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The three-dimensional data-driven Allen Gene Expression Atlas of the adult mouse brain consists of numerized in-situ hybridization data for thousands of genes, co-registered to the Allen Reference Atlas. We propose quantitative criteria to…
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…
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…
We explore encoding brain symmetry into a neural network for a brain tumor segmentation task. A healthy human brain is symmetric at a high level of abstraction, and the high-level asymmetric parts are more likely to be tumor regions. Paying…
Medical images used in clinical practice are heterogeneous and not the same quality as scans studied in academic research. Preprocessing breaks down in extreme cases when anatomy, artifacts, or imaging parameters are unusual or protocols…
Deep brain stimulation (DBS) has the potential to improve the quality of life of people with a variety of neurological diseases. A key challenge in DBS is in the placement of a stimulation electrode in the anatomical location that maximizes…
Advances in experimental neuroscience have transformed our ability to explore the structure and function of neural circuits. At the same time, advances in machine learning have unleashed the remarkable computational power of artificial…
We describe coordinate systems adapted for the space between two surfaces, such as those delineating the highly folded cortex in mammalian brains. These systems are estimated in order to satisfy geometric priors, including streamline…
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,…
Brain mapping research in most neuroanatomical laboratories relies on conventional processing techniques, which often introduce histological artifacts such as tissue tears and tissue loss. In this paper we present techniques and algorithms…
Automated segmentation of anatomical sub-regions with high precision has become a necessity to enable the quantification and characterization of cells/ tissues in histology images. Currently, a machine learning model to analyze…
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,…
We present a novel method for quantifying the microscopic structure of brain tissue. It is based on the automated recognition of interpretable features obtained by analyzing the shapes of cells. This contrasts with prevailing methods of…
The Allen Atlas of the adult mouse brain is used to estimate the region-specificity of 64 cell types whose transcriptional profile in the mouse brain has been measured in microarray experiments. We systematically analyze the preliminary…
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,…
Whole-brain neural connectivity data are now available from viral tracing experiments, which reveal the connections between a source injection site and elsewhere in the brain. These hold the promise of revealing spatial patterns of…
Fast and automatic algorithm to segment Brain (intracranial region) from computed tomography (CT) head images using combination of HU thresholding, identification of intracranial voxels through ray intersection with cranium, special binary…
The Scalable Brain Atlas (SBA) is a collection of web services that provide unified access to a large collection of brain atlas templates for different species. Its main component is an atlas viewer that displays brain atlas data as a stack…
Quantitative criteria are proposed to identify genes (and sets of genes) whose expression marks a specific brain region (or a set of brain regions). Gene-expression energies, obtained for thousands of mouse genes by numerization of in-situ…
Cytoarchitectonic parcellations of the human brain serve as anatomical references in multimodal atlas frameworks. They are based on analysis of cell-body stained histological sections and the identification of borders between brain areas.…