In-vivo and ex-vivo optical clearing methods for biological tissues: review

Achieving transient and reversible optical transparency in live mice with tartrazine

Optical imaging provides real-time visualization of tissues and cells at high spatial and temporal resolutions through techniques such as fluorescence microscopy, optical coherence tomography and photoacoustic imaging. However, overcoming light scattering, caused by mismatches in the refractive indices of tissue components such as water and lipids, still represents a major challenge, particularly when imaging through the thicker biological tissues of living animals. Despite advances in deep-tissue imaging, many optical methods struggle to achieve diffraction-limited resolution at depth or are unsuitable for use in live animals. Here we introduce a noninvasive approach to achieving transient and reversible optical transparency in live mice using absorbing dye molecules, using tartrazine as a representative example. Rooted in the fundamental physics of light-matter interactions, this approach enables reversible optical transparency in live animals and can be further applied ex vivo in freshly dissected tissues. In this Protocol, we detail the procedures for visualizing in vivo internal organs and muscle sarcomeres in the mouse abdomen and hindlimb through their respective transparency windows, showcasing a versatile approach for a variety of optical imaging applications in live animals. The entire protocol for an in vivo application can be implemented in just over 2 weeks by users with expertise in optical imaging and animal handling.

Myelinated fiber labeling and orientation mapping of the human brain with light-sheet fluorescence microscopy

The convoluted network of myelinated fibers that supports behavior, cognition, and sensory processing in the human brain is the source of its extraordinary complexity. Advancements in tissue optical clearing, 3D fluorescence microscopy, and automated image analysis have enabled unprecedented insights into the architecture of these networks. Here, we investigate the multiscale organization of myelinated fibers in human brain tissue from the brainstem, Broca's area, hippocampus, and primary visual cortex by exploiting a specific fiber staining method, light-sheet fluorescence microscopy (LSFM), and an advanced spatial orientation analysis tool. Using an optimized protocol that integrates tissue clearing with the lipophilic DiD probe to achieve uniform and deep myelinated fiber labeling, we generate micrometerresolution volumetric reconstructions of multiple brain regions through an inverted LSFM. Automated image processing, employing unsupervised 3D multiscale Frangi filters, provides orientation distribution functions and local orientation dispersion maps. This enables precise characterization of the directionality of white matter bundles, linking mesoscopic structural properties to orientation details computed at the native micrometric resolution of the LSFM apparatus. The presented workflow illustrates a robust platform for large-scale, high-resolution brain mapping, which may facilitate the investigation of pathological alterations with unparalleled spatial resolution and, furthermore, the validation of other neuroimaging modalities.

Brain-wide immunolabeling and tissue clearing applications for engram research

In recent years, there has been significant progress in memory research, driven by genetic and imaging technological advances that have given unprecedented access to individual memory traces or engrams. Although Karl Lashley argued since the 1930s that an engram is not confined to a particular area but rather distributed across the entire brain, most current studies have focused exclusively on a single or few brain regions. However, this compartmentalized approach overlooks the interactions between multiple brain regions, limiting our understanding of engram mechanisms. More recently, several studies have begun to investigate engrams across the brain, but research is still limited by a lack of standardized techniques capable of reconstructing multiple ensembles at single-cell resolution across the entire brain. In this review, we guide researchers through the latest technological advancements and discoveries in immediate early gene (IEG) techniques, tissue clearing methods, microscope modalities, and automated large-scale analysis. These innovations could propel the field forward in building brain-wide engram maps of normal and disease states, thus, providing unprecedented new insights. Ultimately, this review aims to bridge the gap between research focused on single brain regions and the need for a comprehensive understanding of whole-brain engrams, revealing new approaches for exploring the neuronal mechanisms underlying engrams.

Delivery and kinetics of immersion optical clearing agents in tissues: Optical imaging from ex vivo to in vivo

Advanced optical imaging provides a powerful tool for the structural and functional analysis of tissues with high resolution and contrast, but the imaging performance decreases as light propagates deeper into the tissue. Tissue optical clearing technique demonstrates an innovative way to realize deep-tissue imaging and have emerged substantially in the last two decades. Here, we briefly reviewed the basic principles of tissue optical clearing techniques in the view of delivery strategies via either free diffusion or external forces-driven advection, and the commonly-used optical techniques for monitoring kinetics of clearing agents in tissue, as well as their ex vivo to in vivo applications in multiple biomedical research fields. With future efforts on the even distribution of both clearing agents and probes, excavation of more effective clearing agents, and automation of tissue clearing processes, tissue optical clearing should provide more insights into the fundamental questions in biological events clinical diagnostics.

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.

T-CLEARE: a pilot community-driven tissue clearing protocol repository

Selecting and implementing a tissue clearing protocol is challenging. Established more than 100 years ago, tissue clearing is still a rapidly evolving field of research. There are currently many published protocols to choose from, and each performs better or worse across a range of key evaluation factors (e.g., speed, cost, tissue stability, fluorescence quenching). Additionally, tissue clearing protocols are often optimized for specific experimental contexts, and applying an existing protocol to a new problem can require a lengthy period of adaptation by trial and error. Although the primary literature and review articles provide a useful starting point for optimization, there is growing recognition that results can vary dramatically with changes to tissue type or antibody used. To help address this issue, we have developed a novel, freely available repository of tissue clearing protocols named T-CLEARE (Tissue CLEAring protocol REpository; https://doryworkspace.org/doryviz). T-CLEARE incorporates community responses to an open survey designed to capture details not commonly found in the scientific literature, including modifications to published protocols required for specific use cases and instances when tissue clearing protocols did not perform well (negative results). The goal of T-CLEARE is to help the community share evaluations and modifications of tissue clearing protocols for various tissue types and potentially identify best-in-class methods for a given application.

Quantitative cytoarchitectural phenotyping of deparaffinized human brain tissues

Advanced 3D imaging techniques and image segmentation and classification methods can profoundly transform biomedical research by offering deep insights into the cytoarchitecture of the human brain in relation to pathological conditions. Here, we propose a comprehensive pipeline for performing 3D imaging and automated quantitative cellular phenotyping on Formalin-Fixed Paraffin-Embedded (FFPE) human brain specimens, a valuable yet underutilized resource. We exploited the versatility of our method by applying it to different human specimens from both adult and pediatric, normal and abnormal brain regions. Quantitative data on neuronal volume, ellipticity, local density, and spatial clustering level were obtained from a machine learning-based analysis of the 3D cytoarchitectural organization of cells identified by different molecular markers in two subjects with malformations of cortical development (MCD). This approach will grant access to a wide range of physiological and pathological paraffin-embedded clinical specimens, allowing for volumetric imaging and quantitative analysis of human brain samples at cellular resolution. Possible genotype-phenotype correlations can be unveiled, providing new insights into the pathogenesis of various brain diseases and enlarging treatment opportunities.

Achieving optical transparency in live animals with absorbing molecules

Optical imaging plays a central role in biology and medicine but is hindered by light scattering in live tissue. We report the counterintuitive observation that strongly absorbing molecules can achieve optical transparency in live animals. We explored the physics behind this observation and found that when strongly absorbing molecules dissolve in water, they can modify the refractive index of the aqueous medium through the Kramers-Kronig relations to match that of high-index tissue components such as lipids. We have demonstrated that our straightforward approach can reversibly render a live mouse body transparent to allow visualization of a wide range of deep-seated structures and activities. This work suggests that the search for high-performance optical clearing agents should focus on strongly absorbing molecules.

Light in evaluation of molecular diffusion in tissues: Discrimination of pathologies

The evaluation of the diffusion properties of different molecules in tissues is a subject of great interest in various fields, such as dermatology/cosmetology, clinical medicine, implantology and food preservation. In this review, a discussion of recent studies that used kinetic spectroscopy measurements to evaluate such diffusion properties in various tissues is made. By immersing ex vivo tissues in agents or by topical application of those agents in vivo, their diffusion properties can be evaluated by kinetic collimated transmittance or diffuse reflectance spectroscopy. Using this method, recent studies were able to discriminate the diffusion properties of agents between healthy and diseased tissues, especially in the cases of cancer and diabetes mellitus. In the case of cancer, it was also possible to evaluate an increase of 5% in the mobile water content from the healthy to the cancerous colorectal and kidney tissues. Considering the application of some agents to living organisms or food products to protect them from deterioration during low temperature preservation (cryopreservation), and knowing that such agent inclusion may be reversed, some studies in these fields are also discussed. Considering the broadband application of the optical spectroscopy evaluation of the diffusion properties of agents in tissues and the physiological diagnostic data that such method can acquire, further studies concerning the optimization of fruit sweetness or evaluation of poison diffusion in tissues or antidote application for treatment optimization purposes are indicated as future perspectives.

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.

Functional ultrasound imaging of the human spinal cord

Utilizing the first in-human functional ultrasound imaging (fUSI) of the spinal cord, we demonstrate the integration of spinal functional responses to electrical stimulation. We record and characterize the hemodynamic responses of the spinal cord to a neuromodulatory intervention commonly used for treating pain and increasingly used for the restoration of sensorimotor and autonomic function. We found that the hemodynamic response to stimulation reflects a spatiotemporal modulation of the spinal cord circuitry not previously recognized. Our analytical capability offers a mechanism to assess blood flow changes with a new level of spatial and temporal precision in vivo and demonstrates that fUSI can decode the functional state of spinal networks in a single trial, which is of fundamental importance for developing real-time closed-loop neuromodulation systems. This work is a critical step toward developing a vital technique to study spinal cord function and effects of clinical neuromodulation.

Applications of Tissue Clearing in Central and Peripheral Nerves

The techniques of tissue clearing have been proposed and applied in anatomical and biomedical research since the 19th century. As we all know, the original study of the nervous system relied on serial ultrathin sections and stereoscopic techniques. The 3D visualization of the nervous system was established by software splicing and reconstruction. With the development of science and technology, microscope equipment had constantly been upgraded. Despite the great progress that has been made in this field, the workload is too complex, and it needs high technical requirements. Abundant mistakes due to manual sections were inescapable and structural integrity remained questionable. According to the classification of tissue transparency methods, we introduced the latest application of transparency methods in central and peripheral nerve research from optical imaging, molecular markers and data analysis. This review summarizes the application of transparent technology in neural pathways. We hope to provide some inspiration for the continuous optimization of tissue clearing methods.

Current Landscape of Advanced Imaging Tools for Pathology Diagnostics

Histopathology relies on century-old workflows of formalin fixation, paraffin embedding, sectioning, and staining tissue specimens on glass slides. Despite being robust, this conventional process is slow, labor-intensive, and limited to providing two-dimensional views. Emerging technologies promise to enhance and accelerate histopathology. Slide-free microscopy allows rapid imaging of fresh, unsectioned specimens, overcoming slide preparation delays. Methods such as fluorescence confocal microscopy, multiphoton microscopy, along with more recent innovations including microscopy with UV surface excitation and fluorescence-imitating brightfield imaging can generate images resembling conventional histology directly from the surface of tissue specimens. Slide-free microscopy enable applications such as rapid intraoperative margin assessment and, with appropriate technology, three-dimensional histopathology. Multiomics profiling techniques, including imaging mass spectrometry and Raman spectroscopy, provide highly multiplexed molecular maps of tissues, although clinical translation remains challenging. Artificial intelligence is aiding the adoption of new imaging modalities via virtual staining, which converts methods such as slide-free microscopy into synthetic brightfield-like or even molecularly informed images. Although not yet commonplace, these emerging technologies collectively demonstrate the potential to modernize histopathology. Artificial intelligence-assisted workflows will ease the transition to new imaging modalities. With further validation, these advances may transform the century-old conventional histopathology pipeline to better serve 21st-century medicine. This review provides an overview of these enabling technology platforms and discusses their potential impact.

Influence of optical clearing agents on the scattering properties of human nail bed and blood microrheological properties: In vivo and in vitro study

Optical clearing agents (OCAs) are substances that temporarily modify tissue's optical properties, enabling better imaging and light penetration. This study aimed to assess the impact of OCAs on the nail bed and blood using in vivo and in vitro optical methods. In the in vivo part, OCAs were applied to the nail bed, and optical coherence tomography and optical digital capillaroscopy were used to evaluate their effects on optical clearing and capillary blood flow, respectively. In the in vitro part, the collected blood samples were incubated with the OCA and blood aggregation properties were estimated using diffuse light scattering techniques. The results indicate that OCAs significantly influence the optical properties of the nail bed and blood microrheology. These findings suggest that OCAs hold promise for improving optical imaging and diagnostics, particularly for nail bed applications, and can modify blood microrheology.

Optical clearing of human skin: Molecular modeling and in vivo OCT study

The results of in vivo immersion optical clearing of human skin under the action of two different optical clearing agents (OCAs), such as an aqueous sucrose solution and a radiographic contrast agent Omnipaque™ 300 (iohexol), were obtained with the use of optical coherence tomography (OCT) method. The rate of reduction of light scattering coefficient, obtained through an averaged A-scan of the OCT image in the region of dermis within the depths from 350 to 700 μm, were determined to evaluate the efficiency of optical clearing (EOC). The correlations between the EOC and the energy of intermolecular interaction of OCAs with a fragment of collagen peptide have been established as a result of molecular modeling by quantum chemistry methods HF/STO3G/DFT/B3LYP/6-311G(d) of a number of OCAs (glycerol, iohexol, sucrose, ribose, fructose, glucose) with mimetic peptide of collagen (GPH)3 .

A novel computer-assisted tool for 3D imaging of programmed death-ligand 1 expression in immunofluorescence-stained and optically cleared breast cancer specimens

BACKGROUND

Programmed death-1 (PD-1) and programmed death-ligand 1 (PD-L1) are the two most common immune checkpoints targeted in triple-negative breast cancer (BC). Refining patient selection for immunotherapy is non-trivial and finding an appropriate digital pathology framework for spatial analysis of theranostic biomarkers for PD-1/PD-L1 inhibitors remains an unmet clinical need.

METHODS

We describe a novel computer-assisted tool for three-dimensional (3D) imaging of PD-L1 expression in immunofluorescence-stained and optically cleared BC specimens (n = 20). The proposed 3D framework appeared to be feasible and showed a high overall agreement with traditional, clinical-grade two-dimensional (2D) staining techniques. Additionally, the results obtained for automated immune cell detection and analysis of PD-L1 expression were satisfactory.

RESULTS

The spatial distribution of PD-L1 expression was heterogeneous across various BC tissue layers in the 3D space. Notably, there were six cases (30%) wherein PD-L1 expression levels along different layers crossed the 1% threshold for admitting patients to PD-1/PD-L1 inhibitors. The average PD-L1 expression in 3D space was different from that of traditional immunohistochemistry (IHC) in eight cases (40%). Pending further standardization and optimization, we expect that our technology will become a valuable addition for assessing PD-L1 expression in patients with BC.

CONCLUSION

Via a single round of immunofluorescence imaging, our approach may provide a considerable improvement in patient stratification for cancer immunotherapy as compared with standard techniques.

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.

Near-Infrared Transillumination for Macroscopic Functional Imaging of Animal Bodies

The classical transillumination technique has been revitalized through recent advancements in optical technology, enhancing its applicability in the realm of biomedical research. With a new perspective on near-axis scattered light, we have harnessed near-infrared (NIR) light to visualize intricate internal light-absorbing structures within animal bodies. By leveraging the principle of differentiation, we have extended the applicability of the Beer-Lambert law even in cases of scattering-dominant media, such as animal body tissues. This approach facilitates the visualization of dynamic physiological changes occurring within animal bodies, thereby enabling noninvasive, real-time imaging of macroscopic functionality in vivo. An important challenge inherent to transillumination imaging lies in the image blur caused by pronounced light scattering within body tissues. By extracting near-axis scattered components from the predominant diffusely scattered light, we have achieved cross-sectional imaging of animal bodies. Furthermore, we have introduced software-based techniques encompassing deconvolution using the point spread function and the application of deep learning principles to counteract the scattering effect. Finally, transillumination imaging has been elevated from two-dimensional to three-dimensional imaging. The effectiveness and applicability of these proposed techniques have been validated through comprehensive simulations and experiments involving human and animal subjects. As demonstrated through these studies, transillumination imaging coupled with emerging technologies offers a promising avenue for future biomedical applications.

A cellular resolution atlas of Broca's area

Brain cells are arranged in laminar, nuclear, or columnar structures, spanning a range of scales. Here, we construct a reliable cell census in the frontal lobe of human cerebral cortex at micrometer resolution in a magnetic resonance imaging (MRI)-referenced system using innovative imaging and analysis methodologies. MRI establishes a macroscopic reference coordinate system of laminar and cytoarchitectural boundaries. Cell counting is obtained with a digital stereological approach on the 3D reconstruction at cellular resolution from a custom-made inverted confocal light-sheet fluorescence microscope (LSFM). Mesoscale optical coherence tomography enables the registration of the distorted histological cell typing obtained with LSFM to the MRI-based atlas coordinate system. The outcome is an integrated high-resolution cellular census of Broca's area in a human postmortem specimen, within a whole-brain reference space atlas.

Ex vivo ocular perfusion model to study vascular physiology in the mouse eye

Several hypotheses have been tested to understand whole organ regulation in other organs such as the brain and kidney, but no such hypothesis has yet been proposed for ocular circulations. To some extent resolve this deficit our ex vivo mouse eye perfusion model takes the first step in elucidating the mechanisms controlling the individual components of the ocular circulation. Various isolated ocular vascular preparations have been utilized in studies of ocular vascular biology, physiology, and pharmacology, including studies on both normal and pathological conditions. However, there is still significant potential for further studies to improve our understanding of ocular circulation and its regulation. The choroid specifically is inaccessible to direct visualization due to the retina's high metabolic requirement with a transparency that cannot be compromised by an overly rich vascular network on the inner retinal side hindering the visualization of the choroid. In this technical paper, we provide a detailed description of all the steps to be followed from the enucleation of mouse eyes to cannulation of the ophthalmic artery and perfusion and ex vivo confocal microscopy imaging of the dynamic nature of the choroid circulation.

Tissue optical clearing and 3D imaging of virus infections

Imaging pathogens within 3D environment of biological tissues provides spatial information about their localization and interactions with the host. Technological advances in fluorescence microscopy and 3D image analysis now permit visualization and quantification of pathogens directly in large tissue volumes and in great detail. In recent years large volume imaging became an important tool in virology research helping to understand the properties of viruses and the host response to infection. In this chapter we give a review of fluorescence microscopy modalities and tissue optical clearing methods used for large volume tissue imaging. A summary of recent applications for virus research is provided with particular emphasis on studies using light sheet fluorescence microscopy. We describe the challenges and approaches for volumetric image analysis. Practical examples of volumetric imaging implemented in virology laboratories and addressing specialized research questions, such as virus tropism and immune host response are described. We conclude with an overview of the emerging technologies and their potential for virus research.

Computational approaches for evaluating morphological changes in the corneal stroma associated with decellularization

Decellularized corneas offer a promising and sustainable source of replacement grafts, mimicking native tissue and reducing the risk of immune rejection post-transplantation. Despite great success in achieving acellular scaffolds, little consensus exists regarding the quality of the decellularized extracellular matrix. Metrics used to evaluate extracellular matrix performance are study-specific, subjective, and semi-quantitative. Thus, this work focused on developing a computational method to examine the effectiveness of corneal decellularization. We combined conventional semi-quantitative histological assessments and automated scaffold evaluations based on textual image analyses to assess decellularization efficiency. Our study highlights that it is possible to develop contemporary machine learning (ML) models based on random forests and support vector machine algorithms, which can identify regions of interest in acellularized corneal stromal tissue with relatively high accuracy. These results provide a platform for developing machine learning biosensing systems for evaluating subtle morphological changes in decellularized scaffolds, which are crucial for assessing their functionality.

A scalable corneal xenograft platform: simultaneous opportunities for tissue engineering and circular economic sustainability by repurposing slaughterhouse waste

Introduction: Corneal disease is a leading cause of blindness globally that stems from various etiologies. High-throughput platforms that can generate substantial quantities of corneal grafts will be invaluable in addressing the existing global demand for keratoplasty. Slaughterhouses generate substantial quantities of underutilized biological waste that can be repurposed to reduce current environmentally unfriendly practices. Such efforts to support sustainability can simultaneously drive the development of bioartificial keratoprostheses. Methods: Scores of discarded eyes from the prominent Arabian sheep breeds in our surrounding region of the United Arab Emirates (UAE) were repurposed to generate native and acellular corneal keratoprostheses. Acellular corneal scaffolds were created using a whole-eye immersion/agitation-based decellularization technique with a widely available, eco-friendly, and inexpensive 4% zwitterionic biosurfactant solution (Ecover, Malle, Belgium). Conventional approaches like DNA quantification, ECM fibril organization, scaffold dimensions, ocular transparency and transmittance, surface tension measurements, and Fourier-transform infrared (FTIR) spectroscopy were used to examine corneal scaffold composition. Results: Using this high-throughput system, we effectively removed over 95% of the native DNA from native corneas while retaining the innate microarchitecture that supported substantial light transmission (over 70%) after reversing opacity, a well-established hallmark of decellularization and long-term native corneal storage, with glycerol. FTIR data revealed the absence of spectral peaks in the frequency range 2849 cm-1 to 3075 cm-1, indicating the effective removal of the residual biosurfactant post-decellularization. Surface tension studies confirmed the FTIR data by capturing the surfactant's progressive and effectual removal through tension measurements ranging from approximately 35 mN/m for the 4% decellularizing agent to 70 mN/m for elutes highlighting the effective removal of the detergent. Discussion: To our knowledge, this is the first dataset to be generated outlining a platform that can produce dozens of ovine acellular corneal scaffolds that effectively preserve ocular transparency, transmittance, and ECM components using an eco-friendly surfactant. Analogously, decellularization technologies can support corneal regeneration with attributes comparable to native xenografts. Thus, this study presents a simplified, inexpensive, and scalable high-throughput corneal xenograft platform to support tissue engineering, regenerative medicine, and circular economic sustainability.

A Guide to Perform 3D Histology of Biological Tissues with Fluorescence Microscopy

The analysis of histological alterations in all types of tissue is of primary importance in pathology for highly accurate and robust diagnosis. Recent advances in tissue clearing and fluorescence microscopy made the study of the anatomy of biological tissue possible in three dimensions. The combination of these techniques with classical hematoxylin and eosin (H&E) staining has led to the birth of three-dimensional (3D) histology. Here, we present an overview of the state-of-the-art methods, highlighting the optimal combinations of different clearing methods and advanced fluorescence microscopy techniques for the investigation of all types of biological tissues. We employed fluorescence nuclear and eosin Y staining that enabled us to obtain hematoxylin and eosin pseudo-coloring comparable with the gold standard H&E analysis. The computational reconstructions obtained with 3D optical imaging can be analyzed by a pathologist without any specific training in volumetric microscopy, paving the way for new biomedical applications in clinical pathology.

A novel ex vivo assay to define charge-balanced electrical stimulation parameters for neural precursor cell activation in vivo

Endogenous neural stem cells and their progeny (together termed neural precursor cells (NPCs)) are promising candidates to facilitate neuroregeneration. Charge-balanced biphasic monopolar stimulation (BPMP) is a clinically relevant approach that can activate NPCs both in vitro and in vivo. Herein, we established a novel ex vivo stimulation system to optimize the efficacy of BPMP electric field (EF) application in activating endogenous NPCs. Using the ex vivo system, we discerned that cathodal amplitude of 200 μA resulted in the greatest NPC pool expansion and enhanced cathodal migration. Application of the same stimulation parameters in vivo resulted in the same NPC activation in the mouse brain. The design and implementation of the novel ex vivo model bridges the gap between in vitro and in vivo systems, enabling a moderate throughput stimulation system to explore and optimize EF parameters that can be applied to clinically relevant brain injury/disease models.

T-CLEARE: A Pilot Community-Driven Tissue-Clearing Protocol Repository

Selecting and implementing a tissue-clearing protocol is challenging. Established more than 100 years ago, tissue clearing is still a rapidly evolving field of research. There are currently many published protocols to choose from, and each performs better or worse across a range of key evaluation factors (e.g., speed, cost, tissue stability, fluorescence quenching). Additionally, tissue-clearing protocols are often optimized for specific experimental contexts, and applying an existing protocol to a new problem can require a lengthy period of adaptation by trial and error. Although the primary literature and review articles provide a useful starting point for optimization, there is growing recognition that many articles do not provide sufficient detail to replicate or reproduce experimental results. To help address this issue, we have developed a novel, freely available repository of tissue-clearing protocols named T-CLEARE (Tissue CLEAring protocol REpository; https://doryworkspace.org/doryviz). T-CLEARE incorporates community responses to an open survey designed to capture details not commonly found in the scientific literature, including modifications to published protocols required for specific use cases and instances when tissue-clearing protocols did not perform well (negative results). The goal of T-CLEARE is to provide a forum for the community to share evaluations and modifications of tissue-clearing protocols for various tissue types and potentially identify best-in-class methods for a given application.

Label-free cleared tissue microscopy and machine learning for 3D histopathology of biomaterial implants

Tissue clearing of whole intact organs has enhanced imaging by enabling the exploration of tissue structure at a subcellular level in three-dimensional space. Although clearing and imaging of the whole organ have been used to study tissue biology, the microenvironment in which cells evolve to adapt to biomaterial implants or allografts in the body is poorly understood. Obtaining high-resolution information from complex cell-biomaterial interactions with volumetric landscapes represents a key challenge in the fields of biomaterials and regenerative medicine. To provide a new approach to examine how tissue responds to biomaterial implants, we apply cleared tissue light-sheet microscopy and three-dimensional reconstruction to utilize the wealth of autofluorescence information for visualizing and contrasting anatomical structures. This study demonstrates the adaptability of the clearing and imaging technique to provide sub-cellular resolution (0.6 μm isotropic) 3D maps of various tissue types, using samples from fully intact peritoneal organs to volumetric muscle loss injury specimens. Specifically, in the volumetric muscle loss injury model, we provide 3D visualization of the implanted extracellular matrix biomaterial in the wound bed of the quadricep muscle groups and further apply computational-driven image classification to analyze the autofluorescence spectrum at multiple emission wavelengths to categorize tissue types at the injured site interacting with the biomaterial scaffolds.

Spatio-Temporal Dynamics of Diffusion-Associated Deformations of Biological Tissues and Polyacrylamide Gels Observed with Optical Coherence Elastography

In this work, we use the method of optical coherence elastography (OCE) to enable quantitative, spatially resolved visualization of diffusion-associated deformations in the areas of maximum concentration gradients during diffusion of hyperosmotic substances in cartilaginous tissue and polyacrylamide gels. At high concentration gradients, alternating sign, near-surface deformations in porous moisture-saturated materials are observed in the first minutes of diffusion. For cartilage, the kinetics of osmotic deformations visualized by OCE, as well as the optical transmittance variations caused by the diffusion, were comparatively analyzed for several substances that are often used as optical clearing agents, i.e., glycerol, polypropylene, PEG-400 and iohexol, for which the effective diffusion coefficients were found to be 7.4 ± 1.8, 5.0 ± 0.8, 4.4 ± 0.8 and 4.6 ± 0.9 × 10^-6 cm²/s, respectively. For the osmotically induced shrinkage amplitude, the influence of the organic alcohol concentration appears to be more significant than the influence of its molecular weight. The rate and amplitude of osmotically induced shrinkage and dilatation in polyacrylamide gels is found to clearly depend on the degree of their crosslinking. The obtained results show that observation of osmotic strains with the developed OCE technique can be applied for structural characterization of a wide range of porous materials, including biopolymers. In addition, it may be promising for revealing alterations in the diffusivity/permeability of biological tissues that are potentially associated with various diseases.

ROCKETS - a novel one-for-all toolbox for light sheet microscopy in drug discovery

Advancing novel immunotherapy strategies requires refined tools in preclinical research to thoroughly assess drug targets, biodistribution, safety, and efficacy. Light sheet fluorescence microscopy (LSFM) offers unprecedented fast volumetric ex vivo imaging of large tissue samples in high resolution. Yet, to date laborious and unstandardized tissue processing procedures have limited throughput and broader applications in immunological research. Therefore, we developed a simple and harmonized protocol for processing, clearing and imaging of all mouse organs and even entire mouse bodies. Applying this Rapid Optical Clearing Kit for Enhanced Tissue Scanning (ROCKETS) in combination with LSFM allowed us to comprehensively study the in vivo biodistribution of an antibody targeting Epithelial Cell Adhesion Molecule (EpCAM) in 3D. Quantitative high-resolution scans of whole organs did not only reveal known EpCAM expression patterns but, importantly, uncovered several new EpCAM-binding sites. We identified gustatory papillae of the tongue, choroid plexi in the brain and duodenal papillae as previously unanticipated locations of high EpCAM expression. Subsequently, we confirmed high EpCAM expression also in human tongue and duodenal specimens. Choroid plexi and duodenal papillae may be considered as particularly sensitive sites due to their importance for liquor production or as critical junctions draining bile and digestive pancreatic enzymes into the small bowel, respectively. These newly gained insights appear highly relevant for clinical translation of EpCAM-addressing immunotherapies. Thus, ROCKETS in combination with LSFM may help to set new standards for preclinical evaluation of immunotherapeutic strategies. In conclusion, we propose ROCKETS as an ideal platform for a broader application of LSFM in immunological research optimally suited for quantitative co-localization studies of immunotherapeutic drugs and defined cell populations in the microanatomical context of organs or even whole mice.

Multiscale Label-Free Imaging of Fibrillar Collagen in the Tumor Microenvironment

With recent advances in cancer therapeutics, there is a great need for improved imaging methods for characterizing cancer onset and progression in a quantitative and actionable way. Collagen, the most abundant extracellular matrix protein in the tumor microenvironment (and the body in general), plays a multifaceted role, both hindering and promoting cancer invasion and progression. Collagen deposition can defend the tumor with immunosuppressive effects, while aligned collagen fiber structures can enable tumor cell migration, aiding invasion and metastasis. Given the complex role of collagen fiber organization and topology, imaging has been a tool of choice to characterize these changes on multiple spatial scales, from the organ and tumor scale to cellular and subcellular level. Macroscale density already aids in the detection and diagnosis of solid cancers, but progress is being made to integrate finer microscale features into the process. Here we review imaging modalities ranging from optical methods of second harmonic generation (SHG), polarized light microscopy (PLM), and optical coherence tomography (OCT) to the medical imaging approaches of ultrasound and magnetic resonance imaging (MRI). These methods have enabled scientists and clinicians to better understand the impact collagen structure has on the tumor environment, at both the bulk scale (density) and microscale (fibrillar structure) levels. We focus on imaging methods with the potential to both examine the collagen structure in as natural a state as possible and still be clinically amenable, with an emphasis on label-free strategies, exploiting intrinsic optical properties of collagen fibers.

High-fidelity optical diffraction tomography of live organisms using iodixanol refractive index matching

Optical diffraction tomography (ODT) enables the three-dimensional (3D) refractive index (RI) reconstruction. However, when the RI difference between a sample and a medium increases, the effects of light scattering become significant, preventing the acquisition of high-quality and accurate RI reconstructions. Herein, we present a method for high-fidelity ODT by introducing non-toxic RI matching media. Optimally reducing the RI contrast enhances the fidelity and accuracy of 3D RI reconstruction, enabling visualization of the morphology and intra-organization of live biological samples without producing toxic effects. We validate our method using various biological organisms, including C. albicans and C. elegans.

MAX: a simple, affordable, and rapid tissue clearing reagent for 3D imaging of wide variety of biological specimens

Transparency of biological specimens is crucial to obtaining detailed 3-dimensional images and understanding the structure and function of biological specimens. This transparency or tissue clearing can be achieved by adjusting the refractive index (RI) with embedding media and removing light barriers such as lipids, inorganic deposits, and pigments. Many currently available protocols consist of multiple steps to achieve sufficient transparency, making the process complex and time-consuming. Thus, in this study, we tailored the recipe for RI adjustment media named MAX based on the recently reported MACS protocol to achieve a single-step procedure, especially for ECM-rich tissues. This was achieved by the improvement of the tissue penetrability of the RI-matching reagent by combining MXDA with sucrose or iodixanol. While this was sufficient for the 3D imaging in many applications, MAX can also be combined with modular processes for de-lipidation, de-coloration, and de-calcification to further maximize the transparency depending on the special features of the tissues. Our approach provides an easy alternative for tissue clearing and 3D imaging.

Post mortem mapping of connectional anatomy for the validation of diffusion MRI

Diffusion MRI (dMRI) is a unique tool for the study of brain circuitry, as it allows us to image both the macroscopic trajectories and the microstructural properties of axon bundles in vivo. The Human Connectome Project ushered in an era of impressive advances in dMRI acquisition and analysis. As a result of these efforts, the quality of dMRI data that could be acquired in vivo improved substantially, and large collections of such data became widely available. Despite this progress, the main limitation of dMRI remains: it does not image axons directly, but only provides indirect measurements based on the diffusion of water molecules. Thus, it must be validated by methods that allow direct visualization of axons but that can only be performed in post mortem brain tissue. In this review, we discuss methods for validating the various features of connectional anatomy that are extracted from dMRI, both at the macro-scale (trajectories of axon bundles), and at micro-scale (axonal orientations and other microstructural properties). We present a range of validation tools, including anatomic tracer studies, Klingler's dissection, myelin stains, label-free optical imaging techniques, and others. We provide an overview of the basic principles of each technique, its limitations, and what it has taught us so far about the accuracy of different dMRI acquisition and analysis approaches.

Immersion optical clearing of adipose tissue in rats: ex vivo and in vivo studies

Optical clearing (OC) of adipose tissue has not been studied enough, although it can be promising in medical applications, including surgery and cosmetology, for example, to visualize blood vessels or increase the permeability of tissues to laser beams. The main objective of this work is to develop technology for OC of abdominal adipose tissue in vivo using hyperosmotic optical clearing agents (OCAs). The maximum OC effect (77%) was observed for ex vivo rat adipose tissue samples exposed to OCA on fructose basis for 90 minutes. For in vivo studies, the maximum effect of OC (65%) was observed when using OCA based on diatrizoic acid and dimethylsulfoxide for 120 minutes. Histological analysis showed that in vivo application of OCAs may induce a limited local necrosis of fat cells. The efficiency of OC correlated with local tissue damage through cell necrosis due to accompanied cell lipolysis.

Challenges and advances in optical 3D mesoscale imaging

Optical mesoscale imaging is a rapidly developing field that allows the visualisation of larger samples than is possible with standard light microscopy, and fills a gap between cell and organism resolution. It spans from advanced fluorescence imaging of micrometric cell clusters to centimetre-size complete organisms. However, with larger volume specimens, new problems arise. Imaging deeper into tissues at high resolution poses challenges ranging from optical distortions to shadowing from opaque structures. This manuscript discusses the latest developments in mesoscale imaging and highlights limitations, namely labelling, clearing, absorption, scattering, and also sample handling. We then focus on approaches that seek to turn mesoscale imaging into a more quantitative technique, analogous to quantitative tomography in medical imaging, highlighting a future role for digital and physical phantoms as well as artificial intelligence.

3D molecular phenotyping of cleared human brain tissues with light-sheet fluorescence microscopy

The combination of optical tissue transparency with immunofluorescence allows the molecular characterization of biological tissues in 3D. However, adult human organs are particularly challenging to become transparent because of the autofluorescence contributions of aged tissues. To meet this challenge, we optimized SHORT (SWITCH-H2O2-antigen Retrieval-TDE), a procedure based on standard histological treatments in combination with a refined clearing procedure to clear and label portions of the human brain. 3D histological characterization with multiple molecules is performed on cleared samples with a combination of multi-colors and multi-rounds labeling. By performing fast 3D imaging of the samples with a custom-made inverted light-sheet fluorescence microscope (LSFM), we reveal fine details of intact human brain slabs at subcellular resolution. Overall, we proposed a scalable and versatile technology that in combination with LSFM allows mapping the cellular and molecular architecture of the human brain, paving the way to reconstruct the entire organ.

Long-term in vivo imaging of mouse spinal cord through an optically cleared intervertebral window

The spinal cord accounts for the main communication pathway between the brain and the peripheral nervous system. Spinal cord injury is a devastating and largely irreversible neurological trauma, and can result in lifelong disability and paralysis with no available cure. In vivo spinal cord imaging in mouse models without introducing immunological artifacts is critical to understand spinal cord pathology and discover effective treatments. We developed a minimally invasive intervertebral window by retaining the ligamentum flavum to protect the underlying spinal cord. By introducing an optical clearing method, we achieve repeated two-photon fluorescence and stimulated Raman scattering imaging at subcellular resolution with up to 15 imaging sessions over 6-167 days and observe no inflammatory response. Using this optically cleared intervertebral window, we study neuron-glia dynamics following laser axotomy and observe strengthened contact of microglia with the nodes of Ranvier during axonal degeneration. By enabling long-term, repetitive, stable, high-resolution and inflammation-free imaging of mouse spinal cord, our method provides a reliable platform in the research aiming at interpretation of spinal cord physiology and pathology.

Optical Clearing Agents for Optical Imaging Through Cartilage Tympanoplasties: A Preclinical Feasibility Study

HYPOTHESIS

Optical clearing agents (OCAs) can render cartilage tympanoplasty grafts sufficiently transparent to permit visualization of middle ear structures in an operated ear using optical coherence tomography (OCT) imaging.

METHODS

Pieces of human tragal cartilage were treated with glycerol, a commonly used OCA. A reference reflector was imaged with OCT through the tympanoplasty as it cleared and the optical attenuation of the graft was measured. The reversibility of clearing and the dimensional changes associated with glycerol absorption were also measured. In a separate experiment, a human cadaveric temporal bone was prepared to simulate an ossiculoplasty surgery with cartilage replacement of the tympanic membrane. A partial ossicular replacement prosthesis (PORP) inserted in the ear was imaged with OCT through a 0.4mm cartilage graft optically cleared with glycerol.

MAIN OUTCOME MEASURE

The optical attenuation of 0.4mm cartilage grafts decreased at 2.3+/-1.1 dB/min following treatment with glycerol, reaching a total decrease in attenuation of 13.6+/-5.9 dB after 7 minutes. The optical and dimensional effects of glycerol absorption were reversable following saline washout. In the temporal bone preparation, treatment of a cartilage graft with glycerol resulted in a 13 dB increase in signal-to-noise ratio and a 13 dB increase in contrast for visualizing the PORP through the graft with OCT.

CONCLUSIONS

Optical clearing agents offer a potential pathway towards optical coherence tomography imaging of the middle ear in post-surgical ears with cartilage grafts.

Improving SERS bioimaging of subcutaneous phantom in vivo with optical clearing

Surface-enhanced Raman scattering (SERS) has proven to be a promising technique for different types of imaging including preoperative and intraoperative in vivo tumor visualization. However, the strong scattering of the turbid tissue limits its use in subcutaneous areas. In this article, we used an optical clearing technique to improve the SERS signal from a subcutaneous tumor phantom. The phantom is a 2 mm sphere of calcium alginate with incorporated petal-like gap-enhanced Raman tags. The use of optical clearing increases the SERS signal target-to-background ratio for 5 times and allow to decrease the total imaging time for at least 10 times. In addition, SERS imaging assisted with optical clearing made it possible to more precisely determine the shape and boundaries of the implanted phantom. The combination of optical clearing and SERS is a promising strategy for the clinical imaging of subcutaneous objects that are usually shielded by dermal tissue.

Assessment of Extramammary Paget Disease by Two-Photon Microscopy

Two-photon microscopy techniques are non-linear optical imaging methods which are gaining momentum in the investigation of fixed tissue sections, fresh tissue or even for in vivo experiments. Two-photon excited fluorescence and second harmonic generation are two non-linear optical contrast mechanisms which can be simultaneously used for offering complementary information on the tissue architecture. While the former can originate from endogenous autofluorescence sources (e.g., NADH, FAD, elastin, keratin, lipofuscins, or melanin), or exogenous eosin, the latter is generated in fibrillar structures within living organisms (e.g., collagen and myosin). Here we test the ability of both these contrast mechanisms to highlight features of the extramammary Paget disease on fixed tissue sections prepared for standard histological examination using immunohistochemical markers and hematoxylin and eosin staining. We also demonstrate the label-free abilities of both imaging techniques to highlight histological features on unstained fixed tissue sections. The study demonstrated that two-photon microscopy can detect specific cellular features of the extramammary Paget disease in good correlation with histopathological results.

Exploiting Nanomaterials for Optical Coherence Tomography and Photoacoustic Imaging in Nanodentistry

There is already a societal awareness of the growing impact of nanoscience and nanotechnology, with nanomaterials (with at least one dimension less than 100 nm) now incorporated in items as diverse as mobile phones, clothes or dentifrices. In the healthcare area, nanoparticles of biocompatible materials have already been used for cancer treatment or bioimaging enhancement. Nanotechnology in dentistry, or nanodentistry, has already found some developments in dental nanomaterials for caries management, restorative dentistry and orthodontic adhesives. In this review, we present state-of-the-art scientific development in nanodentistry with an emphasis on two imaging techniques exploiting nanomaterials: optical coherence tomography (OCT) and photoacoustic imaging (PAI). Examples will be given using OCT with nanomaterials to enhance the acquired imaging, acting as optical clearing agents for OCT. A novel application of gold nanoparticles and nanorods for imaging enhancement of incipient occlusal caries using OCT will be described. Additionally, we will highlight how the OCT technique can be properly managed to provide imaging with spatial resolution down to 10's-100's nm resolution. For PAI, we will describe how new nanoparticles, namely TiN, prepared by femtosecond laser ablation, can be used in nanodentistry and will show photoacoustic microscopy and tomography images for such exogenous agents.

Slide Over: Advances in Slide-Free Optical Microscopy as Drivers of Diagnostic Pathology

Conventional analysis using clinical histopathology is based on bright-field microscopy of thinly sliced tissue specimens. Although bright-field microscopy is a simple and robust method of examining microscope slides, the preparation of the slides needed is a lengthy and labor-intensive process. Slide-free histopathology, however, uses direct imaging of intact, minimally processed tissue samples using advanced optical-imaging systems, bypassing the extended workflow now required for the preparation of tissue sections. This article explains the technical basis of slide-free microscopy, reviews common slide-free optical microscopy techniques, and discusses the opportunities and challenges involved in clinical implementation.

Use of High-Refractive Index Hydrogels and Tissue Clearing for Large Biological Sample Imaging

Recent advances in tissue clearing and light sheet fluorescence microscopy have improved insights into and understanding of tissue morphology and disease pathology by imaging large samples without the requirement of histological sectioning. However, sample handling and conservation of sample integrity during lengthy staining and acquisition protocols remains a challenge. This study overcomes these challenges with acrylamide hydrogels synthesised to match the refractive index of solutions typically utilised in aqueous tissue clearing protocols. These hydrogels have a high-water content (82.0 ± 3.7% by weight). The gels are stable over time and FITC-IgG readily permeated into and effluxed out of them. Whilst the gels deformed and/or swelled over time in some commonly used solutions, this was overcome by using a previously described custom refractive index matched solution. To validate their use, CUBIC cleared mouse tissues and whole embryos were embedded in hydrogels, stained using fluorescent small molecule dyes, labels and antibodies and successfully imaged using light sheet fluorescence microscopy. In conclusion, the high water content, high refractive index hydrogels described in this study have broad applicability to research that delves into pathophysiological processes by stabilising and protecting large and fragile samples.

Optical clearing of tissues: Issues of antimicrobial phototherapy and drug delivery

This review presents principles and novelties in the field of tissue optical clearing (TOC) technology, as well as application for optical monitoring of drug delivery and effective antimicrobial phototherapy. TOC is based on altering the optical properties of tissue through the introduction of immersion optical cleaning agents (OCA), which impregnate the tissue of interest. We also analyze various methods and kinetics of delivery of photodynamic agents, nanoantibiotics and their mixtures with OCAs into the tissue depth in the context of antimicrobial and antifungal phototherapy. In vitro and in vivo studies of antimicrobial phototherapies, such as photodynamic, photothermal plasmonic and photocatalytic, are summarized, and the prospects of a new TOC technology for effective killing of pathogens are discussed.

Neurophotonic tools for microscopic measurements and manipulation: status report

Neurophotonics was launched in 2014 coinciding with the launch of the BRAIN Initiative focused on development of technologies for advancement of neuroscience. For the last seven years, Neurophotonics' agenda has been well aligned with this focus on neurotechnologies featuring new optical methods and tools applicable to brain studies. While the BRAIN Initiative 2.0 is pivoting towards applications of these novel tools in the quest to understand the brain, this status report reviews an extensive and diverse toolkit of novel methods to explore brain function that have emerged from the BRAIN Initiative and related large-scale efforts for measurement and manipulation of brain structure and function. Here, we focus on neurophotonic tools mostly applicable to animal studies. A companion report, scheduled to appear later this year, will cover diffuse optical imaging methods applicable to noninvasive human studies. For each domain, we outline the current state-of-the-art of the respective technologies, identify the areas where innovation is needed, and provide an outlook for the future directions.