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Vervet (Chlorocebus aethiops sabaeus) probabilistic atlas that defines an anatomical space (template) with associated tissue and regional prior probability maps. The atlas was produced from whole head MRI of 10 normal adult animal subjects. The package consists of two atlases. The Biased directory contains the average template and probabilistic atlases for selected tissue classes constructed by registering the training population to one subject. The Unbiased directory contains the atlas constructed using unbiased estimation. The atlas is suitable for use in any segmentation tool using a probabilistic atlas, for example those in Slicer.

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• SciCrunch
• 13 years ago - by Anonymous

Software toolbox for counting the frequency of K-tuple from sequencing datasets and calculate the dissimilarity.

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 2, 2022. Software that is an open-source distribution of a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wide range of shape analysis problems, including nonmanifold surfaces and objects of arbitrary topology. The proposed correspondence point optimization uses an entropy-based minimization that balances the simplicity of the model (compactness) with the accuracy of the surface representations. The ShapeWorks software includes tools for preprocessing data, computing point-based shape models, and visualizing the results.

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• SciCrunch
• 13 years ago - by Anonymous

Scribe encodes papers to populate the BrainMap Database

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• SciCrunch
• 13 years ago - by Anonymous

Software for detecting artifacts and performing individual region-of-interest based statistical analysis of fMRI data and enables users of fMRI technology to produce more detailed, consistent and reliable results.

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• SciCrunch
• 13 years ago - by Anonymous

Atlas of segmented and normalized high-resolution postmortem MRI of the human hippocampus. Additional data (raw images) is available through the SCM link. It requires knowing how to use CVS.

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• SciCrunch
• 13 years ago - by Anonymous

Software that uses a Bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins.

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• SciCrunch
• 12 years ago - by Anonymous

This project is meant for planning the NITRC Grantee meetings. A website for organizing meetings for the Neuroimaging Informatics Tools and Resources Clearinghouse, to facilitate participants meeting one another, and promote discussion of common interests and collaboration.

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• SciCrunch
• 13 years ago - by Anonymous

A resource for online accredited courses in a wide variety of areas, including accounting, animal care, beauty, building and construction, business, education, design and writing. This resource is based in Australia.

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• SciCrunch
• 13 years ago - by Anonymous

Software R package for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.

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• SciCrunch
• 12 years ago - by Anonymous

Understanding the mechanisms underlying the expression and perception of auditory communication in nonhuman primates provides important insights for understanding the neural systems that mediate nonverbal auditory communication in humans. Our research is devoted to understanding the changes in vocal behavior that are associated with maturation and social experience under normative conditions, and to investigating neural systems to define their roles in auditory communication. The anterior cingulate gyrus, in the frontal cerebral cortex, is an essential neural system for the expression of the primate isolation call, a structural and functional equivalent of the cry sounds of humans. Bilateral removal of this structure in adult squirrel monkeys resulted in a long-lasting inability to emit isolation calls. Partial recovery, often over many weeks, initially took the form of production of short, faint and uninflected versions of the typical isolation call. Humans suffering infarct damage to this region likewise show an initial recovery in the form of short, faint, monosyllabic sounds, suggesting that the anterior cingulate gyrus of nonhuman primates is the evolutionary precursor of a neural structure involved in human affective expression and speech. Our working model of isolation call production is that the anterior cingulate gyrus is the site where the command to produce this vocalization is initiated. Since the anterior cingulate region also has reciprocal connections with temporal lobe auditory cortex, a presumptive feedback pathway exists for registering commands to initiate vocalization with the temporal lobe cortex, which plays a major role in perceiving and decoding the acoustic details of species-specific vocalizations. At present, we do not know the role of the anterior cingulate gyrus in the production of infant vocalizations. However, we have found that neonatal removal of the amygdala, an important forebrain component of the limbic system, or portions of the inferotemporal gyrus, which sends projections to the amygdala, result in significant changes in the vocal behavior of infant rhesus macaques. Vocal development is a dynamic process, and a pattern shared by several nonhuman primates has emerged regarding the nature of this process. Infants are highly vocal during periods of brief separation from their caregiver, and we take advantage of this to document the range of vocalizations produced by infants of different ages. In the neonatal period, infants of 3 species of nonhuman primate (rhesus macaque, squirrel monkey and common marmoset) all produce sounds that vary widely in their acoustic structure. Many of these bear a striking similarity to sounds used in a variety of social settings by adults, suggesting that neural systems responsible for generating adult vocalizations are already in place during early infancy. As infants mature, their vocal behavior during brief periods of social separation becomes much more stereotyped. It isn't until much later in development, as individuals engage in a variety of social interactions with peers and adults, that the sounds expressed in early infancy begin to re-appear in adult contexts. The role of individual experience during development is currently being explored to determine the mechanisms leading to the acquisition of adult vocal skills.

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• SciCrunch
• 14 years ago - by Anonymous

Software package for control of automated microscopes. Cross-platform desktop application, to control motorized microscopes, scientific cameras, stages, illuminators, and other microscope accessories.

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• SciCrunch
• 13 years ago - by Anonymous

R software package for transcription factor (TF) target gene prediction based on ChIP-seq data. Version 0.4 contains code to compute FDR-corrected q-values via permutations of the peak-to-gene assignments (ClosestGene only).

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• SciCrunch
• 12 years ago - by Anonymous

OpenGL based medical image viewer that contains useful tools such as a DICOM anonymizer and format conversion utility. MIView can read DICOM, Analyze/Nifti, and raster images, and can write Analyze/Nifti and raster images.

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• SciCrunch
• 13 years ago - by Anonymous

The packaged tools perform Local Binary Pattern on Three Orthogonal Planes (LBP-TOP) analysis on MR brain images. One can use them to extract LBP texture features for machine learning applications or other advance analysis. Bash scripts performing simple preprocessing with FSL and AFNI as well as LBP mapping programs written by Java are both including in this package. The output is the histogram describing the brain morphology.

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• SciCrunch
• 13 years ago - by Anonymous

Discussion forum on licensing issues in software and data. All are invited to participate or join the project and contribute. A listing of software licenses are available.

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• SciCrunch
• 13 years ago - by Anonymous

A Bioconductor package that can import gates defined by the commercial package FlowJo and work with them in a manner consistent with the other flow packages in Bioconductor. FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the FlowJo Workspace. This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm.

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• SciCrunch
• 12 years ago - by Anonymous

An R/Bioconductor package that interfaces the X!Tandem protein identification algorithm.

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• SciCrunch
• 12 years ago - by Anonymous

Software R package for meta-analysis for microarrays. It combines either p-values or modified effect sizes from different studies to find differentially expressed genes.

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• SciCrunch
• 12 years ago - by Anonymous

Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.

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• SciCrunch
• 12 years ago - by Anonymous