Neuroinformatics

http://link.springer.com/journal/12021

List of Papers (Total 95)

A Topological Representation of Branching Neuronal Morphologies

Many biological systems consist of branching structures that exhibit a wide variety of shapes. Our understanding of their systematic roles is hampered from the start by the lack of a fundamental means of standardizing the description of complex branching patterns, such as those of neuronal trees. To solve this problem, we have invented the Topological Morphology Descriptor (TMD), a ...

Touching Soma Segmentation Based on the Rayburst Sampling Algorithm

Neuronal soma segmentation is essential for morphology quantification analysis. Rapid advances in light microscope imaging techniques have generated such massive amounts of data that time-consuming manual methods cannot meet requirements for high throughput. However, touching soma segmentation is still a challenge for automatic segmentation methods. In this paper, we propose a soma ...

CAS: Cell Annotation Software – Research on Neuronal Tissue Has Never Been so Transparent

CAS (Cell Annotation Software) is a novel tool for analysis of microscopic images and selection of the cell soma or nucleus, depending on the research objectives in medicine, biology, bioinformatics, etc. It replaces time-consuming and tiresome manual analysis of single images not only with automatic methods for object segmentation based on the Statistical Dominance Algorithm, but ...

Multimodal Neuroimaging in Schizophrenia: Description and Dissemination

In this paper we describe an open-access collection of multimodal neuroimaging data in schizophrenia for release to the community. Data were acquired from approximately 100 patients with schizophrenia and 100 age-matched controls during rest as well as several task activation paradigms targeting a hierarchy of cognitive constructs. Neuroimaging data include structural MRI, ...

A Comparison of Accelerated and Non-accelerated MRI Scans for Brain Volume and Boundary Shift Integral Measures of Volume Change: Evidence from the ADNI Dataset

The aim of this study was to assess whether the use of accelerated MRI scans in place of non-accelerated scans influenced brain volume and atrophy rate measures in controls and subjects with mild cognitive impairment and Alzheimer’s disease. We used data from 861 subjects at baseline, 573 subjects at 6 months and 384 subjects at 12 months from the Alzheimer’s Disease Neuroimaging ...

Multi-View Ensemble Classification of Brain Connectivity Images for Neurodegeneration Type Discrimination

Brain connectivity analyses using voxels as features are not robust enough for single-patient classification because of the inter-subject anatomical and functional variability. To construct more robust features, voxels can be aggregated into clusters that are maximally coherent across subjects. Moreover, combining multi-modal neuroimaging and multi-view data integration techniques ...

A Stereotactic Probabilistic Atlas for the Major Cerebral Arteries

Improved whole brain angiographic and velocity-sensitive MRI is pushing the boundaries of noninvasively obtained cerebral vascular flow information. The complexity of the information contained in such datasets calls for automated algorithms and pipelines, thus reducing the need of manual analyses by trained radiologists. The objective of this work was to lay the foundation for such ...

Collection of Simulated Data from a Thalamocortical Network Model

A major challenge in experimental data analysis is the validation of analytical methods in a fully controlled scenario where the justification of the interpretation can be made directly and not just by plausibility. In some sciences, this could be a mathematical proof, yet biological systems usually do not satisfy assumptions of mathematical theorems. One solution is to use ...

SpineCreator: a Graphical User Interface for the Creation of Layered Neural Models

There is a growing requirement in computational neuroscience for tools that permit collaborative model building, model sharing, combining existing models into a larger system (multi-scale model integration), and are able to simulate models using a variety of simulation engines and hardware platforms. Layered XML model specification formats solve many of these problems, however they ...

Dendritic and Axonal Wiring Optimization of Cortical GABAergic Interneurons

The way in which a neuronal tree expands plays an important role in its functional and computational characteristics. We aimed to study the existence of an optimal neuronal design for different types of cortical GABAergic neurons. To do this, we hypothesized that both the axonal and dendritic trees of individual neurons optimize brain connectivity in terms of wiring length. We took ...

NiftyFit: a Software Package for Multi-parametric Model-Fitting of 4D Magnetic Resonance Imaging Data

Multi-modal, multi-parametric Magnetic Resonance (MR) Imaging is becoming an increasingly sophisticated tool for neuroimaging. The relationships between parameters estimated from different individual MR modalities have the potential to transform our understanding of brain function, structure, development and disease. This article describes a new software package for such ...

Using the Gene Ontology to Annotate Key Players in Parkinson’s Disease

The Gene Ontology (GO) is widely recognised as the gold standard bioinformatics resource for summarizing functional knowledge of gene products in a consistent and computable, information-rich language. GO describes cellular and organismal processes across all species, yet until now there has been a considerable gene annotation deficit within the neurological and immunological ...

A Fast Method for the Segmentation of Synaptic Junctions and Mitochondria in Serial Electron Microscopic Images of the Brain

Recent electron microscopy (EM) imaging techniques permit the automatic acquisition of a large number of serial sections from brain samples. Manual segmentation of these images is tedious, time-consuming and requires a high degree of user expertise. Therefore, there is considerable interest in developing automatic segmentation methods. However, currently available methods are ...

Fuzzy-Logic Based Detection and Characterization of Junctions and Terminations in Fluorescence Microscopy Images of Neurons

Digital reconstruction of neuronal cell morphology is an important step toward understanding the functionality of neuronal networks. Neurons are tree-like structures whose description depends critically on the junctions and terminations, collectively called critical points, making the correct localization and identification of these points a crucial task in the reconstruction ...

Possum—A Framework for Three-Dimensional Reconstruction of Brain Images from Serial Sections

Techniques based on imaging serial sections of brain tissue provide insight into brain structure and function. However, to compare or combine them with results from three dimensional imaging methods, reconstruction into a volumetric form is required. Currently, there are no tools for performing such a task in a streamlined way. Here we propose the Possum volumetric reconstruction ...

NSDF: Neuroscience Simulation Data Format

Data interchange is emerging as an essential aspect of modern neuroscience. In the areas of computational neuroscience and systems biology there are multiple model definition formats, which have contributed strongly to the development of an ecosystem of simulation and analysis tools. Here we report the development of the Neuroscience Simulation Data Format (NSDF) which extends this ...

Quantitative Evaluation of Intensity Inhomogeneity Correction Methods for Structural MR Brain Images

The correction of intensity non-uniformity (INU) in magnetic resonance (MR) images is extremely important to ensure both within-subject and across-subject reliability. Here we tackled the problem of objectively comparing INU correction techniques for T1-weighted images, which are the most commonly used in structural brain imaging. We focused our investigations on the methods ...