143 research outputs found
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 m and 1.3 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 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
Open access resource for cellular-resolution analyses of corticocortical connectivity in the marmoset monkey
Understanding the principles of neuronal connectivity requires tools for efficient quantification and visualization of large datasets. The primate cortex is particularly challenging due to its complex mosaic of areas, which in many cases lack clear boundaries. Here, we introduce a resource that allows exploration of results of 143 retrograde tracer injections in the marmoset neocortex. Data obtained in different animals are registered to a common stereotaxic space using an algorithm guided by expert delineation of histological borders, allowing accurate assignment of connections to areas despite interindividual variability. The resource incorporates tools for analyses relative to cytoarchitectural areas, including statistical properties such as the fraction of labeled neurons and the percentage of supragranular neurons. It also provides purely spatial (parcellation-free) data, based on the stereotaxic coordinates of 2 million labeled neurons. This resource helps bridge the gap between high-density cellular connectivity studies in rodents and imaging-based analyses of human brains
Insight into the fundamental trade-offs of diffusion MRI from polarization-sensitive optical coherence tomography in ex vivo human brain
In the first study comparing high angular resolution diffusion MRI (dMRI) in the human brain to axonal orientation measurements from polarization-sensitive optical coherence tomography (PSOCT), we compare the accuracy of orientation estimates from various dMRI sampling schemes and reconstruction methods. We find that, if the reconstruction approach is chosen carefully, single-shell dMRI data can yield the same accuracy as multi-shell data, and only moderately lower accuracy than a full Cartesian-grid sampling scheme. Our results suggest that current dMRI reconstruction approaches do not benefit substantially from ultra-high b-values or from very large numbers of diffusion-encoding directions. We also show that accuracy remains stable across dMRI voxel sizes of 1 ​mm or smaller but degrades at 2 ​mm, particularly in areas of complex white-matter architecture. We also show that, as the spatial resolution is reduced, axonal configurations in a dMRI voxel can no longer be modeled as a small set of distinct axon populations, violating an assumption that is sometimes made by dMRI reconstruction techniques. Our findings have implications for in vivo studies and illustrate the value of PSOCT as a source of ground-truth measurements of white-matter organization that does not suffer from the distortions typical of histological techniques.Published versio
On the development of the chondrocranium and the histological anatomy of the head in perinatal stages of marsupial mammals
An overview of the literature on the chondrocranium of marsupial mammals reveals a relative conservatism in shape and structures. We document the histological cranial anatomy of individuals representing Monodelphis domestica, Dromiciops gliroides, Perameles sp. and Macropus eugenii. The marsupial chondrocranium is generally characterized by the great breadth of the lamina basalis, absence of pila metoptica and large otic capsules. Its most anterior portion (cupula nasi anterior) is robust, and anterior to it there are well-developed tactile sensory structures, functionally important in the neonate. Investigations of ossification centers at and around the nasal septum are needed to trace the presence of certain bones (e.g., mesethmoid, parasphenoid) across marsupial taxa. In many adult marsupials, the tympanic floor is formed by at least three bones: alisphenoid (alisphenoid tympanic process), ectotympanic and petrosal (rostral and caudal tympanic processes); the squamosal also contributes in some diprotodontians. The presence of an entotympanic in marsupials has not been convincingly demonstrated. The tubal element surrounding the auditory tube in most marsupials is fibrous connective tissue rather than cartilage; the latter is the case in most placentals recorded to date. However, we detected fibrocartilage in a late juvenile of Dromiciops, and a similar tissue has been reported for Tarsipes. Contradictory reports on the presence of the tegmen tympani can be found in the literature. We describe a small tegmen tympani in Macropus. Several heterochronic shifts in the timing of development of the chondocranium and associated structures (e.g., nerves, muscles) and in the ossification sequence have been interpreted as largely being influenced by functional requirements related to the altriciality of the newborn marsupial during early postnatal life. Comparative studies of chondocranial development of mammals can benefit from a solid phylogenetic framework, research on non-classical model organisms, and integration with imaging and sectional data derived from computer-tomography.Fil: Sánchez Villagra, Marcelo R.. Universitat Zurich; SuizaFil: Forasiepi, Analia Marta. Consejo Nacional de Investigaciones CientÃficas y Técnicas. Centro CientÃfico Tecnológico Conicet - Mendoza. Instituto Argentino de NivologÃa, GlaciologÃa y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de NivologÃa, GlaciologÃa y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de NivologÃa, GlaciologÃa y Ciencias Ambientales; Argentin
Navigating the Murine Brain: Toward Best Practices for Determining and Documenting Neuroanatomical Locations in Experimental Studies
In experimental neuroscientific research, anatomical location is a key attribute of experimental observations and critical for interpretation of results, replication of findings, and comparison of data across studies. With steadily rising numbers of publications reporting basic experimental results, there is an increasing need for integration and synthesis of data. Since comparison of data relies on consistently defined anatomical locations, it is a major concern that practices and precision in the reporting of location of observations from different types of experimental studies seem to vary considerably. To elucidate and possibly meet this challenge, we have evaluated and compared current practices for interpreting and documenting the anatomical location of measurements acquired from murine brains with different experimental methods. Our observations show substantial differences in approach, interpretation and reproducibility of anatomical locations among reports of different categories of experimental research, and strongly indicate that ambiguous reports of anatomical location can be attributed to missing descriptions. Based on these findings, we suggest a set of minimum requirements for documentation of anatomical location in experimental murine brain research. We furthermore demonstrate how these requirements have been applied in the EU Human Brain Project to optimize workflows for integration of heterogeneous data in common reference atlases. We propose broad adoption of some straightforward steps for improving the precision of location metadata and thereby facilitating interpretation, reuse and integration of data
Registration of histology and magnetic resonance imaging of the brain
Combining histology and non-invasive imaging has been attracting the attention of the medical imaging community for a long time, due to its potential to correlate macroscopic information with the underlying microscopic properties of tissues. Histology is an invasive procedure that disrupts the spatial arrangement of the tissue components but enables visualisation and characterisation at a cellular level. In contrast, macroscopic imaging allows non-invasive acquisition of volumetric information but does not provide any microscopic details. Through the establishment of spatial correspondences obtained via image registration, it is possible to compare micro- and macroscopic information and to recover the original histological arrangement in three dimensions. In this thesis, I present: (i) a survey of the literature relative to methods for histology reconstruction with and without the help of 3D medical imaging; (ii) a graph-theoretic method for histology volume reconstruction from sets of 2D sections, without external information; (iii) a method for multimodal 2D linear registration between histology and MRI based on partial matching of shape-informative boundaries
Towards efficient neurosurgery: Image analysis for interventional MRI
Interventional magnetic resonance imaging (iMRI) is being increasingly used for performing imageguided
neurosurgical procedures. Intermittent imaging through iMRI can help a neurosurgeon visualise
the target and eloquent brain areas during neurosurgery and lead to better patient outcome. MRI plays
an important role in planning and performing neurosurgical procedures because it can provide highresolution
anatomical images that can be used to discriminate between healthy and diseased tissue, as
well as identify location and extent of functional areas. This is of significant clinical utility as it helps
the surgeons maximise target resection and avoid damage to functionally important brain areas.
There is clinical interest in propagating the pre-operative surgical information to the intra-operative
image space as this allows the surgeons to utilise the pre-operatively generated surgical plans during
surgery. The current state of the art neuronavigation systems achieve this by performing rigid registration
of pre-operative and intra-operative images. As the brain undergoes non-linear deformations after
craniotomy (brain shift), the rigidly registered pre-operative images do not accurately align anymore
with the intra-operative images acquired during surgery. This limits the accuracy of these neuronavigation
systems and hampers the surgeon’s ability to perform more aggressive interventions. In addition,
intra-operative images are typically of lower quality with susceptibility artefacts inducing severe geometric
and intensity distortions around areas of resection in echo planar MRI images, significantly reducing
their utility in the intraoperative setting.
This thesis focuses on development of novel methods for an image processing workflow that aims
to maximise the utility of iMRI in neurosurgery. I present a fast, non-rigid registration algorithm that
can leverage information from both structural and diffusion weighted MRI images to localise target
lesions and a critical white matter tract, the optic radiation, during surgical management of temporal
lobe epilepsy. A novel method for correcting susceptibility artefacts in echo planar MRI images is also
developed, which combines fieldmap and image registration based correction techniques. The work
developed in this thesis has been validated and successfully integrated into the surgical workflow at the
National Hospital for Neurology and Neurosurgery in London and is being clinically used to inform
surgical decisions
3D Reconstruction of Anatomical Structures Using Interpolation Techniques and local Approaches
The reconstruction of the surface is the process by which a 3D object is reproduced from a collection of discrete values that sample the shape. These values are generally called point cloud. Commonly, the reconstruction methods are based on the fundamental properties of the point clouds, which are the density samples, noise, missing data, and outliers. We aim to reconstruct the surface of anatomical structures from medical images; Consider two main problems that are missing data and the presence of noise. We resolve the missing data by generating new samples from a set of contours based on Shape Morphing techniques. If we add noise to the previous problem, we must change the focus and therefore use an implicit rebuild method that is solid for the problems presented above. Finally, we combine part of the previous proposals to solve a specific problem, that occurs when we reconstruct medical images, when a contour is bifurcated into another. The methods are evaluated with the public database from medical images and compared with the standardized algorithms of state of the art and the Hausdorff distance is used to measure the perfanceResumen La reconstrucción de superficie es el proceso mediante el cual un objeto 3D se reproduce de una colección de valores discretos que muestran la forma. Estos valores generalmente son llamados nubes de puntos. Comúnmente, los métodos de reconstrucción se basan en las propiedades básicas de las nubes de puntos, que son la densidad de muestras, ruido, datos faltantes y los valores atÃpicos. Nuestro objetivo es reconstruir la superficie de estructuras anatómicas a partir de imágenes médicas. Consideraremos dos problemas principales que son los datos faltantes y la presencia de ruido. Resolvemos la falta de datos generando nuevas muestras a partir de un conjunto de contornos, basándonos en técnicas de Shape Morphing (forma cambiante). Si adicionamos ruido al problema anterior, debemos cambiar de enfoque por lo tanto utilizamos un método de reconstrucción implÃcita que se ha demostrado que es robusto a los problemas anteriormente mencionados. Por ´ultimo combinamos parte de las propuestas anteriores para resolver un problema especÃfico, que se presenta cuando reconstruimos imágenes médicas, que se trata, cuando un contorno se bifurca en otros contornos. Los métodos se evaluarán sobre bases de datos públicas de imágenes médicas y se compararon con dos algoritmos estándar del estado del arte y la medición de rendimiento de reconstrucción será la distancia de HausdorffMaestrÃ
Spatio-temporal gene expression analysis from 3D in situ hybridization images
In developmental biology, the expression of genes is studied to understand development, phenotypes and to construct models to understand disease. In this thesis, we explore and validate biological as well as computerized tools, to address research questions in developmental biology. Based on these techniques, we developed a workflow to generate a large number of 3D spatio-temporal patterns of gene expression. Though several techniques for gene expression analysis are available, most spatial gene expression data are only in 2D. In order to study gene expression and differentiation of structures during development at the same time, both spatial 3D information, and temporal data are essential. These spatio-temporal patterns of gene expression have to be generated. To that end, we have developed a workflow based on fluorescent in situ hybridization (FISH) (ZebraFISH;), confocal laser scanning microscopy (CLSM) and subsequent three-dimensional modeling with, in our case, TDR-3Dbase software- resulting in a large amount of 3D spatio-temporal patterns of gene expression, obtained in a straightforward and non-destructive manner. In the work described in this thesis, we applied the workflow to 30 genes in 5 developmental processes. 3D modeling and data mining software are used to analyse gene expression patterns in zebrafish embryos and across speciesZF Screens B.V.UBL - phd migration 201
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