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A significant challenge for brain histological data analysis is to precisely identify anatomical regions in order to perform accurate local quantifications and evaluate therapeutic solutions. Usually, this task is performed manually,…
Brightfield and fluorescent imaging of whole brain sections are funda- mental tools of research in mouse brain study. As sectioning and imaging become more efficient, there is an increasing need to automate the post-processing of sec- tions…
While modern imaging technologies such as fMRI have opened exciting new possibilities for studying the brain in vivo, histological sections remain the best way to study the anatomy of the brain at the level of single neurons. The…
Magnetic Resonance Imaging (MRI) is a technology for non-invasive imaging of anatomical features in detail. It can help in functional analysis of organs of a specimen but it is very costly. In this work, methods for (i) virtual…
We present a novel approach to automatically segment magnetic resonance (MR) images of the human brain into anatomical regions. Our methodology is based on a deep artificial neural network that assigns each voxel in an MR image of the brain…
Neuropathological analyses benefit from spatially precise volumetric reconstructions that enhance anatomical delineation and improve morphometric accuracy. Our prior work has shown the feasibility of reconstructing 3D brain volumes from 2D…
The Allen Brain Atlas (ABA) of the adult mouse consists of digitized expression profiles of thousands of genes in the mouse brain, co-registered to a common three-dimensional template (the Allen Reference Atlas). This brain-wide,…
In this paper, we propose a computational framework for 3D volume reconstruction from 2D histological slices using registration algorithms in feature space. To improve the quality of reconstructed 3D volume, first, intensity variations in…
Automated sample preparation and electron microscopy enables acquisition of very large image data sets. These technical advances are of special importance to the field of neuroanatomy, as 3D reconstructions of neuronal processes at the nm…
Nonlinear registration of 2D histological sections with corresponding slices of MRI data is a critical step of 3D histology reconstruction. This task is difficult due to the large differences in image contrast and resolution, as well as the…
Precise segmentation of brain structures in magnetic resonance imaging (MRI) is essential for reliable neuroimaging analysis, yet voxel-wise deep models often yield anatomically inconsistent results that diverge from expert-defined…
The reconstruction of cerebral cortex surfaces from brain MRI scans is instrumental for the analysis of brain morphology and the detection of cortical thinning in neurodegenerative diseases like Alzheimer's disease (AD). Moreover, for a…
The Allen Atlas of the adult mouse brain is a brain-wide, genome-wide data set that has been made available online, triggering a renaissance in neuroanatomy. In particular, it has been used to define brain regions in a computational,…
Surface analysis of the cortex is ubiquitous in human neuroimaging with MRI, e.g., for cortical registration, parcellation, or thickness estimation. The convoluted cortical geometry requires isotropic scans (e.g., 1mm MPRAGEs) and good…
Whole brain neuroanatomy using tera-voxel light-microscopic data sets is of much current interest. A fundamental problem in this field is the mapping of individual brain data sets to a reference space. Previous work has not rigorously…
Advances in image registration and machine learning have recently enabled volumetric analysis of postmortem brain tissue from conventional photographs of coronal slabs, which are routinely collected in brain banks and neuropathology…
Joint registration of a stack of 2D histological sections to recover 3D structure (``3D histology reconstruction'') finds application in areas such as atlas building and validation of \emph{in vivo} imaging. Straightforward pairwise…
In brain tumor diagnosis and surgical planning, segmentation of tumor regions and accurate analysis of surrounding normal tissues are necessary for physicians. Pathological variability often renders difficulty to register a well-labeled…
In modern medical diagnostics, magnetic resonance imaging (MRI) is an important technique that provides detailed insights into anatomical structures. In this paper, we present a comprehensive methodology focusing on streamlining the…
Medical image segmentation has become an essential technique in clinical and research-oriented applications. Because manual segmentation methods are tedious, and fully automatic segmentation lacks the flexibility of human intervention or…