Automated Vascular Smooth Muscle Segmentation, Reconstruction, Classification and Simulation on Whole-Slide Histology

Histology of the microvasculature depicts detailed characteristics relevant to tissue perfusion. One important histologic feature is the smooth muscle component of the microvessel wall, which is responsible for controlling vessel caliber. Abnormalities can cause disease and organ failure, as seen in hypertensive retinopathy, diabetic ischemia, Alzheimer’s disease and improper cardiovascular development. However, assessments of smooth muscle cell content are conventionally performed on selected fields of view on 2D sections, which may lead to measurement bias. We have developed a software platform for automated (1) 3D vascular reconstruction, (2) detection and segmentation of muscularized microvessels, (3) classification of vascular subtypes, and (4) simulation of function through blood flow modeling. Vessels were stained for α-actin using 3,3\u27-Diaminobenzidine, assessing both normal (n=9 mice) and regenerated vasculature (n=5 at day 14, n=4 at day 28). 2D locally adaptive segmentation involved vessel detection, skeletonization, and fragment connection. 3D reconstruction was performed using our novel nucleus landmark-based registration. Arterioles and venules were categorized using supervised machine learning based on texture and morphometry. Simulation of blood flow for the normal and regenerated vasculature was performed at baseline and during demand based on the structural measures obtained from the above tools. Vessel medial area and vessel wall thickness were found to be greater in the normal vasculature as compared to the regenerated vasculature (p\u3c0.001) and a higher density of arterioles was found in the regenerated tissue (p\u3c0.05). Validation showed: a Dice coefficient of 0.88 (compared to manual) for the segmentations, a 3D reconstruction target registration error of 4 μm, and area under the receiver operator curve of 0.89 for vessel classification. We found 89% and 67% decreases in the blood flow through the network for the regenerated vasculature during increased oxygen demand as compared to the normal vasculature, respectively for 14 and 28 days post-ischemia. We developed a software platform for automated vasculature histology analysis involving 3D reconstruction, segmentation, and arteriole vs. venule classification. This advanced the knowledge of conventional histology sampling compared to whole slide analysis, the morphological and density differences in the regenerated vasculature, and the effect of the differences on blood flow and function

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

© 2019, The Author(s). 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

Spectral Domain-optical Coherence Tomography for the Assessment of Cerebrovascular Plasticity

Vascular pathologies represent the leading causes of mortality worldwide, accounting for 31% of all deaths in 2012. Cerebral hypoxia is a condition that often manifests as a result of these medical conditions. Remarkably, the nervous system has evolved mechanisms to compensate for oxygen deprivation. The dilation of existing vessels and the growth of new blood vessels are two prominent physiological responses to hypoxia, both of which play a critical role in maintaining cerebral homeostasis. More recently, exercise has been shown to induce a mild state of hypoxia in the brain, leading to several robust morphological changes within the cerebrovascular system (e.g., angiogenesis, vasodilation). Thus, exercise serves as a viable model for investigating hypoxia-induced adaptations. The present study introduces spectral domain optical coherence tomography (SD-OCT) as a novel technique for examining these micro-level changes in the rat motor cortex. SD-OCT produces high resolution, three-dimensional angiograms, and allows for moderately invasive imaging within the same animal at multiple time points. The independent effect of exercise training on cerebrovascular structure and function has never been explored using SD-OCT. Thus, the primary goal of this study was to determine the relative efficacy of SD-OCT utility. To validate this novel technology, we employed SD-OCT in the examination of exercise-dependent blood vessel growth, as well as real-time capillary dilation in response to a laboratory-induced condition of hypoxia (i.e., 10% oxygen). In addition, histology data was collected to provide comparative measures for statistical analyses. At the start of this investigation, animals were pseudo-randomly assigned to one of two groups: 26-week voluntary exercise (VX), or an inactive control (IC). Upon completing the exercise treatment, animals were anesthetized and prepared for imaging. Vascular anatomy and blood velocity data was captured during three experimental conditions: [1] normal oxygen baseline, [2] hypoxia – 10% oxygen, and [3] normoxia, return to baseline. A two-way analysis of variance revealed a significant difference in total blood vessel density between treatment groups, independent of condition. That is, VX animals had a greater density of blood vessels in the scanned region of interest when compared to IC. These findings were confirmed using unbiased stereology techniques to analyze tissue in the scanned region of interest. Furthermore, statistical analyses revealed a significant increase in small arteriole diameter in both VX and IC animals. However, the dilation captured by SD-OCT was significantly greater in VX animals when compared to IC. In sum, exercise induces potent adaptations that promote greater flexibility during hypoxia. Moreover, these micro-level changes can be effectively probed using SD-OCT

Raman Scattering:From Structural Biology to Medical Applications

This is a review of relevant Raman spectroscopy (RS) techniques and their use in structural biology, biophysics, cells, and tissues imaging towards development of various medical diagnostic tools, drug design, and other medical applications. Classical and contemporary structural studies of different water-soluble and membrane proteins, DNA, RNA, and their interactions and behavior in different systems were analyzed in terms of applicability of RS techniques and their complementarity to other corresponding methods. We show that RS is a powerful method that links the fundamental structural biology and its medical applications in cancer, cardiovascular, neurodegenerative, atherosclerotic, and other diseases. In particular, the key roles of RS in modern technologies of structure-based drug design are the detection and imaging of membrane protein microcrystals with the help of coherent anti-Stokes Raman scattering (CARS), which would help to further the development of protein structural crystallography and would result in a number of novel high-resolution structures of membrane proteins—drug targets; and, structural studies of photoactive membrane proteins (rhodopsins, photoreceptors, etc.) for the development of new optogenetic tools. Physical background and biomedical applications of spontaneous, stimulated, resonant, and surface- and tip-enhanced RS are also discussed. All of these techniques have been extensively developed during recent several decades. A number of interesting applications of CARS, resonant, and surface-enhanced Raman spectroscopy methods are also discussed

Estudio del armazón arquitectónico y del sistema vascular de los tumores neuroblásticos

Los pacientes con tumores neuroblásticos presentan una evolución clínica heterogénea, desde la regresión espontánea hasta una alta propensión para la diseminación metastática generalizada. Aunque la aplicación de una clasificación de riesgo pre-tratamiento bien definida tiene un papel central en la mejora de la supervivencia durante los últimos años, han de llevarse a cabo más avances para mejorar la superviencia de los pacientes en general y específicamente el subgrupo de pacientes de alto riesgo. El estudio morfológico del tejido tumoral está contribuyendo a dicha mejora. La categoría histológica o el porcentaje de estroma tumoral, así como el grado de diferenciación de las células neuroblásticas, determinadas por el patólogo con el microscopio óptico, son factores con un papel importante en el diagnóstico y el pronóstico de los pacientes. Actualmente, dada la relevancia de la matriz extracelular tumoral en la biotensegridad y la mecanotransducción, su arquitectura y la topología de sus elementos, así como su interacción están siendo cada vez más considerados. Su cuantificación y caracterización con técnicas de imagen microscópicas empiezan a ser utilizadas. Nuestra hipótesis es que el destino de una célula tumoral neuroblástica es complejo y entre otros factores, está determinado por las características de un grupo de elementos estructurales no celulares de la matriz extracelular. Además pensamos que aplicando los patrones derivados del análisis morfométrico de estos elementos y asociandolos al impacto de los factores pronósticos conocidos, se mejorará la supervivencia de los pacientes. Nuestro objetivo es el desarrollo de técnicas morfométricas para caracterizar distintos elementos del andamiaje de la matriz extracelular y de la vascularización con el fin de encontrar usos potenciales como nuevos marcadores con valor pronóstico para mejorar la estratificación de los pacientes, o como dianas terapéuticas para ser capaces de remodelar los elementos aberrantes del andamiaje tisular, incluyendo la microvascularización. Hemos construido 19 micromatrices de tejido incluyendo más de 500 neuroblastomas, que fueron teñidos con alzul alcián a pH 2,5, Gomori, tricrómico de Masson, orceína y anti-CD31 para glicosaminoglicanos, fibras de reticulina, fibras de colágeno tipo I, fibras elásticas y vasos sanguíneos, respectivamente. Las laminillas fueron digitalizadas con un escáner de preparaciones y distintos algoritmos de análisis de imagen fueron diseñados o personalizados para detectar y caracterizar la cantidad, el tamaño y la forma de los distintos elementos estudiados de la matriz extracelular. Estos parámetros se relacionaron con los distintos subgrupos de neuroblastoma, teniendo en cuenta varias características clínicas, histopatológicas y genéticas. Los resultados obtenidos mostraron que las fibras de reticulina eran los componentes mayoritarios del andamiaje fibroso y que la abundancia y arquitectura de la microvascularización era relevante para el pronóstico de los niños con neuroblastoma. Una matriz extracelular rígida y poco porosa con vasos sanguíneos con luces irregulares se detectó principalmente en tumores pertenecientes a pacientes con pronóstico desfavorable. Un subgrupo de la cohorte de alto riesgo con muy mala supervivencia pudo ser definido por variables morfométricas de las fibras de reticulina y de los vasos sanguíneos. Concretamente, las muestras con un mayores áreas ocupadas tanto por fibras de reticulina formando grandes redes entrecruzadas, ramificadas y de organización compleja, como por vasos sanguíneos, junto con capilares y vasos tipo sinusoide de forma irregular y vénulas y arteriolas dilatas, estaban asociadas a un pronóstico muy desfavorable. En esta cohorte, las células con amplificación del gen MYCN conllevaron cambios topológicos detectables en relación a las fibras de reticulina y los vasos sanguíneos. Podemos concluir que es possible y conveniente cuantificar la sustancia fundamental, caracterizar el andamiaje fibroso y el sistema vascular de los tumors neuroblásticos gracias al análisis morfométrico de imágenes microscópicas. Algunas de las características morfométricas relaciondas con los distintos elementos de la matriz extracelular estudiados podrían ser usadas como ayuda diagnóstica del grupo de pacientes con riesgo ultra alto, tras estudiar una mayor cohorte. Los resultados obtenidos sugieren la necesidad de realizar trabajos multidisciplinarios para integrar de estos estudios a nivel internacional y que la información morfométrica de los elementos de la matriz extracelular, incluyendo el sistema vascular, pueda ser utilizada para una terapia basada en la mecanotransducción.Neuroblastic tumor patients present an heterogeneous clinical evolution, from spontaneous regression to a high propensity for widespread metastatic dissemination. Although the application of a well-defined pre-treatment risk classification plays a central role in the improvement of survival during the last years, more efforts must be done to improve patient’s survival in general and specifically in the subgroup of high risk patients. The morphological study of the tumoral tissue is contributing to such improvement. The histological category or the percentage of tumoral stroma, as well as the degree of differentiation of neuroblastic cells, evaluated by the pathologist with light microscopy, are factors that play a role in the diagnosis and prognosis of the patients. Given the role of tumoral extracellular matrix in biotensegrity and mechanotransduction, its architecture and the topology of its elements, as well as their interaction are being increasingly considered. Its quantification and characterization with microscopic image techniques start to be used. We hypothesize that the destiny of a neuroblastic tumor cell is complex and, is in part directed by characteristics of a set of non-cellular extracellular matrix structural elements. Additionally, we think that the application of the patterns derived from the morphometric analysis of such elements and their association with the impact of the known prognostic factors, patient’s survival will be improved. We aim to develop morphometric techniques to characterize different extracellular matrix scaffolding and vascular elements to find out potential uses as new prognostic markers for a better pre-treatment stratification of the patients or as therapeutic targets to be able to remodel the aberrant elements of the tissue scaffolding, including microvascularization. We constructed 19 tissue microarrays including more than 500 neuroblastomas which were stained with alcian blue pH 2.5, Gomori, Masson’s trichrome, orcein and anti-CD31 for glycosaminoglycans, reticulin fibers, collagen type I fibers, elastic fibers and blood vessels, respectively. The slides were digitized with a whole-slide scanner and different image-analysis algorithms were designed or customized to specifically detect and characterize the amount, the size and the shape of the different extracellular matrix elements studied. These parameters were related to different neuroblastoma subgroups, taking into account several clinical, histopathological and genetic features. The results obtained showed that reticulin fibers were the main components of the fibrous scaffolding and that microvasculature amount and architecture were relevant in the prognosis of neuroblastoma patients. A stiff and poorly porous extracellular matrix with irregularly-shaped vascular lumens was mainly detected in tumors belonging to patients with unfavorable prognosis. A subgroup of the high risk cohort with very poor survival could be defined by morphometric variables of reticulin fibers and blood vessels. Specificallly, those samples with high stained areas occupied by reticulin fibers forming large, crosslinking, branching and disorganized networks and by blood vessels, as well as with irregularly-shaped capillaries and sinusoid-like vessels and dilated venules, presented a very unfavorable survival. In this cohort, cells with MYCN gene amplification led to detectable topological changes regarding reticulin fibers and bood vessels. We can conclude that it is possible and convenient to quantify the fundamental substance and characterize the architecture of the fibrous scaffolding and the vascular system of neuroblastic tumors by means of the morphometric analysis of microscopic images. Some of the morphometric features related to the different extracellular matrix elements studied could be used as a diagnostic support for the ultra-high risk group of patients, after studying a larger cohort. The obtained results suggest the need of developing multidisciplinary efforts for an international integration of these studies, and that the morphometric information of the elements of the extracellular matrix, including the vascular system, could be used for a therapy based on mechanotransduction