相关论文: Cell-type-specific computational neuroanatomy, sim…
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,…
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…
We review quantitative methods and software developed to analyze genome-scale, brain-wide spatially-mapped gene-expression data. We expose new methods based on the underlying high-dimensional geometry of voxel space and gene space, and on…
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…
The voxelized Allen Atlas of the adult mouse brain (at a resolution of 200 microns) has been used in [arXiv:1303.0013] to estimate the region-specificity of 64 cell types whose transcriptional profile in the mouse brain has been measured in…
Cataloging the neuronal cell types that comprise circuitry of individual brain regions is a major goal of modern neuroscience and the BRAIN initiative. Single-cell RNA sequencing can now be used to measure the gene expression profiles of…
We use the Allen Gene Expression Atlas (AGEA) and the OMA ortholog dataset to investigate the evolution of mouse-brain neuroanatomy from the standpoint of the molecular evolution of brain-specific genes. For each such gene, using the…
The Allen Brain Atlas project (ABA) generated a genome-scale collection of gene-expression profiles using in-situ hybridization. These profiles were co-registered to the three-dimensional Allen Reference Atlas (ARA) of the adult mouse…
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…
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…
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 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…
Two cliques of genes identified computationally for their high co-expression in the mouse brain according to the Allen Brain Atlas, and for their enrichment in genes related to autism spectrum disorder, have recently been shown to be highly…
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…
In recent years, several studies have provided insight on the functioning of the brain which consists of neurons and form networks via interconnection among them by synapses. Neural networks are formed by interconnected systems of neurons,…
Morphology based analysis of cell types has been an area of great interest to the neuroscience community for several decades. Recently, high resolution electron microscopy (EM) datasets of the mouse brain have opened up opportunities for…
Numerical simulations rely on constructing accurate and detailed models to produce reliable results - a task that is often challenging. This task becomes notably more difficult when the model is of the human brain. We create an anatomically…
Precise identification of mouse brain microscopy images is a crucial first step when anatomical structures in the mouse brain are to be registered to a reference atlas. Practitioners usually rely on manual comparison of images or tools that…
Given an atlas of the brain and a number of injections to be performed in order to map out the connections between parts of the brain, we propose an algorithm to compute the coordinates of the injections. The algorithm is designed to sample…
For constructing neuronal network models computational neuroscientists have access to wide-ranging anatomical data that nevertheless tend to cover only a fraction of the parameters to be determined. Finding and interpreting the most…