stabilization to harsh conditions via intramolecular epoxide linkages to prevent degradation (SHIELD) were comprehensively compared with the ultimate dimensional imaging of solvent-cleared organs (uDISCO) approach selected for clearing lymphoma tissues. A Bessel-beam light-sheet fluorescence microscope (B-LSFM) was developed to three-dimensionally image the clarified tissues at high speed and high resolution. A customized MATLAB program was used to quantify the number and colocalization of the cell subtypes based on the acquired multichannel 3D images. By combining these cutting-edge methods, we successfully carried out high-efficiency 3D visualization and high-content cellular analyses of the lymphoma TME. Results: Several antibodies, including CD3, CD8, CD20, CD68, CD163, CD14, CD15, FOXP3 and Ki67, were screened for labeling the TME in lymphoma tumors. The 3D imaging results of the TME from three types of lymphoma, reactive lymphocytic hyperplasia (RLN), diffuse large B-cell lymphoma (DLBCL), and angioimmunoblastic T-cell lymphoma (AITL), were quantitatively analyzed, and their cell number, localization, and spatial correlation were comprehensively revealed. Conclusion: We present an advanced imaging-based method for efficient 3D visualization and high-content cellular analysis of the lymphoma TME, rendering it a valuable tool for tumor pathological diagnosis and other clinical research.

Increased multiplexity in optical tissue clearing-based 3D immunofluorescence microscopy of the tumor microenvironment by LED photobleaching

Optical tissue clearing and three-dimensional (3D) immunofluorescence (IF) microscopy have been transforming imaging of the complex tumor microenvironment (TME). However, current 3D IF microscopy has restricted multiplexity; only three or four cellular and non-cellular TME components can be localized in a cleared tumor tissue. Here we report a LED photobleaching method and its application for 3D multiplexed optical mapping of the TME. We built a high-power LED light irradiation device and temperature-controlled chamber for completely bleaching fluorescent signals throughout optically cleared tumor tissues without compromise of tissue and protein antigen integrity. With newly developed tissue mounting and selected region-tracking methods, we established a cyclic workflow involving IF staining, tissue clearing, 3D confocal microscopy, and LED photobleaching. By registering microscope channel images generated through three work cycles, we produced 8-plex image data from individual 400 μm-thick tumor macrosections that visualize various vascular, immune, and cancer cells in the same TME at tissue-wide and cellular levels in 3D. Our method was also validated for quantitative 3D spatial analysis of cellular remodeling in the TME after immunotherapy. These results demonstrate that our LED photobleaching system and its workflow offer a novel approach to increase the multiplexing power of 3D IF microscopy for studying tumor heterogeneity and response to therapy.

Comparison of Light-Sheet Fluorescence Microscopy and Fast-Confocal Microscopy for Three-Dimensional Imaging of Cleared Mouse Brain

Whole-brain imaging is important for understanding brain functions through deciphering tissue structures, neuronal circuits, and single-neuron tracing. Thus, many clearing methods have been developed to acquire whole-brain images or images of three-dimensional thick tissues. However, there are several limitations to imaging whole-brain volumes, including long image acquisition times, large volumes of data, and a long post-image process. Based on these limitations, many researchers are unsure about which light microscopy is most suitable for imaging thick tissues. Here, we compared fast-confocal microscopy with light-sheet fluorescence microscopy for whole-brain three-dimensional imaging, which can acquire images the fastest. To compare the two types of microscopies for large-volume imaging, we performed tissue clearing of a whole mouse brain, and changed the sample chamber and low- magnification objective lens and modified the sample holder of a light-sheet fluorescence microscope. We found out that light-sheet fluorescence microscopy using a 2.5× objective lens possesses several advantages, including saving time, large-volume image acquisitions, and high Z-resolution, over fast-confocal microscopy, which uses a 4× objective lens. Therefore, we suggest that light-sheet fluorescence microscopy is suitable for whole mouse brain imaging and for obtaining high-resolution three-dimensional images.

Multimodal Diagnostics of Changes in Rat Lungs after Vaping

(1) Background: The use of electronic cigarettes has become widespread in recent years. The use of e-cigarettes leads to milder pathological conditions compared to traditional cigarette smoking. Nevertheless, e-liquid vaping can cause morphological changes in lung tissue, which affects and impairs gas exchange. This work studied the changes in morphological and optical properties of lung tissue under the action of an e-liquid aerosol. To do this, we implemented the "passive smoking" model and created the specified concentration of aerosol of the glycerol/propylene glycol mixture in the chamber with the animal. (2) Methods: In ex vivo studies, the lungs of Wistar rats are placed in the e-liquid for 1 h. For in vivo studies, Wistar rats were exposed to the e-liquid vapor in an aerosol administration chamber. After that, lung tissue samples were examined ex vivo using optical coherence tomography (OCT) and spectrometry with an integrating sphere. Absorption and reduced scattering coefficients were estimated for the control and experimental groups. Histological sections were made according to the standard protocol, followed by hematoxylin and eosin staining. (3) Results: Exposure to e-liquid in ex vivo and aerosol in in vivo studies was found to result in the optical clearing of lung tissue. Histological examination of the lung samples showed areas of emphysematous expansion of the alveoli, thickening of the alveolar septa, and the phenomenon of plasma permeation, which is less pronounced in in vivo studies than for the exposure of e-liquid ex vivo. E-liquid aerosol application allows for an increased resolution and improved imaging of lung tissues using OCT. Spectral studies showed significant differences between the control group and the ex vivo group in the spectral range of water absorption. It can be associated with dehydration of lung tissue owing to the hyperosmotic properties of glycerol and propylene glycol, which are the main components of e-liquids. (4) Conclusions: A decrease in the volume of air in lung tissue and higher packing of its structure under e-liquid vaping causes a better contrast of OCT images compared to intact lung tissue.

Advancing Dentistry through Bioprinting: Personalization of Oral Tissues

Despite significant advancements in dental tissue restoration and the use of prostheses for addressing tooth loss, the prevailing clinical approaches remain somewhat inadequate for replicating native dental tissue characteristics. The emergence of three-dimensional (3D) bioprinting offers a promising innovation within the fields of regenerative medicine and tissue engineering. This technology offers notable precision and efficiency, thereby introducing a fresh avenue for tissue regeneration. Unlike the traditional framework encompassing scaffolds, cells, and signaling factors, 3D bioprinting constitutes a contemporary addition to the arsenal of tissue engineering tools. The ongoing shift from conventional dentistry to a more personalized paradigm, principally under the guidance of bioprinting, is poised to exert a significant influence in the foreseeable future. This systematic review undertakes the task of aggregating and analyzing insights related to the application of bioprinting in the context of regenerative dentistry. Adhering to PRISMA guidelines, an exhaustive literature survey spanning the years 2019 to 2023 was performed across prominent databases including PubMed, Scopus, Google Scholar, and ScienceDirect. The landscape of regenerative dentistry has ushered in novel prospects for dentoalveolar treatments and personalized interventions. This review expounds on contemporary accomplishments and avenues for the regeneration of pulp-dentin, bone, periodontal tissues, and gingival tissues. The progressive strides achieved in the realm of bioprinting hold the potential to not only enhance the quality of life but also to catalyze transformative shifts within the domains of medical and dental practices.

Compact organ-tissue electrophoresis system (CORES)

Electrophoretic tissue clearing has been a commonly used laboratory method since the early twentieth century. Infrastructure for standard procedures has yet to be formed. In particular, control of the heat produced by electrophoresis, the voltage applied to the electrodes, the resistance, and the speed of liquid circulation create difficulty for researchers. We aimed to develop a compact organ electrophoresis system that enables the researcher to have easy, rapid, and inexpensive working opportunities. The system includes an electronic control unit, a liquid tank, a temperature control unit, and an electrophoresis chamber. The control unit software can keep the system stable by using information on temperature and circulation rate received through the sensors using the feedback principle. Corrosion and particle collection are reduced to a minimum as platinum wires are used for electrophoresis electrodes. A temperature control unit can heat and cool via a liquid tank base. The CORES is an all-in-one, easy-to-use solution for electrophoretic tissue clearing. It assures efficient, rapid, and consistent tissue clearing. The system was stable with 72 h of continuous operation. Patent applications and trial version studies for introducing the system to researchers are still in progress.

Spatial mapping of cellular senescence: emerging challenges and opportunities

Cellular senescence is a well-established driver of aging and age-related diseases. There are many challenges to mapping senescent cells in tissues such as the absence of specific markers and their relatively low abundance and vast heterogeneity. Single-cell technologies have allowed unprecedented characterization of senescence; however, many methodologies fail to provide spatial insights. The spatial component is essential, as senescent cells communicate with neighboring cells, impacting their function and the composition of extracellular space. The Cellular Senescence Network (SenNet), a National Institutes of Health (NIH) Common Fund initiative, aims to map senescent cells across the lifespan of humans and mice. Here, we provide a comprehensive review of the existing and emerging methodologies for spatial imaging and their application toward mapping senescent cells. Moreover, we discuss the limitations and challenges inherent to each technology. We argue that the development of spatially resolved methods is essential toward the goal of attaining an atlas of senescent cells.

Multiresolution 3D Optical Mapping of Immune Cell Infiltrates in Mouse Asthmatic Lung

Asthma is a chronic inflammatory airway disease driven by various infiltrating immune cell types into the lung. Optical microscopy has been used to study immune infiltrates in asthmatic lungs. Confocal laser scanning microscopy (CLSM) identifies the phenotypes and locations of individual immune cells in lung tissue sections by employing high-magnification objectives and multiplex immunofluorescence staining. In contrast, light-sheet fluorescence microscopy (LSFM) can visualize the macroscopic and mesoscopic architecture of whole-mount lung tissues in three dimensions (3D) by adopting an optical tissue-clearing method. Despite each microscopy method producing image data with unique resolution from a tissue sample, CLSM and LSFM have not been applied together because of different tissue-preparation procedures. Here, we introduce a new approach combining LSFM and CLSM into a sequential imaging pipeline. We built a new optical tissue clearing workflow in which the immersion clearing agent can be switched from an organic solvent to an aqueous sugar solution for sequential 3D LSFM and CLSM of mouse lungs. This sequential combination microscopy offered quantitative 3D spatial analyses of the distribution of immune infiltrates in the same mouse asthmatic lung tissue at the organ, tissue, and cell levels. These results show that our method facilitates multiresolution 3D fluorescence microscopy as a new imaging approach providing comprehensive spatial information for a better understanding of inflammatory lung diseases.

Triglyceride-Rich Lipoprotein-Mediated Polymer Dots for Multimodal Imaging Interscapular Brown Adipose Tissue Capillaries

Brown adipose tissues (BATs) have been identified as a promising target of metabolism disorders. [18F]FDG-PET (FDG = fluorodeoxyglucose; PET = positron emission tomography) has been predominantly employed for BAT imaging, but its limitations drive the urgent need for novel functional probes combined with multimodal imaging approaches. It has been reported that polymer dots (Pdots) display rapid BAT imaging without additional cold stimulation. However, the mechanism by which Pdots image BAT remains unclear. Here, we made an intensive study of the imaging mechanism and found that Pdots can bind to triglyceride-rich lipoproteins (TRLs). By virtue of their high affinity to TRLs, Pdots selectively accumulate in capillary endothelial cells (ECs) in interscapular brown adipose tissues (iBATs). Compared to poly(styrene-co-maleic anhydride)cumene terminated (PSMAC)-Pdots with a short half-life and polyethylene glycol (PEG)-Pdots with low lipophilicity, naked-Pdots have good lipophilicity, with a half-life of about 30 min and up to 94% uptake in capillary ECs within 5 min, increasing rapidly after acute cold stimulation. These results suggested that the accumulation changes of Pdots in iBAT can reflect iBAT activity sensitively. Based on this mechanism, we further developed a strategy to detect iBAT activity and quantify the TRL uptake in vivo using multimodal Pdots.

Deep learning-based adaptive optics for light sheet fluorescence microscopy

Light sheet fluorescence microscopy (LSFM) is a high-speed imaging technique that is often used to image intact tissue-cleared specimens with cellular or subcellular resolution. Like other optical imaging systems, LSFM suffers from sample-induced optical aberrations that decrement imaging quality. Optical aberrations become more severe when imaging a few millimeters deep into tissue-cleared specimens, complicating subsequent analyses. Adaptive optics are commonly used to correct sample-induced aberrations using a deformable mirror. However, routinely used sensorless adaptive optics techniques are slow, as they require multiple images of the same region of interest to iteratively estimate the aberrations. In addition to the fading of fluorescent signal, this is a major limitation as thousands of images are required to image a single intact organ even without adaptive optics. Thus, a fast and accurate aberration estimation method is needed. Here, we used deep-learning techniques to estimate sample-induced aberrations from only two images of the same region of interest in cleared tissues. We show that the application of correction using a deformable mirror greatly improves image quality. We also introduce a sampling technique that requires a minimum number of images to train the network. Two conceptually different network architectures are compared; one that shares convolutional features and another that estimates each aberration independently. Overall, we have presented an efficient way to correct aberrations in LSFM and to improve image quality.

Optical attenuation coefficient of skin under low compression

In various biomedical optics therapies, knowledge of how light is absorbed or scattered by tissues is crucial. Currently, it is suspected that a low compression applied to the skin surface may improve light delivery into tissue. However, the minimum pressure needed to be applied to significantly increase the light penetration into the skin has not been determined. In this study, we used optical coherence tomography (OCT) to measure the optical attenuation coefficient of the human forearm dermis in a low compression regime (<8k P a). Our results show low pressures such as 4 kPa to 8 kPa are sufficient to significantly increase light penetration by decreasing the attenuation coefficient by at least 1.0m m ^-1.

Combining tissue clearing and Fluoro-Jade C labeling for neurotoxicity assessments

Tissue clearing refers to laboratory methods that make tissue transparent by chemical means. This approach allows the labeling, visualization, and analysis of specific targets without cutting the tissue into sections, thereby maintaining three-dimensional architecture. More than two dozen tissue-clearing methods have been developed by different research teams to date. While tissue clearing has been successfully applied in several studies concerning basic science or diseases, little is known about the utilization of tissue clearing for neurotoxicity evaluation. In this study, several tissue-clearing methods were combined with Fluoro-Jade C (FJ-C), a standard marker of neurodegeneration. The results suggest that some but not all tissue-clearing media are compatible with the FJ-C fluorophore. By utilizing a neurotoxicity animal model, the results further suggest that FJ-C labeling can be combined with tissue clearing for neurotoxicity assessments. This approach has the potential to be expanded further by combining multicolor labeling of molecular targets involved in the development and/or mechanisms of neurotoxicity and neurodegeneration.

Tissue clearing and immunostaining to visualize the spatial organization of vasculature and tumor cells in mouse liver

The liver has a complex and hierarchical segmental organization of arteries, portal veins, hepatic veins and lymphatic vessels. In-depth imaging of liver vasculature and malignancies could improve knowledge on tumor micro-environment, local tumor growth, invasion, as well as metastasis. Non-invasive imaging techniques such as computed tomography (CT), magnetic resonance imaging (MRI) and positron-emission transmission (PET) are routine for clinical imaging, but show inadequate resolution at cellular and subcellular level. In recent years, tissue clearing – a technique rendering tissues optically transparent allowing enhanced microscopy imaging – has made great advances. While mainly used in the neurobiology field, recently more studies have used clearing techniques for imaging other organ systems as well as tumor tissues. In this study, our aim was to develop a reproducible tissue clearing and immunostaining model for visualizing intrahepatic blood microvasculature and tumor cells in murine colorectal liver metastases. CLARITY and 3DISCO/iDISCO+ are two established clearing methods that have been shown to be compatible with immunolabelling, most often in neurobiology research. In this study, CLARITY unfortunately resulted in damaged tissue integrity of the murine liver lobes and no specific immunostaining. Using the 3DISCO/iDISCO+ method, liver samples were successfully rendered optically transparent. After which, successful immunostaining of the intrahepatic microvasculature using panendothelial cell antigen MECA-32 and colorectal cancer cells using epithelial cell adhesion molecule (EpCAM) was established. This approach for tumor micro-environment tissue clearing would be especially valuable for allowing visualization of spatial heterogeneity and complex interactions of tumor cells and their environment in future studies.

Label-free, fast, 2-photon volume imaging of the organization of neurons and glia in the enteric nervous system

The enteric nervous system (ENS), sometimes referred to as a "second brain" is a quasi-autonomous nervous system, made up of interconnected plexuses organized in a mesh-like network lining the gastrointestinal tract. Originally described as an actor in the regulation of digestion, bowel contraction, and intestinal secretion, the implications of the ENS in various central neuropathologies has recently been demonstrated. However, with a few exceptions, the morphology and pathologic alterations of the ENS have mostly been studied on thin sections of the intestinal wall or, alternatively, in dissected explants. Precious information on the three-dimensional (3-D) architecture and connectivity is hence lost. Here, we propose the fast, label-free 3-D imaging of the ENS, based on intrinsic signals. We used a custom, fast tissue-clearing protocol based on a high refractive-index aqueous solution to increase the imaging depth and allow us the detection of faint signals and we characterized the autofluorescence (AF) from the various cellular and sub-cellular components of the ENS. Validation by immunofluorescence and spectral recordings complete this groundwork. Then, we demonstrate the rapid acquisition of detailed 3-D image stacks from unlabeled mouse ileum and colon, across the whole intestinal wall and including both the myenteric and submucosal enteric nervous plexuses using a new spinning-disk two-photon (2P) microscope. The combination of fast clearing (less than 15 min for 73% transparency), AF detection and rapid volume imaging [less than 1 min for the acquisition of a z-stack of 100 planes (150*150 μm) at sub-300-nm spatial resolution] opens up the possibility for new applications in fundamental and clinical research.

Clearing of hemozoin crystals in malaria parasites enables whole-cell STED microscopy

Malaria is a devastating mosquito-borne parasitic disease that manifests when Plasmodium parasites replicate within red blood cells. During the development within the red blood cell, the parasite digests hemoglobin and crystalizes the otherwise toxic heme. The resulting hemozoin crystals limit imaging by STED nanoscopy owing to their high light-absorbing capacity, which leads to immediate cell destruction upon contact with the laser. Here, we establish CUBIC-P-based clearing of hemozoin crystals, enabling whole-cell STED nanoscopy of parasites within red blood cells. Hemozoin-cleared infected red blood cells could reliably be stained with antibodies, and hence proteins in the hemozoin-containing digestive vacuole membrane, as well as in secretory vesicles of gametocytes, could be imaged at high resolution. Thus, this process is a valuable tool to study and understand parasite biology and the potential molecular mechanisms mediating drug resistance. This article has an associated First Person interview with the first author of the paper.

Three-dimensional visualization of human brain tumors using the CUBIC technique

Application of tissue clearing techniques on human brain tumors is still limited. This study was to investigate the application of CUBIC on 3D pathological studies of human brain tumors. Brain tumor specimens derived from 21 patients were cleared with CUBIC. Immunostaining was conducted on cleared specimens to label astrocytes, microglia and microvessels, respectively. All tumor specimens achieved transparency after clearing. Immunostaining and CUBIC are well compatible in a variety of human brain tumors. Spatial morphologies of microvessels, astrocytes and microglia of tumors were clearly visualized in 3D, and their 3D morphological parameters were easily quantified. By comparing the quantitative morphological parameters of microvessels among brain tumors of different malignancy, we found that mean vascular diameter was positively correlated with tumor malignancy. Our study demonstrates that CUBIC can be successfully applied to 3D pathological studies of various human brain tumors, and 3D studies of human brain tumors hold great promise in helping us better understand brain tumor pathology in the future.

Broadband spectral verification of optical clearing reversibility in lung tissue

The increase of tissue transparency through sequential optical immersion clearing treatments and treatment reversibility have high interest for clinical applications. To evaluate the clearing reversibility in a broad spectral range and the magnitude of the transparency created by a second treatment, the present study consisted on measuring the spectral collimated transmittance of lung tissues during a sequence of two treatments with electronic cigarette (e-cig) fluid, which was intercalated with an immersion in saline. The saline immersion clearly reverted the clearing effect in the lung tissue in the spectral range between 220 and 1000 nm. By a later application of a second treatment with the e-cig fluid, the magnitude of the optical clearing effect was observed to be about the double as the one observed in the first treatment, showing that the molecules of the optical clearing agent might have converted some bound water into mobile water during the first treatment.

Development of a 3D-immunofluorescence analysis for sensory nerve endings in human ligaments

BACKGROUND

The analysis of ligamentous mechanoreceptors is difficult due to a high amount of unclassifiable mechanoreceptors, which result from incomplete visualization through limited microscopic techniques.

NEW METHOD

The method was developed using dorsal intercarpal ligaments and dorsal regions of the scapholunate interosseous ligament from human cadaver wrists. Consecutive 70 µm thick cryosections were stained with immunofluorescence markers for protein S100B, neurotrophin receptor p75 (p75), protein gene product 9.5 (PGP 9.5) and 4',6-diamidino-2-phenylindole (DAPI). 3D images of sensory nerve endings were obtained using a confocal laser scanning microscope. Experimental point spread functions (PSF) were used to deconvolve images. Sensory nerve endings were localised in each section plane and classified according to Freeman and Wyke. Finally, confocal data was visualized as 3D-images.

RESULTS

The method produced excellent image quality, revealing detailed three-dimensional structures. The created 3D-model of sensory nerve endings could be analyzed in all three dimensions, augmenting visualization of the form and immunoreactive pattern of sensory nerve endings. Deconvolution with experimentally measured PSFs aided in enhancing image quality.

COMPARISON WITH EXISTING METHODS

Using a triple immunofluorescent staining method allows to visualize the structure of sensory nerve endings more precisely than techniques with serial analysis of different monostaining of neural markers. Imaging in three dimensions enhances morphologic details, which are limited in 2D-microscopy.

CONCLUSION

3D-triple immunofluorescence produces high quality visualization of mechanoreceptors, thereby improving their analysis. As an elaborate technique, it is ideal for defined research questions concerning the microstructure of sensory nerve endings.

Optical Tissue Clearing to Study the Intra-Pulmonary Biodistribution of Intravenously Delivered Mesenchymal Stromal Cells and Their Interactions with Host Lung Cells

Mesenchymal stromal cells (MSCs) injected intravenously are trapped in the capillaries of the lungs and die within the first 24 h. Studying the biodistribution and fate of labelled therapeutic cells in the 3D pulmonary context is important to understand their function in this organ and gain insights into their mechanisms of action. Optical tissue clearing enables volumetric cell tracking at single-cell resolution. Thus, we compared three optical tissue-clearing protocols (Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis (CUBIC), modified stabilised 3D imaging of solvent-cleared organs (s-DISCO) and ethyl cinnamate (ECi)) to evaluate their potential to track the biodistribution of human umbilical cord MSCs expressing the tdTomato fluorescence reporter and investigate how they interact with host cells in the mouse lung. The results showed that although CUBIC clearing is the only method that enables direct imaging of fluorescently labelled MSCs, combining s-DISCO or ECi with immunofluorescence or dye labelling allows the interaction of MSCs with endothelial and immune cells to be studied. Overall, this comparative study offers guidance on selecting an optical tissue-clearing method for cell tracking applications.

Fluorescent transgenic mouse models for whole-brain imaging in health and disease

A paradigm shift is occurring in neuroscience and in general in life sciences converting biomedical research from a descriptive discipline into a quantitative, predictive, actionable science. Living systems are becoming amenable to quantitative description, with profound consequences for our ability to predict biological phenomena. New experimental tools such as tissue clearing, whole-brain imaging, and genetic engineering technologies have opened the opportunity to embrace this new paradigm, allowing to extract anatomical features such as cell number, their full morphology, and even their structural connectivity. These tools will also allow the exploration of new features such as their geometrical arrangement, within and across brain regions. This would be especially important to better characterize brain function and pathological alterations in neurological, neurodevelopmental, and neurodegenerative disorders. New animal models for mapping fluorescent protein-expressing neurons and axon pathways in adult mice are key to this aim. As a result of both developments, relevant cell populations with endogenous fluorescence signals can be comprehensively and quantitatively mapped to whole-brain images acquired at submicron resolution. However, they present intrinsic limitations: weak fluorescent signals, unequal signal strength across the same cell type, lack of specificity of fluorescent labels, overlapping signals in cell types with dense labeling, or undetectable signal at distal parts of the neurons, among others. In this review, we discuss the recent advances in the development of fluorescent transgenic mouse models that overcome to some extent the technical and conceptual limitations and tradeoffs between different strategies. We also discuss the potential use of these strains for understanding disease.

Three-dimensional visualization of cerebral blood vessels and neural changes in thick ischemic rat brain slices using tissue clearing

Blood vessels are three-dimensional (3D) in structure and precisely connected. Conventional histological methods are unsuitable for their analysis because of the destruction of functionally important topological 3D vascular structures. Tissue optical clearing techniques enable extensive volume imaging and data analysis without destroying tissue. This study therefore applied a tissue clearing technique to acquire high-resolution 3D images of rat brain vasculature using light-sheet and confocal microscopies. Rats underwent middle cerebral artery occlusion for 45 min followed by 24 h reperfusion with lectin injected directly into the heart for vascular staining. For acquiring 3D images of rat brain vasculature, 3-mm-thick brain slices were reconstructed using tissue clearing and light-sheet microscopy. Subsequently, after 3D rendering, the fitting of blood vessels to a filament model was used for analysis. The results revealed a significant reduction in vessel diameter and density in the ischemic region compared to those in contralesional non-ischemic regions. Immunostaining of 0.5-mm-thick brain slices revealed considerable neuronal loss and increased astrocyte fluorescence intensity in the ipsilateral region. Thus, these methods can provide more accurate data by broadening the scope of the analyzed regions of interest for examining the 3D cerebrovascular system and neuronal changes occurring in various brain disorders.

Understanding Breast Cancers through Spatial and High-Resolution Visualization Using Imaging Technologies

Breast cancer is the most common cancer affecting women worldwide. Although many analyses and treatments have traditionally targeted the breast cancer cells themselves, recent studies have focused on investigating entire cancer tissues, including breast cancer cells. To understand the structure of breast cancer tissues, including breast cancer cells, it is necessary to investigate the three-dimensional location of the cells and/or proteins comprising the tissues and to clarify the relationship between the three-dimensional structure and malignant transformation or metastasis of breast cancers. In this review, we aim to summarize the methods for analyzing the three-dimensional structure of breast cancer tissue, paying particular attention to the recent technological advances in the combination of the tissue-clearing method and optical three-dimensional imaging. We also aimed to identify the latest methods for exploring the relationship between the three-dimensional cell arrangement in breast cancer tissues and the gene expression of each cell. Finally, we aimed to describe the three-dimensional imaging features of breast cancer tissues using noninvasive photoacoustic imaging methods.

cGAN-assisted imaging through stationary scattering media

Analyzing images taken through scattering media is challenging, owing to speckle decorrelations from perturbations in the media. For in-line imaging modalities, which are appealing because they are compact, require no moving parts, and are robust, negating the effects of such scattering becomes particularly challenging. Here we explore the use of conditional generative adversarial networks (cGANs) to mitigate the effects of the additional scatterers in in-line geometries, including digital holographic microscopy. Using light scattering simulations and experiments on objects of interest with and without additional scatterers, we find that cGANs can be quickly trained with minuscule datasets and can also efficiently learn the one-to-one statistical mapping between the cross-domain input-output image pairs. Importantly, the output images are faithful enough to enable quantitative feature extraction. We also show that with rapid training using only 20 image pairs, it is possible to negate this undesired scattering to accurately localize diffraction-limited impulses with high spatial accuracy, therefore transforming a shift variant system to a linear shift invariant (LSI) system.

Three-Dimensional Visualization With Tissue Clearing Uncovers Dynamic Alterations of Renal Resident Mononuclear Phagocytes After Acute Kidney Injury

Traditional histologic methods are limited in detecting dynamic changes in immune cells during acute kidney injury (AKI). Recently, optical tissue clearing combined with multiphoton microscopy (MPM) or light sheet fluorescence microscopy (LSFM) has become an emerging method for deep tissue evaluation and three-dimensional visualization. These new approaches have helped expand our understanding of tissue injury and repair processes, including tracing the changes in immune cells. We designed this study to investigate the morphological and functional alterations of renal mononuclear phagocytes (MNPs) in lipopolysaccharide (LPS)-induced AKI using renal clearing in CD11c-YFP mice. We also evaluated the effect of the NLRP3 inhibitor MCC950 to determine whether NLRP3 inhibition attenuates the activation of CD11c+ cells in an LPS-induced AKI model. Transverse sectioned whole mouse kidney imaging by LSFM showed that CD11c+ cells were mainly distributed in the cortex, especially the tubulointerstitial area. The number of CD11c+ cells was significantly more densely interspersed, particularly in periglomerular and perivascular lesions, in the saline-treated LPS-exposed kidney than in the control kidney. Deep imaging of the kidney cortex by MPM demonstrated an increased number of CD11c+ cells in the saline-treated LPS group compared with the control group. This quantitative alteration of CD11c+ cells in AKI was accompanied by morphological changes at high resolution, showing an increased number and level of dendrites. These morphological and behavioral changes in the saline-treated LPS group were accompanied by increased MHC class II and CD86 on CD11c-YFP+ cells. MCC950 attenuated the activation of CD11c+ cells after AKI and improved renal function. In conclusion, wide and deep three-dimensional visualization using MPM or LSFM combined with kidney clearing uncovers dynamic changes of renal MNPs, which are directly linked to renal function in AKI.