3D virtual histology of murine kidneys -high resolution visualization of pathological alterations by micro computed tomography

X-Ray-Based 3D Histopathology of the Kidney Using Cryogenic Contrast-Enhanced MicroCT

The kidney's microstructure, which comprises a highly convoluted tubular and vascular network, can only be partially revealed using classical 2D histology. Considering that the kidney's microstructure is closely related to its function and is often affected by pathologies, there is a need for powerful and high-resolution 3D imaging techniques to visualize the microstructure. Here, we present how cryogenic contrast-enhanced microCT (cryo-CECT) allowed 3D visualization of glomeruli, tubuli, and vasculature. By comparing different contrast-enhancing staining agents and freezing protocols, we found that the preferred sample preparation protocol was the combination of staining with 1:2 hafnium(IV)-substituted Wells-Dawson polyoxometalate and freezing by submersion in isopentane at -78°C. This optimized protocol showed to be highly sensitive, allowing to detect small pathology-induced microstructural changes in a mouse model of mild trauma-related acute kidney injury after thorax trauma and hemorrhagic shock. In summary, we demonstrated that cryo-CECT is an effective 3D histopathological tool that allows to enhance our understanding of kidney tissue microstructure and their related function.

Engineering the future of 3D pathology

In recent years, technological advances in tissue preparation, high-throughput volumetric microscopy, and computational infrastructure have enabled rapid developments in nondestructive 3D pathology, in which high-resolution histologic datasets are obtained from thick tissue specimens, such as whole biopsies, without the need for physical sectioning onto glass slides. While 3D pathology generates massive datasets that are attractive for automated computational analysis, there is also a desire to use 3D pathology to improve the visual assessment of tissue histology. In this perspective, we discuss and provide examples of potential advantages of 3D pathology for the visual assessment of clinical specimens and the challenges of dealing with large 3D datasets (of individual or multiple specimens) that pathologists have not been trained to interpret. We discuss the need for artificial intelligence triaging algorithms and explainable analysis methods to assist pathologists or other domain experts in the interpretation of these novel, often complex, large datasets.

Optimal Agents for Visualizing Collagen Tissue Microarchitecture Using Contrast-Enhanced MicroCT

Micro-computed tomography (microCT) is a common tool for the visualization of the internal composition of organic tissues. Collagen comprises approximately 25-35% of the whole-body protein content in mammals, and the structure and arrangement of collagen fibers contribute significantly to the integrity of tissues. Collagen type I is also frequently used as a key structural component in tissue-engineered and bioprinted tissues. However, the imaging of collagenous tissues is limited by their inherently low X-ray attenuation, which makes them indistinguishable from most other soft tissues. An imaging contrast agent that selectively alters X-ray attenuation is thus essential to properly visualize collagenous tissue using a standard X-ray tube microCT scanner. This review compares various contrast-enhanced techniques reported in the literature for MicroCT visualization of collagen-based tissues. An ideal microCT contrast agent would meet the following criteria: (1) it diffuses through the tissue quickly; (2) it does not deform or impair the object being imaged; and (3) it provides sufficient image contrast for reliable visualization of the orientation of individual fibers within the collagen network. The relative benefits and disadvantages of each method are discussed. Lugol's solution (I3K), phosphotungstic acid (H3PW12O40), mercury(II) chloride (HgCl2), and Wells-Dawson polyoxometalates came closest to fitting the criteria. While none of the contrast agents discussed in the literature met all criteria, each one has advantages to consider in the context of specific lab capabilities and imaging priorities.

A hybrid approach to full-scale reconstruction of renal arterial network

The renal vasculature, acting as a resource distribution network, plays an important role in both the physiology and pathophysiology of the kidney. However, no imaging techniques allow an assessment of the structure and function of the renal vasculature due to limited spatial and temporal resolution. To develop realistic computer simulations of renal function, and to develop new image-based diagnostic methods based on artificial intelligence, it is necessary to have a realistic full-scale model of the renal vasculature. We propose a hybrid framework to build subject-specific models of the renal vascular network by using semi-automated segmentation of large arteries and estimation of cortex area from a micro-CT scan as a starting point, and by adopting the Global Constructive Optimization algorithm for generating smaller vessels. Our results show a close agreement between the reconstructed vasculature and existing anatomical data obtained from a rat kidney with respect to morphometric and hemodynamic parameters.

Three-dimensional analysis of human pancreatic cancer specimens by phase-contrast based X-ray tomography - the next dimension of diagnosis

BACKGROUND

The worldwide increase of pancreatic ductal adenocarcinoma (PDAC), which still has one of the lowest survival rates, requires novel imaging tools to improve early detection and to refine diagnosis. Therefore, the aim of this study was to assess the feasibility of propagation-based phase-contrast X-ray computed tomography of already paraffin-embedded and unlabeled human pancreatic tumor tissue to achieve a detailed three-dimensional (3D) view of the tumor sample in its entirety.

METHODS

Punch biopsies of areas of particular interest were taken from paraffin blocks after initial histological analysis of hematoxylin and eosin stained tumor sections. To cover the entire 3.5 mm diameter of the punch biopsy, nine individual tomograms with overlapping regions were acquired in a synchrotron parallel beam configuration and stitched together after data reconstruction. Due to the intrinsic contrast based on electron density differences of tissue components and a voxel size of 1.3 μm achieved PDAC and its precursors were clearly identified.

RESULTS

Characteristic tissue structures for PDAC and its precursors, such as dilated pancreatic ducts, altered ductal epithelium, diffuse immune cell infiltrations, increased occurrence of tumor stroma and perineural invasion were clearly identified. Certain structures of interest were visualized in three dimensions throughout the tissue punch. Pancreatic duct ectasia of different caliber and atypical shape as well as perineural infiltration could be contiguously traced by viewing serial tomographic slices and by applying semi-automatic segmentation. Histological validation of corresponding sections confirmed the former identified PDAC features.

CONCLUSION

In conclusion, virtual 3D histology via phase-contrast X-ray tomography visualizes diagnostically relevant tissue structures of PDAC in their entirety, preserving tissue integrity in label-free, paraffin embedded tissue biopsies. In the future, this will not only enable a more comprehensive diagnosis but also a possible identification of new 3D imaging tumor markers.

Analysis of RNA processing directly from spatial transcriptomics data reveals previously unknown regulation

Technical advances have led to an explosion in the amount of biological data available in recent years, especially in the field of RNA sequencing. Specifically, spatial transcriptomics (ST) datasets, which allow each RNA molecule to be mapped to the 2D location it originated from within a tissue, have become readily available. Due to computational challenges, ST data has rarely been used to study RNA processing such as splicing or differential UTR usage. We apply the ReadZS and the SpliZ, methods developed to analyze RNA process in scRNA-seq data, to analyze spatial localization of RNA processing directly from ST data for the first time. Using Moran's I metric for spatial autocorrelation, we identify genes with spatially regulated RNA processing in the mouse brain and kidney, re-discovering known spatial regulation in Myl6 and identifying previously-unknown spatial regulation in genes such as Rps24, Gng13, Slc8a1, Gpm6a, Gpx3, ActB, Rps8, and S100A9. The rich set of discoveries made here from commonly used reference datasets provides a small taste of what can be learned by applying this technique more broadly to the large quantity of Visium data currently being created.

Phosphotungstic acid-enhanced microcomputed tomography for quantitative visualization of mouse mammary gland morphology

Purpose

Even though current techniques provide two-dimensional (2D) imaging of the mouse mammary gland, they fail to achieve high-resolution three-dimensional (3D) reconstruction and quantification. The objective of this study is to establish and evaluate quantitative visualization of the mouse mammary epithelium through microcomputed tomography (microCT) using phosphotungstic acid (PTA) as a contrast agent.

Approach

Ex vivo microCT scan images of the mouse mammary glands were obtained following staining by PTA, whereas for quantification we adapted volumetric parameters that are used for assessing trabecular bone morphometry and can be structurally applicable in the mammary ductal system. The proposed method was validated in distinct developmental stages and upon short-term treatment with synthetic progesterone, using the carmine alum staining for comparison.

Results

We demonstrate a simple PTA staining procedure that allows high contrast 3D imaging of mammary glands and quantitation of mammary duct structures using microCT. We validated the proposed method in distinct developmental stages, such as at puberty, adult mice, pregnancy as well as upon progesterone treatment. Compared with carmine alum staining, the microCT analysis provided higher resolution 2D and 3D images of the mammary gland morphology, with lower background that enabled the detection of subtle changes.

Conclusions

This work is the first study that employs PTA-enhanced microCT for 3D imaging and volumetric analysis of mouse mammary glands. Our results establish PTA-enhanced microCT as a useful tool for comparative studies of the mouse mammary gland morphology that can apply in mutant mice and for the preclinical evaluation of pharmaceuticals in breast cancer models.

Semibulk RNA-seq analysis as a convenient method for measuring gene expression statuses in a local cellular environment

When biologically interpretation of the data obtained from the single-cell RNA sequencing (scRNA-seq) analysis is attempted, additional information on the location of the single cells, behavior of the surrounding cells, and the microenvironment they generate, would be very important. We developed an inexpensive, high throughput application while preserving spatial organization, named “semibulk RNA-seq” (sbRNA-seq). We utilized a microfluidic device specifically designed for the experiments to encapsulate both a barcoded bead and a cell aggregate (a semibulk) into a single droplet. Using sbRNA-seq, we firstly analyzed mouse kidney specimens. In the mouse model, we could associate the pathological information with the gene expression information. We validated the results using spatial transcriptome analysis and found them highly consistent. When we applied the sbRNA-seq analysis to the human breast cancer specimens, we identified spatial interactions between a particular population of immune cells and that of cancer-associated fibroblast cells, which were not precisely represented solely by the single-cell analysis. Semibulk analysis may provide a convenient and versatile method, compared to a standard spatial transcriptome sequencing platform, to associate spatial information with transcriptome information.

Pericyte-mediated constriction of renal capillaries evokes no-reflow and kidney injury following ischaemia

Acute kidney injury is common, with ~13 million cases and 1.7 million deaths/year worldwide. A major cause is renal ischaemia, typically following cardiac surgery, renal transplant or severe haemorrhage. We examined the cause of the sustained reduction in renal blood flow ('no-reflow'), which exacerbates kidney injury even after an initial cause of compromised blood supply is removed. Adult male Sprague-Dawley rats, or NG2-dsRed male mice were used in this study. After 60 min kidney ischaemia and 30-60 min reperfusion, renal blood flow remained reduced, especially in the medulla, and kidney tubule damage was detected as Kim-1 expression. Constriction of the medullary descending vasa recta and cortical peritubular capillaries occurred near pericyte somata, and led to capillary blockages, yet glomerular arterioles and perfusion were unaffected, implying that the long-lasting decrease of renal blood flow contributing to kidney damage was generated by pericytes. Blocking Rho kinase to decrease pericyte contractility from the start of reperfusion increased the post-ischaemic diameter of the descending vasa recta capillaries at pericytes, reduced the percentage of capillaries that remained blocked, increased medullary blood flow and reduced kidney injury. Thus, post-ischaemic renal no-reflow, contributing to acute kidney injury, reflects pericytes constricting the descending vasa recta and peritubular capillaries. Pericytes are therefore an important therapeutic target for treating acute kidney injury.

Brain virtual histology with X-ray phase-contrast tomography Part I: whole-brain myelin mapping in white-matter injury models

White-matter injury leads to severe functional loss in many neurological diseases. Myelin staining on histological samples is the most common technique to investigate white-matter fibers. However, tissue processing and sectioning may affect the reliability of 3D volumetric assessments. The purpose of this study was to propose an approach that enables myelin fibers to be mapped in the whole rodent brain with microscopic resolution and without the need for strenuous staining. With this aim, we coupled in-line (propagation-based) X-ray phase-contrast tomography (XPCT) to ethanol-induced brain sample dehydration. We here provide the proof-of-concept that this approach enhances myelinated axons in rodent and human brain tissue. In addition, we demonstrated that white-matter injuries could be detected and quantified with this approach, using three animal models: ischemic stroke, premature birth and multiple sclerosis. Furthermore, in analogy to diffusion tensor imaging (DTI), we retrieved fiber directions and DTI-like diffusion metrics from our XPCT data to quantitatively characterize white-matter microstructure. Finally, we showed that this non-destructive approach was compatible with subsequent complementary brain sample analysis by conventional histology. In-line XPCT might thus become a novel gold-standard for investigating white-matter injury in the intact brain. This is Part I of a series of two articles reporting the value of in-line XPCT for virtual histology of the brain; Part II shows how in-line XPCT enables the whole-brain 3D morphometric analysis of amyloid- β (A β ) plaques.

Automated Machine-Learning Framework Integrating Histopathological and Radiological Information for Predicting IDH1 Mutation Status in Glioma

Diffuse gliomas are the most common malignant primary brain tumors. Identification of isocitrate dehydrogenase 1 (IDH1) mutations aids the diagnostic classification of these tumors and the prediction of their clinical outcomes. While histology continues to play a key role in frozen section diagnosis, as a diagnostic reference and as a method for monitoring disease progression, recent research has demonstrated the ability of multi-parametric magnetic resonance imaging (MRI) sequences for predicting IDH genotypes. In this paper, we aim to improve the prediction accuracy of IDH1 genotypes by integrating multi-modal imaging information from digitized histopathological data derived from routine histological slide scans and the MRI sequences including T1-contrast (T1) and Fluid-attenuated inversion recovery imaging (T2-FLAIR). In this research, we have established an automated framework to process, analyze and integrate the histopathological and radiological information from high-resolution pathology slides and multi-sequence MRI scans. Our machine-learning framework comprehensively computed multi-level information including molecular level, cellular level, and texture level information to reflect predictive IDH genotypes. Firstly, an automated pre-processing was developed to select the regions of interest (ROIs) from pathology slides. Secondly, to interactively fuse the multimodal complementary information, comprehensive feature information was extracted from the pathology ROIs and segmented tumor regions (enhanced tumor, edema and non-enhanced tumor) from MRI sequences. Thirdly, a Random Forest (RF)-based algorithm was employed to identify and quantitatively characterize histopathological and radiological imaging origins, respectively. Finally, we integrated multi-modal imaging features with a machine-learning algorithm and tested the performance of the framework for IDH1 genotyping, we also provided visual and statistical explanation to support the understanding on prediction outcomes. The training and testing experiments on 217 pathologically verified IDH1 genotyped glioma cases from multi-resource validated that our fully automated machine-learning model predicted IDH1 genotypes with greater accuracy and reliability than models that were based on radiological imaging data only. The accuracy of IDH1 genotype prediction was 0.90 compared to 0.82 for radiomic result. Thus, the integration of multi-parametric imaging features for automated analysis of cross-modal biomedical data improved the prediction accuracy of glioma IDH1 genotypes.

Three-dimensional reconstruction of testis cords/seminiferous tubules

BACKGROUND

Due to the development of novel equipment for the acquisition of two-dimensional serial images and software capable of displaying three-dimensional (3D) images from serial images, the accurate 3D reconstruction of organs and tissues has become possible.

METHODS

Based on published studies, this review summarizes techniques for the 3D reconstruction of the testis cords/seminiferous tubules, with special reference to our method using serial paraffin sections and 3D visualization software.

MAIN FINDINGS

The testes of mice, rats, and hamsters of various ages were 3D reconstructed and species and age differences in the structures of the testis cords/seminiferous tubules were analyzed. Our method is advantageous because conventional paraffin-embedded normal and pathological specimens may be utilized for the 3D analysis without the need for complicated and expensive equipment.

CONCLUSION

By further decreasing the time and labor required for the procedure and adding information on molecular localization, the technique for 3D reconstruction will contribute to the elucidation of not only the structures, but also the functions of various organs, including the testis.

Micro-CT imaging of Thiel-embalmed and iodine-stained human temporal bone for 3D modeling

Introduction

This pilot study explores whether a human Thiel-embalmed temporal bone is suitable for generating an accurate and complete data set with micro-computed tomography (micro-CT) and whether solid iodine-staining improves visualization and facilitates segmentation of middle ear structures.

Methods

A temporal bone was used to verify the accuracy of the imaging by first digitally measuring the stapes on the tomography images and then physically under the microscope after removal from the temporal bone. All measurements were compared with literature values.

The contralateral temporal bone was used to evaluate segmentation and three-dimensional (3D) modeling after iodine staining and micro-CT scanning.

Results

The digital and physical stapes measurements differed by 0.01–0.17 mm or 1–19%, respectively, but correlated well with the literature values. Soft tissue structures were visible in the unstained scan. However, iodine staining increased the contrast-to-noise ratio by a factor of 3.7 on average. The 3D model depicts all ossicles and soft tissue structures in detail, including the chorda tympani, which was not visible in the unstained scan.

Conclusions

Micro-CT imaging of a Thiel-embalmed temporal bone accurately represented the entire anatomy. Iodine staining considerably increased the contrast of soft tissues, simplified segmentation and enabled detailed 3D modeling of the middle ear.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40463-021-00522-0.

Imaging the Renal Microcirculation in Cell Therapy

Renal microvascular rarefaction plays a pivotal role in progressive kidney disease. Therefore, modalities to visualize the microcirculation of the kidney will increase our understanding of disease mechanisms and consequently may provide new approaches for evaluating cell-based therapy. At the moment, however, clinical practice is lacking non-invasive, safe, and efficient imaging modalities to monitor renal microvascular changes over time in patients suffering from renal disease. To emphasize the importance, we summarize current knowledge of the renal microcirculation and discussed the involvement in progressive kidney disease. Moreover, an overview of available imaging techniques to uncover renal microvascular morphology, function, and behavior is presented with the associated benefits and limitations. Ultimately, the necessity to assess and investigate renal disease based on in vivo readouts with a resolution up to capillary level may provide a paradigm shift for diagnosis and therapy in the field of nephrology.

X-ray Dark-Field Imaging (XDFI)-a Promising Tool for 3D Virtual Histopathology

X-ray dark-field imaging (XDFI) utilizing a thin silicon crystal under Laue case enables visualizing three-dimensional (3D) morphological alterations of human tissue. XDFI uses refraction-contrast derived from phase shift rather than absorption as the main X-ray image contrast source to render 2D and 3D images of tissue specimens in unprecedented detail. The unique features of XDFI are its extremely high sensitivity (approximately 1000:1 compared to absorption for soft tissues under X-ray energy of around 20 keV, theoretically) and excellent resolution (8.5 μm) without requiring contrast medium or staining. Thus, XDFI-computed tomography can generate 3D virtual histological images equivalent to those of stained histological sections pathologists observe under low-power light microscopy as far as organs and tissues selected as samples in preliminary studies. This paper reviews the fundamental principles and the potential of XDFI, describes two optical setups for XDFI with examples, illustrates features of XDFI that are salient for histopathology, and presents XDFI examples of refraction-contrast images of atherosclerotic plaques, musculoskeletal tissue, neuronal tissue, and breast cancer specimens. Availability of this X-ray imaging in routine histopathological evaluations of tissue specimens would help guide clinical decision making by highlighting suspicious areas in unstained, thick sections for further sampling and analysis using conventional histopathological techniques. XDFI is a promising tool for 3D virtual histopathology.

Delayed urea differential enhancement CEST (dudeCEST)-MRI with T1 correction for monitoring renal urea handling

PURPOSE

We demonstrate a method of delayed urea differential enhancement CEST for probing urea recycling action of the kidney using expanded multi-pool Lorentzian fitting and apparent exchange-dependent relaxation compensation.

METHODS

T₁ correction of urea CEST contrast by apparent exchange-dependent relaxation was tested in phantoms. Nine mice were scanned at 7 Tesla following intraperitoneal injection of 2M 150 μL urea, and later saline. T₁ maps and Z-spectra were acquired before and 20 and 40 min postinjection. Z-spectra were fit to a 7-pool Lorentzian model for CEST quantification and compared to urea assay of kidney homogenate. Renal injury was induced by aristolochic acid in 7 mice, and the same scan protocol was performed.

RESULTS

Apparent exchange-dependent relaxation corrected for variable T₁ times in phantoms. Urea CEST contrast at +1 ppm increased significantly at both time points following urea injection in the inner medulla and papilla. When normalizing the postinjection urea CEST contrast to the corresponding baseline value, both urea and saline injection resulted in identical fold changes in urea CEST contrast. Urea assay of kidney homogenate showed a significant correlation to both apparent exchange-dependent relaxation (R² = 0.4687, P = .0017) and non-T₁ -corrected Lorentzian amplitudes (R² = 0.4964, P = .0011). Renal injury resulted in increased T₁ time in the cortex and reduced CEST contrast change upon urea and saline infusion.

CONCLUSION

Delayed urea enhancement following infusion can provide insight into renal urea handling. In addition, changes in CEST contrast at 1.0 ppm following saline infusion may provide insight into renal function.

3D virtual histology of human pancreatic tissue by multiscale phase-contrast X-ray tomography

A multiscale three-dimensional (3D) virtual histology approach is presented, based on two configurations of propagation phase-contrast X-ray tomography, which have been implemented in close proximity at the GINIX endstation at the beamline P10/PETRA III (DESY, Hamburg, Germany). This enables the 3D reconstruction of characteristic morphological features of human pancreatic normal and tumor tissue, as obtained from cancer surgery, first in the form of a large-scale overview by parallel-beam illumination, followed by a zoom into a region-of-interest based on zoom tomography using a Kirkpatrick-Baez mirror with additional waveguide optics. To this end 1 mm punch biopsies of the tissue were taken. In the parallel tomography, a volumetric throughput on the order of 0.01 mm3 s-1 was achieved, while maintaining the ability to segment isolated cells. With a continuous rotation during the scan, a total acquisition time of less than 2 min was required for a full tomographic scan. Using the combination of both setups, islets of Langerhans, a three-dimensional cluster of cells in the endocrine part of the pancreas, could be located. Cells in such an islet were segmented and visualized in 3D. Further, morphological alterations of tumorous tissue of the pancreas were characterized. To this end, the anisotropy parameter Ω, based on intensity gradients, was used in order to quantify the presence of collagen fibers within the entire biopsy specimen. This proof-of-concept experiment of the multiscale approach on human pancreatic tissue paves the way for future 3D virtual pathology.

Challenges of Post-measurement Histology for the Dielectric Characterisation of Heterogeneous Biological Tissues

The dielectric properties of biological tissues are typically measured using the open-ended coaxial probe technique, which is based on the assumption that the tissue sample is homogeneous. Therefore, for heterogeneous tissue samples, additional post-measurement sample processing is conducted. Specifically, post-measurement histological analysis may be performed in order to associate the measured dielectric properties with the tissue types present in a heterogeneous sample. Accurate post-measurement histological analysis enables identification of the constituent tissue types that contributed to the measured dielectric properties, and their relative distributions. There is no standard protocol for conducting post-measurement histological analysis, which leads to high numbers of excluded tissue samples and inconsistencies in the resulting reported data for heterogeneous tissues. To this extent, this study examines the post-measurement histological process and the challenges in associating the acquired dielectric properties with the different tissue types present in heterogeneous samples. The results demonstrate that the histological process inevitably alters the morphology of samples, thus introducing errors in the interpretation of the dielectric properties acquired from heterogeneous biological samples. Notably, sample size was seen to shrink by up to 90% through the histological process, meaning that sensing volume determined from fresh tissues is not directly applicable to histology images.

Fiber orientation in a whole mouse heart reconstructed by laboratory phase-contrast micro-CT

Purpose: We present a phase-contrast x-ray tomography study of wild type C57BL/6 mouse hearts as a nondestructive approach to the microanatomy on the scale of the entire excised organ. Based on the partial coherence at a home-built phase-contrast μ-CT setup installed at a liquid metal jet source, we exploit phase retrieval and hence achieve superior image quality for heart tissue, almost comparable to previous synchrotron data on the whole organ scale.

Approach: In our work, different embedding methods and heavy metal-based stains have been explored. From the tomographic reconstructions, quantitative structural parameters describing the three-dimensional (3-D) architecture have been derived by two different fiber tracking algorithms. The first algorithm is based on the local gradient of the reconstructed electron density. By performing a principal component analysis on the local structure-tensor of small subvolumes, the dominant direction inside the volume can be determined. In addition to this approach, which is already well established for heart tissue, we have implemented and tested an algorithm that is based on a local 3-D Fourier transform.

Results: We showed that the choice of sample preparation influences the 3-D structure of the tissue, not only in terms of contrast but also with respect to the structural preservation. A heart prepared with the evaporation-of-solvent method was used to compare both algorithms. The results of structural orientation were very similar for both approaches. In addition to the determination of the fiber orientation, the degree of filament alignment and local thickness of single muscle fiber bundles were obtained using the Fourier-based approach.

Conclusions: Phase-contrast x-ray tomography allows for investigating the structure of heart tissue with an isotropic resolution below 10  μm. The fact that this is possible with compact laboratory instrumentation opens up new opportunities for screening samples and optimizing sample preparation, also prior to synchrotron beamtimes. Further, results from the structural analysis can help in understanding cardiovascular diseases or can be used to improve computational models of the heart.

Fiber orientation in a whole mouse heart reconstructed by laboratory phase-contrast micro-CT

Purpose: We present a phase-contrast x-ray tomography study of wild type C57BL/6 mouse hearts as a nondestructive approach to the microanatomy on the scale of the entire excised organ. Based on the partial coherence at a home-built phase-contrast μ - CT setup installed at a liquid metal jet source, we exploit phase retrieval and hence achieve superior image quality for heart tissue, almost comparable to previous synchrotron data on the whole organ scale. Approach: In our work, different embedding methods and heavy metal-based stains have been explored. From the tomographic reconstructions, quantitative structural parameters describing the three-dimensional (3-D) architecture have been derived by two different fiber tracking algorithms. The first algorithm is based on the local gradient of the reconstructed electron density. By performing a principal component analysis on the local structure-tensor of small subvolumes, the dominant direction inside the volume can be determined. In addition to this approach, which is already well established for heart tissue, we have implemented and tested an algorithm that is based on a local 3-D Fourier transform. Results: We showed that the choice of sample preparation influences the 3-D structure of the tissue, not only in terms of contrast but also with respect to the structural preservation. A heart prepared with the evaporation-of-solvent method was used to compare both algorithms. The results of structural orientation were very similar for both approaches. In addition to the determination of the fiber orientation, the degree of filament alignment and local thickness of single muscle fiber bundles were obtained using the Fourier-based approach. Conclusions: Phase-contrast x-ray tomography allows for investigating the structure of heart tissue with an isotropic resolution below 10    μ m . The fact that this is possible with compact laboratory instrumentation opens up new opportunities for screening samples and optimizing sample preparation, also prior to synchrotron beamtimes. Further, results from the structural analysis can help in understanding cardiovascular diseases or can be used to improve computational models of the heart.

Phosphotungstic acid-enhanced microCT: Optimized protocols for embryonic and early postnatal mice

BACKGROUND

Given the need for descriptive and increasingly mechanistic morphological analyses, contrast-enhanced microcomputed tomography (microCT) represents perhaps the best method for visualizing 3D biological soft tissues in situ. Although staining protocols using phosphotungstic acid (PTA) have been published with beautiful visualizations of soft tissue structures, these protocols are often aimed at highly specific research questions and are applicable to a limited set of model organisms, specimen ages, or tissue types. We provide detailed protocols for micro-level visualization of soft tissue structures in mice at several embryonic and early postnatal ages using PTA-enhanced microCT.

RESULTS

Our protocols produce microCT scans that enable visualization and quantitative analyses of whole organisms, individual tissues, and organ systems while preserving 3D morphology and relationships with surrounding structures, with minimal soft tissue shrinkage. Of particular note, both internal and external features of the murine heart, lungs, and liver, as well as embryonic cartilage, are captured at high resolution.

CONCLUSION

These protocols have broad applicability to mouse models for a variety of diseases and conditions. Minor experimentation in the staining duration can expand this protocol to additional age groups, permitting ontogenetic studies of internal organs and soft tissue structures within their 3D in situ position.

Three-dimensional visualization of fibrous tissues in cirrhotic rats via X-ray phase-contrast computed tomography with iodine staining

To accurately characterize cirrhosis, knowledge of the 3D fibrous structures is essential. Histology is the gold standard in cirrhosis screening, but it mainly provides structural information in 2D planes and destroys the 3D samples in the process. The aim of this study was to evaluate the potential of X-ray phase-contrast computed tomography (PCCT) with iodine staining for the 3D nondestructive visualization of internal structural details in entire cirrhotic livers with histopathologic correlation. In this study, cirrhotic livers induced by carbon tetrachloride (CCl₄) in rats were imaged via PCCT and then histopathologically processed. Characteristics of the cirrhosis, i.e. abnormal nodules surrounded by annular fibrosis, were established and a 3D reconstruction of these structures was also performed via PCCT. Fibrosis area, septal width and nodular size were measured and the correlation for these quantitative measurements between PCCT and histopathologic findings was analyzed. The results showed that fibrous bands, small nodules and angio-architecture in cirrhosis were clearly presented in the PCCT images, with histopathologic findings as standard reference. In comparison with histopathology, PCCT was associated with a very close value for fibrosis area, septal width and nodular size. The quantitative measurements showed a strong correlation between PCCT and histopathology. Additionally, the 3D structures of fibrous bands and microvasculature were presented simultaneously. PCCT provides excellent results in the assessment of cirrhosis characteristics and 3D presentation of these feature structures compared with histopathology. Thus, the technique may serve as an adjunct nondestructive 3D modality for cirrhosis characterization.

X-ray-Based 3D Virtual Histology-Adding the Next Dimension to Histological Analysis

Histology and immunohistochemistry of thin tissue sections have been the standard diagnostic procedure in many diseases for decades. This method is highly specific for particular tissue regions or cells, but mechanical sectioning of the specimens is required, which destroys the sample in the process and can lead to non-uniform tissue deformations. In addition, regions of interest cannot be located beforehand and the analysis is intrinsically two-dimensional. Micro X-ray computed tomography (μCT) on the other hand can provide 3D images at high resolution and allows for quantification of tissue structures, as well as the localization of small regions of interest. These advantages advocate the use of μCT for virtual histology tool with or without subsequent classical histology. This review summarizes the most recent examples of virtual histology and provides currently known possibilities of improving contrast and resolution of μCT. Following a background in μCT imaging, ex vivo staining procedures for contrast enhancement are presented as well as label-free virtual histology approaches and the technologies, which could rapidly advance it, such as phase-contrast CT. Novel approaches such as zoom tomography and nanoparticulate contrast agents will also be considered. The current evidence suggests that virtual histology may present a valuable addition to the workflow of histological analysis, potentially reducing the workload in pathology, refining tissue classification, and supporting the detection of small malignancies.

Evaluation of X-ray tomography contrast agents: A review of production, protocols, and biological applications

X-ray computed tomography is a strong tool that finds many applications both in medical applications and in the investigation of biological and nonbiological samples. In the clinics, X-ray tomography is widely used for diagnostic purposes whose three-dimensional imaging in high resolution helps physicians to obtain detailed image of investigated regions. Researchers in biological sciences and engineering use X-ray tomography because it is a nondestructive method to assess the structure of their samples. In both medical and biological applications, visualization of soft tissues and structures requires special treatment, in which special contrast agents are used. In this detailed report, molecule-based and nanoparticle-based contrast agents used in biological applications to enhance the image quality were compiled and reported. Special contrast agent applications and protocols to enhance the contrast for the biological applications and works to develop nanoparticle contrast agents to enhance the contrast for targeted drug delivery and general imaging applications were also assessed and listed.

3D vessel-wall virtual histology of whole-body perfused mice using a novel heavy element stain

Virtual histology – utilizing high-resolution three-dimensional imaging – is becoming readily available. Micro-computed tomography (micro-CT) is widely available and is often coupled with x-ray attenuating histological stains that mark specific tissue components for 3D virtual histology. In this study we describe a new tri-element x-ray attenuating stain and perfusion protocol that provides micro-CT contrast of the entire vasculature of an intact mouse. The stain – derived from an established histology stain (Verhoeff’s) – is modified to enable perfusion through the vasculature; the attenuating elements of the stain are iodine, aluminum, and iron. After a 30-minute perfusion through the vasculature (10-minute flushing with detergent-containing saline followed by 15-minute perfusion with the stain and a final 5-minute saline flush), animals are scanned using micro-CT. We demonstrate that the new staining protocol enables sharp delineation of the vessel walls in three dimensions over the whole body; corresponding histological analysis verified that the CT stain is localized primarily in the endothelial cells and media of large arteries and the endothelium of smaller vessels, such as the coronaries. The rapid perfusion and scanning protocol ensured that all tissues are available for further analysis via higher resolution CT of smaller sections or traditional histological sectioning.

Fundamental Understanding of Cellular Water Transport Process in Bio-Food Material during Drying

Bio-food materials are heterogeneous in structure with cellular diversity, where the majority of the water is located in the intracellular spaces. Understanding of the nature of the microscopic behaviour of water transport is crucial to enhance the energy efficiency in food processing and obtain the better quality of processed food. In this research, apoplastic and symplastic transport of cellular water in the bio-food material during drying was investigated using 1H-NMR-T2 relaxometry. We found that intracellular water (ICW) migrates from intracellular spaces to the intercellular spaces by progressive rupturing the cell membranes while drying at a higher temperatures (60 °C-70 °C). In this case, apoplastic process dominates the transport process. However, at lower temperature (45 °C), cell membranes do not rupture and therefore ICW migrates from cell to the neighbouring cell through micro-capillaries, where the symplastic process dominates the mass transfer at different stages of drying.

Studying Osteoarthritis Pathogenesis in Mice

With the increasing availability and complexity of mouse models of disease, either spontaneous or induced, there is a concomitant increase in their use in the analysis of pathogenesis. Among such diseases is osteoarthritis, a debilitating disease with few treatment options. While advances in our understanding of the pathogenesis of osteoarthritis has advanced through clinical investigations and genome-wide association studies, there is still a large gap in our knowledge, hindering advances in therapy. Patient samples are available ex vivo, but these are generally in the very late stages of disease. However, with mice, we are able to induce disease at a defined time and track the progression in vivo and ex vivo, from inception to end stage, to delineate the processes involved in disease development. © 2018 by John Wiley & Sons, Inc.

Synchrotron inline phase contrast µCT enables detailed virtual histology of embedded soft-tissue samples with and without staining

Synchrotron radiation micro-computed tomography (SRµCT) based virtual histology, in combination with dedicated ex vivo staining protocols and/or phase contrast, is an emerging technology that makes use of three-dimensional images to provide novel insights into the structure of tissue samples at microscopic resolution with short acquisition times of the order of minutes or seconds. However, the high radiation dose creates special demands on sample preparation and staining. As a result of the lack of specific staining in virtual histology, it can supplement but not replace classical histology. Therefore, the aim of this study was to establish and compare optimized ex vivo staining and acquisition protocols for SRµCT-based virtual histology of soft-tissue samples, which could be integrated into the standard workflow of classical histology. The high grade of coherence of synchrotron radiation allows the application of propagation-based phase contrast imaging (PBI). In this study, PBI yielded a strong increase in image quality even at lower radiation doses and consequently prevented any damage to the tissue samples or the embedding material. This work has demonstrated that the improvement in contrast-to-noise ratio by PBI enabled label-free virtual histology of soft-tissue specimens embedded in paraffin to a level of detail that exceeds that achieved with staining protocols.

X-ray based virtual histology allows guided sectioning of heavy ion stained murine lungs for histological analysis

Examination of histological or immunohistochemically stained 2D sections of embedded tissue is one of the most frequently used tools in biomedical research and clinical routine. Since to date, targeted sectioning of specific regions of interest (ROI) in the sample is not possible, we aimed at developing a guided sectioning approach based on x-ray 3D virtual histology for heavy ion stained murine lung samples. For this purpose, we increased the contrast to noise ratio of a standard benchtop microCT by 5–10-fold using free-propagation phase contrast imaging and thus substantially improved image quality. We then show that microCT 3D datasets deliver more precise anatomical information and quantification of the sample than traditional histological sections, which display deformations of the tissue. To quantify these deformations caused by sectioning we developed the “Displacement Index (DI)”, which combines block-matching with the calculation of the local mutual information. We show that the DI substantially decreases when a femtosecond laser microtome is used for sections as opposed to a traditional microtome. In conclusion, our microCT based virtual histology approach can be used as a supplement and a guidance tool for traditional histology, providing 3D measurement capabilities and offering the ability to perform sectioning directly at an ROI.