A simple nuclear contrast staining method for microCT-based 3D histology using lead(II) acetate

Air artifact suppression in phase contrast micro-CT using conditional generative adversarial networks

3D virtual histology of formalin-fixed and paraffin-embedded (FFPE) tissue by means of phase contrast micro-computed tomography (micro-CT) is an increasingly popular technique, as it allows the 3D architecture of the tissue to be addressed without the need of additional heavy ion based staining approaches. Therefore, it can be applied on archived standard FFPE tissue blocks. However, one of the major concerns of using phase contrast micro-CT in combination with FFPE tissue blocks is the trapped air within the tissue. While air inclusion within the FFPE tissue block does not strongly impact the workflow and quality of classical histology, it creates serious obstacles in 3D visualization of detailed morphology. In particular, the 3D analysis of structural features is challenging, due to a strong edge effect caused by the phase shift at the air-tissue/paraffin interface. Despite certain improvements in sample preparation to eliminate air inclusion, such as the use of negative pressure, it is not always possible to remove all trapped air, for example in soft tissues such as lung. Here, we present a novel workflow based on conditional generative adversarial networks (cGANs) to effectively replace these air artifact regions with generated tissue, which are influenced by the surrounding content. Our results show that this approach not only improves the visualization of the lung tissue but also eases the use of structural analysis on the air artifact-suppressed phase contrast micro-CT scans. In addition, we demonstrate the transferability of the generative model to FFPE specimens of porcine lung tissue.

Unveiling Another Dimension: Advanced Visualization of Cancer Invasion and Metastasis via Micro-CT Imaging

Invasion and metastasis are well-known hallmarks of cancer, with metastatic disease accounting for 60% to 90% of cancer-related deaths [...].

In situ isotropic 3D imaging of vasculature perfusion specimens using x-ray microscopic dual-energy CT

Ex vivo x-ray angiography provides high-resolution, three-dimensional information on vascular phenotypes down to the level of capillaries. Sample preparation for ex vivo angiography starts with the removal of blood from the vascular system, followed by perfusion with an x-ray dense contrast agent mixed with a carrier such as gelatine or a polymer. Subsequently, the vascular micro-architecture of harvested organs is imaged in the intact fixed organ. In the present study, we present novel microscopic dual-energy CT (microDECT) imaging protocols that allow to visualise and analyse microvasculature in situ with reference to the morphology of hard and soft tissue. We show that the spectral contrast of µAngiofil and Micropaque barium sulphate in perfused specimens allows for the effective separation of vasculature from mineralised skeletal tissues. Furthermore, we demonstrate the counterstaining of perfused specimens using established x-ray dense contrast agents to depict blood vessels together with the morphology of soft tissue. Phosphotungstic acid (PTA) is used as a counterstain that shows excellent spectral contrast in both µAngiofil and Micropaque barium sulphate-perfused specimens. A novel Sorensen-buffered PTA protocol is introduced as a counterstain for µAngiofil specimens, as the polyurethane polymer is susceptible to artefacts when using conventional staining solutions. Finally, we demonstrate that counterstained samples can be automatically processed into three separate image channels (skeletal tissue, vasculature and stained soft tissue), which offers multiple new options for data analysis. The presented microDECT workflows are suited as tools to screen and quantify microvasculature and can be implemented in various correlative imaging pipelines to target regions of interest for downstream light microscopic investigation.

Contrast-Enhanced Micro-CT Imaging of Murine Mandibles: A Multi-Method Approach for Simultaneous Hard and Soft Tissue Analysis

AIM

To develop and evaluate a novel multi-method micro-computed tomography (μCT) imaging protocol for enhanced visualization of both hard and soft tissues in murine mandibles, addressing the limitations of traditional imaging techniques in dental research.

MATERIALS AND METHODS

We employed a contrast-enhanced (CE) μCT imaging technique using Lugol's iodine as a contrast agent to visualize the intricate structures of murine mandibles. The protocol involved the combination of conventional μCT imaging as well as CE-μCT, including decalcification with EDTA, allowing for simultaneous assessment of hard and soft tissues. The method is compared with standard imaging modalities, and the ability to visualize detailed anatomical features is discussed.

RESULTS

The CE-μCT imaging technique provided superior visualization of murine mandibular structures, including dental pulp, periodontal ligaments and the surrounding soft tissues, along with conventional μCT imaging of alveolar bone and teeth. This method revealed detailed anatomical features with high specificity and contrast, surpassing traditional imaging approaches.

CONCLUSION

Our findings demonstrate the potential of CE-μCT imaging with Lugol's iodine as a powerful tool for dental research. This technique offers a comprehensive view of the murine mandible, facilitating advanced studies in tissue engineering, dental pathology and the development of dental materials.

Expanding understanding of chick embryo's nervous system development at HH22-HH41 embryonic stages using X-ray microcomputed tomography

Assessing the embryotoxicity and teratogenicity of various substances and processes is crucial due to their complexity and resource intensity. The chicken embryo (CE) serves an ideal model for simulating the first months of mammalian embryonic development. This makes the CE a reliable model for testing teratogenic effects, particularly in relation to the nervous system (NS), which experiences developmental abnormalities second in frequency only to cardiovascular teratogenic disorders. Microcomputed tomography (μCT) is a promising method for studying these processes. The advantages of μCT include relatively high research speed, diagnostic accuracy, high resolution and the ability to visualize the entire internal 3D structure of an object while preserving for other types of research. At the same time, there are practically no available databases of normative μCT data, both qualitative and quantitative, which would act as a starting point for screening detection of abnormalities in the development of the NS. In this study, we present a simple method for obtaining very detailed quantitative sets of 2D and 3D μCT data of NS structures of the CE (Gallus Gallus domesticus) at HH22-HH41 embryonic stages with contrasting by 1% phosphotungstic acid. The results of μCT demonstrate the exact boundaries, high general and differentiated contrast of the main and specific structures of the NS of CE, which are quantitatively and qualitatively similar to results of histological analysis. Calculations of the X-ray density and volume of the main structures of the NS at constant exponential growth are presented. In addition to the increase in linear dimensions, significant changes in the structures of various parts of the brain were identified and visualized during the CE development at HH22 to HH41 embryonic stages. The data presented establish the first methodology for obtaining normative data, including subtle localized differences in the NS in CE embryogenesis. The data obtained open up new opportunities for modern embryology, teratology, pharmacology and toxicology.

Improved visualisation of ACP-engineered osteoblastic spheroids: a comparative study of contrast-enhanced micro-CT and traditional imaging techniques

This study investigates osteoblastic cell spheroid cultivation methods, exploring flat-bottom, U-bottom, and rotary flask techniques with and without amorphous calcium phosphate (ACP) supplementation to replicate the 3D bone tissue microenvironment. ACP particles derived from eggshell waste exhibit enhanced osteogenic activity in 3D models. However, representative imaging of intricate 3D tissue-engineered constructs poses challenges in conventional imaging techniques due to notable scattering and absorption effects in light microscopy, and hence limited penetration depth. We investigated contrast-enhanced micro-CT as a methodological approach for comprehensive morphological 3D-analysis of thein-vitromodel and compared the technique with confocal laser scanning microscopy, scanning electron microscopy and classical histology. Phosphotungstic acid and iodine-based contrast agents were employed for micro-CT imaging in laboratory and synchrotron micro-CT imaging. Results revealed spheroid shape variations and structural integrity influenced by cultivation methods and ACP particles. The study underscores the advantage of 3D spheroid models over traditional 2D cultures in mimicking bone tissue architecture and cellular interactions, emphasising the growing demand for novel imaging techniques to visualise 3D tissue-engineered models. Contrast-enhanced micro-CT emerges as a promising non-invasive imaging method for tissue-engineered constructs containing ACP particles, offering insights into sample morphology, enabling virtual histology before further analysis.

Advanced soft tissue visualization in conjunction with bone structures using contrast-enhanced micro-CT

Purpose

Micro-computed tomography (CT) analysis of soft tissues alongside bone remains challenging due to significant differences in X-ray absorption, preventing spatial inspection of bone remodeling including the cellular intricacies of mineralized tissues in developmental biology and pathology. The goal was to develop a protocol for contrast-enhanced micro-CT imaging that effectively visualizes soft tissues and cells in conjunction with bone while minimizing bone attenuation by decalcification.

Approach

Murine femur samples were decalcified in ethylenediaminetetraacetic acid and treated with three different contrast agents: (i) iodine in ethanol, (ii) phosphotungstic acid in water, and (iii) Lugol's iodine. Micro-CT scans were performed in the laboratory setup SkyScan 1172 and at the synchrotron radiation for medical physics beamline in synchrotron radiation facility Elettra. Soft and hard tissue contrast-to-noise ratio (CNR) and contrast efficiency after decalcification were measured.

Results

In laboratory micro-CT, Lugol's iodine demonstrated a threefold higher CNR in the bone marrow, representing the soft tissue portion, compared with the bone. Contrast efficiencies, measured in synchrotron micro-CT, were consistent with these findings. Higher resolutions and the specificity of Lugol's iodine to cellular structures enabled detailed visualization of bone-forming cells in the epiphyseal plate.

Conclusions

The combination of decalcification and the utilization of the contrast agent Lugol's iodine facilitated an enhanced soft tissue visualization in conjunction with bone.

Synchrotron X-ray imaging of soft biological tissues - principles, applications and future prospects

Synchrotron-based tomographic phase-contrast X-ray imaging (SRµCT or SRnCT) is a versatile isotropic three-dimensional imaging technique that can be used to study biological samples spanning from single cells to human-sized specimens. SRµCT and SRnCT take advantage of the highly brilliant and coherent X-rays produced by a synchrotron light source. This enables fast data acquisition and enhanced image contrast for soft biological samples owing to the exploitation of phase contrast. In this Review, we provide an overview of the basics behind the technique, discuss its applications for biologists and provide an outlook on the future of this emerging technique for biology. We introduce the latest advances in the field, such as whole human organs imaged with micron resolution, using X-rays as a tool for virtual histology and resolving neuronal connections in the brain.

Three-Dimensional Cell Culture Micro-CT Visualization within Collagen Scaffolds in an Aqueous Environment

Among all of the materials used in tissue engineering in order to develop bioequivalents, collagen shows to be the most promising due to its superb biocompatibility and biodegradability, thus becoming one of the most widely used materials for scaffold production. However, current imaging techniques of the cells within collagen scaffolds have several limitations, which lead to an urgent need for novel methods of visualization. In this work, we have obtained groups of collagen scaffolds and selected the contrasting agents in order to study pores and patterns of cell growth in a non-disruptive manner via X-ray computed microtomography (micro-CT). After the comparison of multiple contrast agents, a 3% aqueous phosphotungstic acid solution in distilled water was identified as the most effective amongst the media, requiring 24 h of incubation. The differences in intensity values between collagen fibers, pores, and masses of cells allow for the accurate segmentation needed for further analysis. Moreover, the presented protocol allows visualization of porous collagen scaffolds under aqueous conditions, which is crucial for the multimodal study of the native structure of samples.

Chondrosarcoma evaluation using hematein-based x-ray staining and high-resolution 3D micro-CT: a feasibility study

BACKGROUND

Chondrosarcomas are rare malignant bone tumors diagnosed by analyzing radiological images and histology of tissue biopsies and evaluating features such as matrix calcification, cortical destruction, trabecular penetration, and tumor cell entrapment.

METHODS

We retrospectively analyzed 16 cartilaginous tumor tissue samples from three patients (51-, 54-, and 70-year-old) diagnosed with a dedifferentiated chondrosarcoma at the femur, a moderately differentiated chondrosarcoma in the pelvis, and a predominantly moderately differentiated chondrosarcoma at the scapula, respectively. We combined a hematein-based x-ray staining with high-resolution three-dimensional (3D) microscopic x-ray computed tomography (micro-CT) for nondestructive 3D tumor assessment and tumor margin evaluation.

RESULTS

We detected trabecular entrapment on 3D micro-CT images and followed bone destruction throughout the volume. In addition to staining cell nuclei, hematein-based staining also improved the visualization of the tumor matrix, allowing for the distinction between the tumor and the bone marrow cavity. The hematein-based staining did not interfere with further conventional histology. There was a 5.97 ± 7.17% difference between the relative tumor area measured using micro-CT and histopathology (p = 0.806) (Pearson correlation coefficient r = 0.92, p = 0.009). Signal intensity in the tumor matrix (4.85 ± 2.94) was significantly higher in the stained samples compared to the unstained counterparts (1.92 ± 0.11, p = 0.002).

CONCLUSIONS

Using nondestructive 3D micro-CT, the simultaneous visualization of radiological and histopathological features is feasible.

RELEVANCE STATEMENT

3D micro-CT data supports modern radiological and histopathological investigations of human bone tumor specimens. It has the potential for being an integrative part of clinical preoperative diagnostics.

KEY POINTS

• Matrix calcifications are a relevant diagnostic feature of bone tumors. • Micro-CT detects all clinically diagnostic relevant features of x-ray-stained chondrosarcoma. • Micro-CT has the potential to be an integrative part of clinical diagnostics.

Contrast-enhanced Micro-CT 3D visualization of cell distribution in hydrated human cornea

Background

The cornea, a vital component of the human eye, plays a crucial role in maintaining visual clarity. Understanding its ultrastructural organization and cell distribution is fundamental for elucidating corneal physiology and pathology. This study comprehensively examines the microarchitecture of the hydrated human cornea using contrast-enhanced micro-computed tomography (micro-CT).

Method

Fresh human corneal specimens were carefully prepared and hydrated to mimic their in vivo state. Contrast enhancement with Lugol's iodine-enabled high-resolution Micro-CT imaging. The cells' three-dimensional (3D) distribution within the cornea was reconstructed and analyzed.

Results

The micro-CT imaging revealed exquisite details of the corneal ultrastructure, including the spatial arrangement of cells throughout its depth. This novel approach allowed for the visualization of cells' density and distribution in different corneal layers. Notably, our findings highlighted variations in cell distribution between non-hydrated and hydrated corneas.

Conclusions

This study demonstrates the potential of contrast-enhanced micro-CT as a valuable tool for non-destructive, 3D visualization and quantitative analysis of cell distribution in hydrated human corneas. These insights contribute to a better understanding of corneal physiology and may have implications for research in corneal diseases and tissue engineering.

Gene expression detection in developing mouse tissue using in situ hybridization and µCT imaging

High resolution and noninvasiveness have made soft-tissue X-ray microtomography (µCT) a widely applicable three-dimensional (3D) imaging method in studies of morphology and development. However, scarcity of molecular probes to visualize gene activity with µCT has remained a challenge. Here, we apply horseradish peroxidase-assisted reduction of silver and catalytic gold enhancement of the silver deposit to in situ hybridization in order to detect gene expression in developing tissues with µCT (here called GECT, gene expression CT). We show that GECT detects expression patterns of collagen type II alpha 1 and sonic hedgehog in developing mouse tissues comparably with an alkaline phosphatase-based detection method. After detection, expression patterns are visualized with laboratory µCT, demonstrating that GECT is compatible with varying levels of gene expression and varying sizes of expression regions. Additionally, we show that the method is compatible with prior phosphotungstic acid staining, a conventional contrast staining approach in µCT imaging of soft tissues. Overall, GECT is a method that can be integrated with existing laboratory routines to obtain spatially accurate 3D detection of gene expression.

OCT Meets micro-CT: A Subject-Specific Correlative Multimodal Imaging Workflow for Early Chick Heart Development Modeling

Structural and Doppler velocity data collected from optical coherence tomography have already provided crucial insights into cardiac morphogenesis. X-ray microtomography and other ex vivo methods have elucidated structural details of developing hearts. However, by itself, no single imaging modality can provide comprehensive information allowing to fully decipher the inner workings of an entire developing organ. Hence, we introduce a specimen-specific correlative multimodal imaging workflow combining OCT and micro-CT imaging which is applicable for modeling of early chick heart development—a valuable model organism in cardiovascular development research. The image acquisition and processing employ common reagents, lab-based micro-CT imaging, and software that is free for academic use. Our goal is to provide a step-by-step guide on how to implement this workflow and to demonstrate why those two modalities together have the potential to provide new insight into normal cardiac development and heart malformations leading to congenital heart disease.

Mouse embryo phenotyping using X-ray microCT

Microscopic X-ray computed tomography (microCT) is a structural ex vivo imaging technique providing genuine isotropic 3D images from biological samples at micron resolution. MicroCT imaging is non-destructive and combines well with other modalities such as light and electron microscopy in correlative imaging workflows. Protocols for staining embryos with X-ray dense contrast agents enable the acquisition of high-contrast and high-resolution datasets of whole embryos and specific organ systems. High sample throughput is achieved with dedicated setups. Consequently, microCT has gained enormous importance for both qualitative and quantitative phenotyping of mouse development. We here summarize state-of-the-art protocols of sample preparation and imaging procedures, showcase contemporary applications, and discuss possible pitfalls and sources for artefacts. In addition, we give an outlook on phenotyping workflows using microscopic dual energy CT (microDECT) and tissue-specific contrast agents.

Elastic transformation of histological slices allows precise co-registration with microCT data sets for a refined virtual histology approach

Although X-ray based 3D virtual histology is an emerging tool for the analysis of biological tissue, it falls short in terms of specificity when compared to conventional histology. Thus, the aim was to establish a novel approach that combines 3D information provided by microCT with high specificity that only (immuno-)histochemistry can offer. For this purpose, we developed a software frontend, which utilises an elastic transformation technique to accurately co-register various histological and immunohistochemical stainings with free propagation phase contrast synchrotron radiation microCT. We demonstrate that the precision of the overlay of both imaging modalities is significantly improved by performing our elastic registration workflow, as evidenced by calculation of the displacement index. To illustrate the need for an elastic co-registration approach we examined specimens from a mouse model of breast cancer with injected metal-based nanoparticles. Using the elastic transformation pipeline, we were able to co-localise the nanoparticles to specifically stained cells or tissue structures into their three-dimensional anatomical context. Additionally, we performed a semi-automated tissue structure and cell classification. This workflow provides new insights on histopathological analysis by combining CT specific three-dimensional information with cell/tissue specific information provided by classical histology.

A simple nuclear contrast staining method for microCT-based 3D histology using lead(II) acetate

X-ray microtomography (microCT) enables histological-scale 3D imaging of many types of biological samples, but it has yet to rival traditional histology for differentiation of tissue types and cell components. This report presents prima facie results indicating that a simple lead(II) acetate staining solution can impart preferential X-ray contrast to cell nuclei. While not strictly selective for nuclei, the staining reflects local cell-density differences. It can be applied in a single overnight treatment and does not require hematoxylin staining or drying of the sample. The stain is removable with EDTA, and it may enhance early calcifications. A basic protocol is given as a guide for further testing and optimization.