Curator Dashboard

THIS RESOURCE IS NO LONGER IN SERVICE, documented Jan. 5, 2016. Tools will be available for biomedical data mining and visualization as well as linkages to Google Maps and other online resources.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software for efficient generation and simulation of models containing stochastic ion channels distributed across dendritic and axonal membranes. It computes the behavior of neurons taking account of the stochastic nature of ion channel gating and the detailed positions of the channels themselves. It is designed as a complement for existing tools.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A Matlab toolbox that computes the Q-Ball Imaging Orientation Distribution Function in Constant Solid Angle (CSA-ODF) for diffusion-weighted MRI.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Open source tool for multi-modal medical and brain data visualization. It is a tool for the scientific user and a powerful framework for the visualization researcher. It is written in Standard C++ and uses a number of portable libraries (e.g. Qt, Boost and OpenSceneGraph). It runs on common GNU/Linux operating systems, Mac OSX and Windows.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A multi-platform software dedicated to designing, testing and using brain-computer interfaces (BCI). OpenViBE is a software for real-time neurosciences that can be used to acquire, filter, process, classify and visualize brain signals in real time.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A diffusion spectrum imaging (DSI) template constructed in the standard ICBM-152 space from 122 healthy adults. The template was built through incorporating the macroscopic anatomical information using high-resolution T1-weighted images and the microscopic structural information obtained from DSI datasets, rendering it to achieve a high anatomical matching to the ICBM-152 space. This template can serve as a representative DSI dataset for a healthy adult population. It is released in its original DWI format.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Standalone software designed to be used by radiology researchers for storage and anonymization of research images.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A repository of schizophrenia neuroimaging data collected from over 450 individuals with schizophrenia, healthy controls and their respective siblings, most with 2-year longitudinal follow-up. The data include neuroimaging data, cognitive data, clinical data, and genetic data.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A set of Matlab scripts for analyzing neuroimaging data from clinical populations. The NiiStat tools are designed to correlate behavioral data (task performance) with brain imaging data.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A MATLAB GUI for segmenting and quantifying PET images with multi-focal and diffuse uptakes. It imports a PET image and allows the user to draw region of interests (ROIs) in 2D or 3D to roughly separate the object of interest from the background. The areas are then segmented using a PET image segmentation method based on Affinity Propagation clustering to cluster the image intensities into meaningful groups. For quantification, the Standardized Uptake Value measurements of the binary or the user defined ROI are SUVmax, SUVmean, and Volume (mm^3) and can be exported into an excel sheet.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A segmentation tool for the segmentation of a lung from CT images. The sofware can be run in two modes: fully automatic and semi-automatic with manual seeding by the user. The software also allows the user to perform basic filtering operations and manual correction to the segmentation. The VTK-based rendering implementation, along with option to view in axial, coronal, and sagittal, provides the user with better visualization of the segmented lung.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A database which contains longitudinal structural MRIs, spectroscopy, DTI and correlated clinical/behavioral data from approximately 500 healthy, normally developing children, ages newborn to young adult.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A simulation language for modeling biophysically realistic neural circuits (1 to 10,000 neurons) and simulating physiology experiments on it. Programs for plotting and displaying data are included.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A Matlab-based toolbox initially created for reading, writing, and processing of BrainVoyager (QX) files in Matlab.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A set of ImageJ plugins for fully automated measurement of neurite outgrowth in fluorescence microscopy images of cultured neurons. The plugin analyzes fluorescence microscopy images of neurites and nuclei of dissociated cultured neurons. Given user-defined thresholds, the plugin counts neuronal nuclei, and traces and measures neurite length. NeuriteTracer accurately measures neurite outgrowth from cerebellar, DRG and hippocampal neurons.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

This tool allows segmenting neonate brain MRI using a subject-specific atlas. It generates a subject-specific atlas based on an atlas population and some diffusion images of the subject to segment. Then a single atlas method is run with this atlas to obtain results.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A tool which computes an automatic segmentation of neonatal brain MRI. It uses a registered probabilistic brain atlas to select training samples and to be used as a spatial prior.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A statistical analysis tool for manifold-valued data. The SPD manifold for diffusion tensor images (DTI) and the Hilbert unit sphere for square root representation of orientation distribution functions (ODF) can be used.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A Matlab-based tool for computational neuroscience-based analysis and data visualization. Its features include: surface mesh visualization in PLY, PIAL, NV, STL,VTK, and GIFTI formats; conversion of NIfTI voxel images to surface meshes and saving as PLY or VTK; track (TRK files) visualization; connectome data (BrainNet Viewer .node and .edge files) visualization; intuitive GUI; that availability of all functions available in the GUI through scripting (automated scripts can be created); and exporting of rendered image as bitmap.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Web tool to provide brain measurement services. Used for modeling the living human brain. Used to make quantitative measurements of the volume, shape, and location of specific neuroanatomical structures using given MRI brain scans.The final measurements result from automated analyses that are manually guided, inspected and certified by a neuroanatomical expert. In addition to raw measurements, graphical presentations, surface renderings, and movies (rotations and fly-throughs) can be provided along with shape and statistical analyses that are calculated with respect to continually growing reference data bases. Databases of neuroanatomically labeled MRI brain scans. Resource for neuroanatomical localization and identification: NeuAtlas.

• Resource
• SciCrunch
• 11 years ago - submitted by Kristen Jensen