In Vivo Imaging With Confirmation by Histopathology for Increased Rigor and Reproducibility in Translational Research: A Review of Examples, Options, and Resources

Convolutional Neural Networks for the segmentation of hippocampal structures in postmortem MRI scans

BACKGROUND

The hippocampus plays a crucial role in memory and is one of the first structures affected by Alzheimer's disease. Postmortem MRI offers a way to quantify the alterations by measuring the atrophy of the inner structures of the hippocampus. Unfortunately, the manual segmentation of hippocampal subregions required to carry out these measures is very time-consuming.

NEW METHOD

In this study, we explore the use of fully automated methods relying on state-of-the-art Deep Learning approaches to produce these annotations. More specifically, we propose a new segmentation framework made of a set of encoder-decoder blocks embedding self-attention mechanisms and atrous spatial pyramidal pooling to produce better maps of the hippocampus and identify four hippocampal regions: the dentate gyrus, the hippocampal head, the hippocampal body, and the hippocampal tail.

RESULTS

Trained using slices extracted from 15 postmortem T1-weighted, T2-weighted, and susceptibility-weighted MRI scans, our new approach produces hippocampus parcellations that are better aligned with the manually delineated parcellations provided by neuroradiologists.

COMPARISON WITH EXISTING METHODS

Four standard deep learning segmentation architectures: UNet, Double UNet, Attention UNet, and Multi-resolution UNet have been utilized for the qualitative and quantitative comparison of the proposed hippocampal region segmentation model.

CONCLUSIONS

Postmortem MRI serves as a highly valuable neuroimaging technique for examining the effects of neurodegenerative diseases on the intricate structures within the hippocampus. This study opens the way to large sample-size postmortem studies of the hippocampal substructures.

A toolkit for stroke infarct volume estimation in rodents

Stroke volume is a key determinant of infarct severity and an important metric for evaluating treatments. However, accurate estimation of stroke volume can be challenging, due to the often confined 2-dimensional nature of available data. Here, we introduce a comprehensive semi-automated toolkit to reliably estimate stroke volumes based on (1) whole brains ex-vivo magnetic resonance imaging (MRI) and (2) brain sections that underwent immunofluorescence staining. We located and quantified infarct areas from MRI three days (acute) and 28 days (chronic) after photothrombotic stroke induction in whole mouse brains. MRI results were compared with measures obtained from immunofluorescent histologic sections of the same brains. We found that infarct volume determined by post-mortem MRI was highly correlated with a deviation of only 6.6 % (acute) and 4.9 % (chronic) to the measurements as determined in the histological brain sections indicating that both methods are capable of accurately assessing brain tissue damage (Pearson r > 0.9, p < 0.001). The Dice similarity coefficient (DC) showed a high degree of coherence (DC > 0.8) between MRI-delineated regions of interest (ROIs) and ROIs obtained from histologic sections at four to six pre-defined landmarks, with histology-based delineation demonstrating higher inter-operator similarity compared to MR images. We further investigated stroke-related scarring and post-ischemic angiogenesis in cortical peri‑infarct regions and described a negative correlation between GFAP+fluorescence intensity and MRI-obtained lesion size.

Comparison of the Eggshell and the Porcine Pericardium Membranes for Guided Tissue Regeneration Applications

Guided bone regeneration is frequently used to reconstruct the alveolar bone to rehabilitate the mastication using dental implants. The purpose of this article is to research the properties of eggshell membrane (ESM) and its potential application in tissue engineering. The study focuses on the structural, mechanical, and histological characteristics of ESM extracted from Gallus domesticus eggs and to compare them to a commercially available porcine pericardium membrane (Jason® membrane, botiss biomaterials GmbH, Zossen, Germany). Thus, histology was performed on the ESM, and a comparison of the microstructure through scanning electron microscopy and atomic force microscopy (AFM) was conducted. Also, mechanical tensile strength was evaluated. Samples of ESM were prepared and treated with alcohol for fixation and disinfection. Histological analysis revealed that the ESM architecture is constituted out of loose collagen fibers. However, due to the random arrangement of collagen fibers within the membrane, it might not be an effective barrier and occlusive barrier. Comparative analyses were performed between the ESM and the AFM examinations and demonstrated differences in the surface topography and mechanical properties between the two membranes. The ESM exhibited rougher surfaces and weaker mechanical cohesion attributed to its glycoprotein content. The study concludes that while the ESM displays favorable biocompatibility and resorb ability, its non-uniform collagen arrangement limits its suitability as a guided bone regeneration membrane in the current non-crosslinked native form. Crosslinking techniques may enhance its properties for such applications. Further research is needed to explore modifications and processing methods that could leverage the ESM's unique properties for tissue engineering purposes.

Biocompatibility and histological responses of eggshell membrane for dental implant-guided bone regeneration

Guided bone regeneration (GBR) utilizing eggshell membrane (ESM) as a potential biomaterial for dental implant therapy augmentation was explored in this study. ESM, an environmentally friendly waste product, possesses collagen-rich characteristics. The biocompatibility and histological responses of ESM were investigated in a rat model. Twelve young adult Wistar rats were used in this study. ESM samples were implanted in subcutaneous and intramuscular pockets, and samples were collected at 48 hours, 4 weeks, and 8 weeks post-implantation. Histological analysis revealed the changes in ESM over time. Results showed that ESM maintained its structural integrity, induced a moderate cellular response, and exhibited slow degradation, indicating potential biocompatibility. However, the lack of organized collagen arrangement in ESM led to the formation of irregular and polymorphic spaces, allowing cell migration. Encapsulation of ESM by newly proliferating collagen fibers and multinucleated giant cells was observed at later time points, indicating a foreign body reaction. Crosslinking might improve its performance as a separation membrane, as it has the potential to resist enzymatic degradation and enhance biomechanical properties. In conclusion, ESM demonstrated biocompatibility, slow degradation, and lack of foreign body reaction. While not suitable as a complete separation membrane due to irregular collagen arrangement, further research involving crosslinking could enhance its properties, making it a viable option for guided bone regeneration applications in dental implant therapy. This study highlights the potential of repurposing waste materials for medical purposes and underscores the importance of controlled collagen structure in biomaterial development.

Development of polarization-sensitive optical coherence tomography imaging platform and metrics to quantify electrostimulation-induced peripheral nerve injury in vivo in a small animal model

Significance

Neuromodulation devices are rapidly evolving for the treatment of neurological diseases and conditions. Injury from implantation or long-term use without obvious functional losses is often only detectable through terminal histology. New technologies are needed that assess the peripheral nervous system (PNS) under normal and diseased or injured conditions.

Aim

We aim to demonstrate an imaging and stimulation platform that can elucidate the biological mechanisms and impacts of neurostimulation in the PNS and apply it to the sciatic nerve to extract imaging metrics indicating electrical overstimulation.

Approach

A sciatic nerve injury model in a 15-rat cohort was observed using a newly developed imaging and stimulation platform that can detect electrical overstimulation effects with polarization-sensitive optical coherence tomography. The sciatic nerve was electrically stimulated using a custom-developed nerve holder with embedded electrodes for 1 h, followed by a 1-h recovery period, delivered at above-threshold Shannon model k -values in experimental groups: sham control (SC, n = 5 , 0.0    mA / 0    Hz ), stimulation level 1 (SL1, n = 5 , 3.4    mA / 50    Hz , and k = 2.57 ), and stimulation level 2 (SL2, n = 5 , 6.8    mA / 100    Hz , and k = 3.17 ).

Results

The stimulation and imaging system successfully captured study data across the cohort. When compared to a SC after a 1-week recovery, the fascicle closest to the stimulation lead showed an average change of + 4 % / - 309 % (SL1/SL2) in phase retardation and - 79 % / - 148 % in optical attenuation relative to SC. Analysis of immunohistochemistry (IHC) shows a + 1 % / - 36 % difference in myelin pixel counts and - 13 % / + 29 % difference in axon pixel counts, and an overall increase in cell nuclei pixel count of + 20 % / + 35 % . These metrics were consistent with IHC and hematoxylin/eosin tissue section analysis.

Conclusions

The poststimulation changes observed in our study are manifestations of nerve injury and repair, specifically degeneration and angiogenesis. Optical imaging metrics quantify these processes and may help evaluate the safety and efficacy of neuromodulation devices.

High-Resolution Episcopic Microscopy (HREM) in Multimodal Imaging Approaches

High-resolution episcopic microscopy (HREM) is a three-dimensional (3D) episcopic imaging modality based on the acquisition of two-dimensional (2D) images from the cut surface of a block of tissue embedded in resin. Such images, acquired serially through the entire length/depth of the tissue block, are aligned and stacked for 3D reconstruction. HREM has proven to be specifically advantageous when integrated in correlative multimodal imaging (CMI) pipelines. CMI creates a composite and zoomable view of exactly the same specimen and region of interest by (sequentially) correlating two or more modalities. CMI combines complementary modalities to gain holistic structural, functional, and chemical information of the entire sample and place molecular details into their overall spatiotemporal multiscale context. HREM has an advantage over in vivo 3D imaging techniques on account of better histomorphologic resolution while simultaneously providing volume data. HREM also has certain advantages over ex vivo light microscopy modalities. The latter can provide better cellular resolution but usually covers a limited area or volume of tissue, with limited 3D structural context. HREM has predominantly filled a niche in the phenotyping of embryos and characterisation of anatomic developmental abnormalities in various species. Under the umbrella of CMI, when combined with histopathology in a mutually complementary manner, HREM could find wider application in additional nonclinical and translational areas. HREM, being a modified histology technique, could also be incorporated into specialised preclinical pathology workflows. This review will highlight HREM as a versatile imaging platform in CMI approaches and present its benefits and limitations.

Computed Tomography as a Characterization Tool for Engineered Scaffolds with Biomedical Applications

The ever-growing field of materials with applications in the biomedical field holds great promise regarding the design and fabrication of devices with specific characteristics, especially scaffolds with personalized geometry and architecture. The continuous technological development pushes the limits of innovation in obtaining adequate scaffolds and establishing their characteristics and performance. To this end, computed tomography (CT) proved to be a reliable, nondestructive, high-performance machine, enabling visualization and structure analysis at submicronic resolutions. CT allows both qualitative and quantitative data of the 3D model, offering an overall image of its specific architectural features and reliable numerical data for rigorous analyses. The precise engineering of scaffolds consists in the fabrication of objects with well-defined morphometric parameters (e.g., shape, porosity, wall thickness) and in their performance validation through thorough control over their behavior (in situ visualization, degradation, new tissue formation, wear, etc.). This review is focused on the use of CT in biomaterial science with the aim of qualitatively and quantitatively assessing the scaffolds’ features and monitoring their behavior following in vivo or in vitro experiments. Furthermore, the paper presents the benefits and limitations regarding the employment of this technique when engineering materials with applications in the biomedical field.

MRI-Based and Histologically Verified 3D Modeling of Spatial Distribution of Intra-Arterially Transplanted Cells in Rat Brain

Visualization of transplanted stem cells in the brain is an important issue in the study of the mechanisms of their therapeutic action. MRI allowing visualization of single transplanted cells previously labeled with superparamagnetic iron oxide particles is among the most informative methods of non-invasive intravital imaging. Verification of MRI data using pathomorphological examination at the microscopic level helps to avoid errors in data interpretation. However, making serial sections of the whole brain and searching for transplanted cells under the microscope is laborious and time-consuming. We have developed a method for 3D modeling of the distribution of transplanted cells in the brain allowing navigating through various brain structures and identifying the areas of accumulation of transplanted cells, which significantly increases the efficiency and reduces the time of histological examination.

Predictive Markers of Immunogenicity and Efficacy for Human Vaccines

Vaccines represent one of the major advances of modern medicine. Despite the many successes of vaccination, continuous efforts to design new vaccines are needed to fight "old" pandemics, such as tuberculosis and malaria, as well as emerging pathogens, such as Zika virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Vaccination aims at reaching sterilizing immunity, however assessing vaccine efficacy is still challenging and underscores the need for a better understanding of immune protective responses. Identifying reliable predictive markers of immunogenicity can help to select and develop promising vaccine candidates during early preclinical studies and can lead to improved, personalized, vaccination strategies. A systems biology approach is increasingly being adopted to address these major challenges using multiple high-dimensional technologies combined with in silico models. Although the goal is to develop predictive models of vaccine efficacy in humans, applying this approach to animal models empowers basic and translational vaccine research. In this review, we provide an overview of vaccine immune signatures in preclinical models, as well as in target human populations. We also discuss high-throughput technologies used to probe vaccine-induced responses, along with data analysis and computational methodologies applied to the predictive modeling of vaccine efficacy.

Noninvasive in vivo cell tracking using molecular imaging: A useful tool for developing mesenchymal stem cell-based cancer treatment

Mounting evidence has emphasized the potential of cell therapies in treating various diseases by restoring damaged tissues or replacing defective cells in the body. Cell therapies have become a strong therapeutic modality by applying noninvasive in vivo molecular imaging for examining complex cellular processes, understanding pathophysiological mechanisms of diseases, and evaluating the kinetics/dynamics of cell therapies. In particular, mesenchymal stem cells (MSCs) have shown promise in recent years as drug carriers for cancer treatment. They can also be labeled with different probes and tracked in vivo to assess the in vivo effect of administered cells, and to optimize therapy. The exact role of MSCs in oncologic diseases is not clear as MSCs have been shown to be involved in tumor progression and inhibition, and the exact interactions between MSCs and specific cancer microenvironments are not clear. In this review, a multitude of labeling approaches, imaging modalities, and the merits/demerits of each strategy are outlined. In addition, specific examples of the use of MSCs and in vivo imaging in cancer therapy are provided. Finally, present limitations and future outlooks in terms of the translation of different imaging approaches in clinics are discussed.

Magnetic Resonance Imaging for Translational Research in Oncology

The translation of results from the preclinical to the clinical setting is often anything other than straightforward. Indeed, ideas and even very intriguing results obtained at all levels of preclinical research, i.e., in vitro, on animal models, or even in clinical trials, often require much effort to validate, and sometimes, even useful data are lost or are demonstrated to be inapplicable in the clinic. In vivo, small-animal, preclinical imaging uses almost the same technologies in terms of hardware and software settings as for human patients, and hence, might result in a more rapid translation. In this perspective, magnetic resonance imaging might be the most translatable technique, since only in rare cases does it require the use of contrast agents, and when not, sequences developed in the lab can be readily applied to patients, thanks to their non-invasiveness. The wide range of sequences can give much useful information on the anatomy and pathophysiology of oncologic lesions in different body districts. This review aims to underline the versatility of this imaging technique and its various approaches, reporting the latest preclinical studies on thyroid, breast, and prostate cancers, both on small laboratory animals and on human patients, according to our previous and ongoing research lines.

An Introduction to Pathology in Biomedical Research: A Mission-Critical Specialty for Reproducibility and Rigor in Translational Research

This issue of ILAR Journal focusses on pathology and pathologists in biomedical research, more specifically in preclinical translational research involving (nonhuman) animals, emphasizing academic settings. Considerations in study design and planning to maximize benefit from pathologists and pathology resources are reviewed. Adjunctive technologies including molecular techniques, digital pathology, and imaging are highlighted. Additional considerations regarding safety and regulatory concerns, and veterinary clinical trials are reviewed as well. Pathology has been fundamental to understanding clinical disease, remains fundamental to diagnosing disease, and is required in drug and device development. Broader integration of pathology expertise and well-designed pathology investigations have much to offer research rigor and reproducibility, and successful translation from biomedical research.