A Method for 3D Histopathology Reconstruction Supporting Mouse Microvasculature Analysis.

Structural abnormalities of the microvasculature can impair perfusion and function. Conventional histology provides good spatial resolution with which to evaluate the microvascular structure but affords no 3-dimensional information; this limitation could lead to misinterpretations of the complex microvessel network in health and disease. The objective of this study was to develop and evaluate an accurate, fully automated 3D histology reconstruction method to visualize the arterioles and venules within the mouse hind-limb. Sections of the tibialis anterior muscle from C57BL/J6 mice (both normal and subjected to femoral artery excision) were reconstructed using pairwise rigid and affine registrations of 5 µm-thick, paraffin-embedded serial sections digitized at 0.25 µm/pixel. Low-resolution intensity-based rigid registration was used to initialize the nucleus landmark-based registration, and conventional high-resolution intensity-based registration method. The affine nucleus landmark-based registration was developed in this work and was compared to the conventional affine high-resolution intensity-based registration method. Target registration errors were measured between adjacent tissue sections (pairwise error), as well as with respect to a 3D reference reconstruction (accumulated error, to capture propagation of error through the stack of sections). Accumulated error measures were lower (

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

Large Deformation Diffeomorphic Metric Mapping Registration of Reconstructed 3D Histological Section Images and in vivo MR Images

Our current understanding of neuroanatomical abnormalities in neuropsychiatric diseases is based largely on magnetic resonance imaging (MRI) and post mortem histological analyses of the brain. Further advances in elucidating altered brain structure in these human conditions might emerge from combining MRI and histological methods. We propose a multistage method for registering 3D volumes reconstructed from histological sections to corresponding in vivo MRI volumes from the same subjects: (1) manual segmentation of white matter (WM), gray matter (GM) and cerebrospinal fluid (CSF) compartments in histological sections, (2) alignment of consecutive histological sections using 2D rigid transformation to construct a 3D histological image volume from the aligned sections, (3) registration of reconstructed 3D histological volumes to the corresponding 3D MRI volumes using 3D affine transformation, (4) intensity normalization of images via histogram matching, and (5) registration of the volumes via intensity based large deformation diffeomorphic metric (LDDMM) image matching algorithm. Here we demonstrate the utility of our method in the transfer of cytoarchitectonic information from histological sections to identify regions of interest in MRI scans of nine adult macaque brains for morphometric analyses. LDDMM improved the accuracy of the registration via decreased distances between GM/CSF surfaces after LDDMM (0.39 ± 0.13 mm) compared to distances after affine registration (0.76 ± 0.41 mm). Similarly, WM/GM distances decreased to 0.28 ± 0.16 mm after LDDMM compared to 0.54 ± 0.39 mm after affine registration. The multistage registration method may find broad application for mapping histologically based information, for example, receptor distributions, gene expression, onto MRI volumes

Robust point correspondence applied to two and three-dimensional image registration

Accurate and robust correspondence calculations are very important in many medical and biological applications. Often, the correspondence calculation forms part of a rigid registration algorithm, but accurate correspondences are especially important for elastic registration algorithms and for quantifying changes over time. In this paper, a new correspondence calculation algorithm, CSM (correspondence by sensitivity to movement), is described. A robust corresponding point is calculated by determining the sensitivity of a correspondence to movement of the point being matched. If the correspondence is reliable, a perturbation in the position of this point should not result in a large movement of the correspondence. A measure of reliability is also calculated. This correspondence calculation method is independent of the registration transformation and has been incorporated into both a 2D elastic registration algorithm for warping serial sections and a 3D rigid registration algorithm for registering pre and postoperative facial range scans. These applications use different methods for calculating the registration transformation and accurate rigid and elastic alignment of images has been achieved with the CSM method. It is expected that this method will be applicable to many different applications and that good results would be achieved if it were to be inserted into other methods for calculating a registration transformation from correspondence

Towards ultra-high resolution 3D reconstruction of a whole rat brain from 3D-PLI data

3D reconstruction of the fiber connectivity of the rat brain at microscopic scale enables gaining detailed insight about the complex structural organization of the brain. We introduce a new method for registration and 3D reconstruction of high- and ultra-high resolution (64 $\mu$m and 1.3 $\mu$m pixel size) histological images of a Wistar rat brain acquired by 3D polarized light imaging (3D-PLI). Our method exploits multi-scale and multi-modal 3D-PLI data up to cellular resolution. We propose a new feature transform-based similarity measure and a weighted regularization scheme for accurate and robust non-rigid registration. To transform the 1.3 $\mu$m ultra-high resolution data to the reference blockface images a feature-based registration method followed by a non-rigid registration is proposed. Our approach has been successfully applied to 278 histological sections of a rat brain and the performance has been quantitatively evaluated using manually placed landmarks by an expert.Comment: 9 pages, Accepted at 2nd International Workshop on Connectomics in NeuroImaging (CNI), MICCAI'201

Registration and Analysis of Developmental Image Sequences

Mapping images into the same anatomical coordinate system via image registration is a fundamental step when studying physiological processes, such as brain development. Standard registration methods are applicable when biological structures are mapped to the same anatomy and their appearance remains constant across the images or changes spatially uniformly. However, image sequences of animal or human development often do not follow these assumptions, and thus standard registration methods are unsuited for their analysis. In response, this dissertation tackles the problems of i) registering developmental image sequences with spatially non-uniform appearance change and ii) reconstructing a coherent 3D volume from serially sectioned images with non-matching anatomies between the sections. There are three major contributions presented in this dissertation. First, I develop a similarity metric that incorporates a time-dependent appearance model into the registration framework. The proposed metric allows for longitudinal image registration in the presence of spatially non-uniform appearance change over time—a common medical imaging problem for longitudinal magnetic resonance images of the neonatal brain. Next, a method is introduced for registering longitudinal developmental datasets with missing time points using an appearance atlas built from a population. The proposed method is applied to a longitudinal study of young macaque monkeys with incomplete image sequences. The final contribution is a template-free registration method to reconstruct images of serially sectioned biological samples into a coherent 3D volume. The method is applied to confocal fluorescence microscopy images of serially sectioned embryonic mouse brains.Doctor of Philosoph

Precise Three-Dimensional Morphology of the Male Anterior Anorectum Reconstructed From Large Serial Histologic Sections: A Cadaveric Study

BACKGROUND: Deep anatomic knowledge of the male anterior anorectum is important to avoid urethral injury and rectal perforation in intersphincteric resection or abdominoperineal resection for very low rectal cancer. However, its structure is difficult to understand, because the anorectum, muscles, and urogenital organs are complicatedly and 3-dimensionally arranged. OBJECTIVE: The purpose of this study was to revisit the anatomic information of the male anterior anorectum for intersphincteric resection and abdominoperineal resection with a focus on the spatial muscular morphology. DESIGN: This was a descriptive cadaveric study. SETTINGS: The study was conducted at Ehime and Kyoto universities. PATIENTS: Tissue specimens from 9 male cadavers were included. MAIN OUTCOME MEASURES: Specimens around the anterior anorectum were serially sectioned in the horizontal, sagittal, or frontal plane; large semiserial histologic sections were created at 250-μm intervals. The series were stained with Elastica van Gieson, and some sections from the series were studied by immunohistochemistry to detect smooth and striated muscles. Two series were digitalized and reconstructed 3-dimensionally. RESULTS: Two regions without a clear anatomic border were elucidated: 1) the anterior region of the external anal sphincter, where the external anal sphincter, bulbospongiosus muscle, and superficial transverse perineal muscle were intertwined; and 2) the rectourethralis muscle, where the smooth muscle of the longitudinal muscle continuously extended to the posteroinferior area of the urethra, which became closest to the anorectum at the prostatic apex level. A tight connection between the striated and smooth muscles was identified at the anterior part of the upper external anal sphincter and anterolateral part of the puborectalis muscle level. LIMITATIONS: This study involved a small sample size of elderly cadavers. CONCLUSIONS: This study clarified the precise spatial relationship between smooth and striated muscles. The detailed anatomic findings will contribute more accurate step-by-step anterior dissection in intersphincteric resection and abdominoperineal resection, especially with the transanal approach, which can magnify the muscle fiber direction and contraction of striated muscle by electrostimulation. MORFOLOGÍA TRIDIMENSIONAL PRECISA DEL ANORRECTO ANTERIOR MASCULINO RECONSTRUIDO A TRAVÉS DE SECCIONES MAYORES HISTOLÓGICAS EN SERIE: UN ESTUDIO CADAVÉRICO: El conocimiento anatómico amplio del anorrecto anterior masculino es importante para evitar lesiones de uretra y perforación de recto en la resección interesfinterica o la resección abdominoperineal para cáncer de recto bajo. Sin embargo, su estructura es difícil de entender porque el anorrecto, los músculos y los órganos urogenitales están aliñados en forma complexa tridimensional. OBJETIVO: Revisar de nuevo el conocimiento anatómico del anorrecto anterior masculino relevante a la resección interesfinterica y la resección abdominoperineal con un enfoque en la morfología muscular espacial. DISEÑO:: Estudio descriptivo cadavérico. ENTORNO: Ehime y la Universidad de Kyoto. SUJETOS: Tejido especímenes de nueve cadáveres masculinos. PUNTOS FINALES DE VALORACIÓN:: Las muestras alrededor del anorrecto anterior se seccionaron en serie en planos horizontal, sagital y coronal. Se crearon mayores secciones histológicas en serie a intervalos de 250 μm. Los especímenes fueron teñidos con Elástica van Gieson, y algunas secciones de la serie se estudiaron mediante inmunohistoquímica para detectar músculos lisos y estriados. Dos series fueron digitalizadas y reconstruidas tridimensionalmente. RESULTADOS: Se demostraron dos regiones sin un borde anatómico definido: (i) la región anterior del esfínter anal externo, donde se entrelazaron el esfínter anal externo, el músculo bulbospongoso y el músculo perineal transverso superficial; y (ii) músculo rectouretral, donde el músculo liso del músculo longitudinal se extiende continuamente a la zona posteroinferior de la uretra, que se acerca más al anorrecto a nivel del ápice prostático. La conexión estrecha entre los músculos estriados y lisos se identificó en la parte anterior del esfínter anal externo superior y la parte anterolateral del nivel del músculo puborrectal. LIMITACIÓN:: Este estudio incluyó una muestra pequeña de cadáveres ancianos. CONCLUSIÓN:: Este estudio aclaró la relación espacial precisa entre los músculos lisos y estriados. Los hallazgos anatómicos detallados ayudarán para una disección anterior paso a paso más precisa en la resección interesfintérica y la resección abdominoperineal, especialmente con el abordaje transanal, que puede magnificar la dirección de las fibras musculares y la contracción del músculo estriado utilizando electroestimulación

The filter-house of the larvacean Oikopleura dioica. A complex extracellular architecture : from fiber production to rudimentary state to inflated house

While cellulose is the most abundant macromolecule in the biosphere, most animals are unable to produce cellulose with the exception of tunicates. Some tunicates have evolved the ability to secrete a complex house containing cellulosic fibers, yet little is known about the early stages of the house building process. Here, we investigate the rudimentary house of Oikopleura dioica for the first time using complementary light and electron microscopic techniques. In addition, we digitally modelled the arrangement of chambers, nets, and filters of the functional, expanded house in three dimensions based on life-video-imaging. Combining 3D-reconstructions based on serial histological semithin-sections, confocal laser scanning microscopy, transmission electron microscopy, scanning electron microscopy (SEM), and focused ion beam (FIB)-SEM, we were able to elucidate the arrangement of structural components, including cellulosic fibers, of the rudimentary house with a focus on the food concentration filter. We developed a model for the arrangement of folded structures in the house rudiment and show it is a precisely preformed structure with identifiable components intricately correlated with specific cells. Moreover, we demonstrate that structural details of the apical surfaces of Nasse cells provide the exact locations and shapes to produce the fibers of the house and interact amongst each other, with Giant Fol cells, and with the fibers to arrange them in the precise positions necessary for expansion of the house rudiment into the functional state. The presented data and hypotheses advance our knowledge about the interrelation of structure and function on different biological levels and prompt investigations into this astonishing biological object