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http://ric.uthscsa.edu/mango/

A viewer for medical research images that provides analysis tools and a user interface to navigate image volumes. There are three versions of Mango, each geared for a different platform: * Mango ? Desktop ? Mac OS X, Windows, and Linux * webMango ? Browser ? Safari, Firefox, Chrome, and Internet Explorer * iMango ? Mobile ? Apple iPad Key Features: * Built-in support for DICOM, NIFTI, Analyze, and NEMA-DES formats * Customizable: Create plugins, custom filters, color tables, file formats, and atlases * ROI Editing: Threshold and component-based tools for painting and tracing ROIs * Surface Rendering: Interactive surface models supporting cut planes and overlays * Image Registration: Semi-automatic image coregistration and manual transform editing * Image Stacking: Threshold and transparency-based image overlay stacking * Analysis: Histogram, cross-section, time-series analysis, image and ROI statistics * Processing: Kernel and rank filtering, arithmetic/logic image and ROI calculators

Proper citation: Mango (RRID:SCR_009603) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/vmagnotta/

A Diffusion Tensor fiber tracking software suite that includes streamline tracking tools. The fiber tracking includes a guided tracking tool that integrates apriori information into a streamlines algorithm. This suite of programs is built using the NA-MIC toolkit and uses the Slicer3 execution model framework to define the command line arguments. These tools can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3. NOTE: All new development is being managed in a github repository. Please visit, https://github.com/BRAINSia/BRAINSTools

Proper citation: GTRACT (RRID:SCR_009651) Copy   

•   Source: SciCrunch Registry

http://www.blueprintnhpatlas.org/

Atlas of gene expression in the developing rhesus macaque brain. This atlas is a free online resource with a unique set of data and tools aimed to create a developmental neuroanatomical framework for exploring the cellular and molecular architecture of the developing postnatal primate brain with direct relevance for human brain development. The atlas includes: * Microarray ** Microdissection: Fine structure transcriptional profiling across postnatal development for fine nuclear subdivisions of the prefrontal cortex, primary visual cortex, hippocampus, amygdala and ventral striatum ** Macrodissection: Gross structure transcriptional profiling across postnatal development for the same structures * ISH: ** Cellular resolution in situ hybridization image data of five major brain regions during postnatal developmental periods for genes clinically important for a variety of human neurodevelopmental disorders, including prefrontal cortex, primary visual cortex, hippocampus, amygdala and ventral striatum. ** Serial analysis of selected genes across the entire adult brain, focusing on cellular marker genes, genes with cortical area specificity and gene families important to neural function. * ISH Anatomic Search: Detailed gene expression search on the ISH data based on expert annotation * Reference Data: Developmental stage-specific reference series, consisting of magnetic resonance imaging (MRI) and Nissl histology to provide a neuroanatomical context for the gene expression data. These data and tools are designed to provide a valuable public resource for researchers and educators to explore neurodevelopment in non-human primates, and a key evolutionary link between other Web-based gene expression atlases for adult and developing mouse and human brain.

Proper citation: NIH Blueprint NHP Atlas (RRID:SCR_010559) Copy   

•   Source: SciCrunch Registry

http://brainandsociety.org/the-brain-observatory

Formerly a topical portal studying the brain which collected and imaged 1000 human brains, the Brain Observatory has partnered with the Institute for Brain and Society to build virtual laboratories that will feed directly into the database of images and knowledge created in the context of the Human Brain Library. The Brain Observatory will also host exhibits, conferences, and events aimed at promoting a heightened awareness of brain research and how its results can benefit personal brain fitness and mental health.

Proper citation: Brain Observatory (RRID:SCR_010641) Copy   

•   Source: SciCrunch Registry

http://nipy.org

Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration.

Proper citation: Neuroimaging in Python (RRID:SCR_013141) Copy   

•   Source: SciCrunch Registry

https://www.delaneycare.org/index.php

The Collaboratory of AIDS Researchers for Eradication (CARE) is a consortium of scientific experts in the field of HIV latency from several U.S. and European academic research institutions as well as Merck Research Laboratories working together to find a cure for HIV.

Proper citation: Collaboratory of AIDS Researchers for Eradciation (CARE) (RRID:SCR_013681) Copy   

•   Source: SciCrunch Registry

http://hbatlas.org/pages/publications

A research paper with supplementary materials reporting the generation and analysis of exon-level transcriptome and associated genotyping data. The experiment represented both males and females of multiple ethnicities and examines gene regulation and expression in different areas of the brain. A data set on the human brain transcriptome as well as insights into the transcriptional foundations of human neurodevelopment is provided.

Proper citation: Spatio-temporal transcriptome of the human brain (RRID:SCR_013743) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/nusdast

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.

Proper citation: Northwestern University Schizophrenia Data and Software Tool (NUSDAST) (RRID:SCR_014153) Copy   

•   Source: SciCrunch Registry

http://brainvis.wustl.edu/wiki/index.php/Caret:About

Software package to visualize and analyze structural and functional characteristics of cerebral and cerebellar cortex in humans, nonhuman primates, and rodents. Runs on Apple (Mac OSX), Linux, and Microsoft Windows operating systems.

Proper citation: Computerized Anatomical Reconstruction and Editing Toolkit (RRID:SCR_006260) Copy   

•   Source: SciCrunch Registry

http://dally.nimh.nih.gov/matoff/matoff.html

An interactive analysis program that searches neurophysiological data and plots the results. MatOFF was developed especially for dealing with the complexities common to behavioral neurophysiological experiments. It runs under Windows 2000 or XP and relies on MATLAB version R11.1 (or above) for all operations. MatOFF searches a data file to locate and plot epochs (trials) of special interest to the investigator. Appropriate input data files have time-stamped event codes, usually including neuron action potential firing events (spikes), and digitized analog data. The user specifies a list of event code numbers that uniquely identify a sequence of events. MatOFF uses this sequence to search the raw data file, select the epochs that meet the criteria, time-shift the trials to align them on a common event, order the epochs based on user-selected criteria, and plot the results based on a collection of page formatting specifications. MatOFF will also save extracted data and some statistics to disk. Features: * Powerful, interactive searching tools for locating relevant experimental events * Compatible with Cortex data acquisition program * Compatible with Plexon data acquisition system * Flexible, publication-quality graphical display and printing * Comprehensive scripting language * Supports learning and other dynamic behavior * Integrated interface to MATLAB functions * Automatic alignment of trial data and generation of histograms * Large variety of options for selecting and ordering trial data * Descriptive and non-parametric statistics * XY analog displays * Data export with flexible format control * Up to 72 plots per page * Display templates can be saved and reloaded * Free for public or private use * Adaptable to almost any data file format

Proper citation: MatOFF (RRID:SCR_006821) Copy   

•   Source: SciCrunch Registry

http://dally.nimh.nih.gov/index.html

A program developed by the NIMH Laboratory of Neuropsychology for data acquisition and experimental control of neurophysiological experiments. The purpose of this website is to make it easier to access new versions of NIMH CORTEX and its supporting documents. Ultimately, it is also hoped that these pages will make it easier for users to report bugs, request enhancements, and obtain help. Download the latest version and unzip it into a new sub-directory. Then read the on-line documentation. For the new user, the User''s Manuals are invaluable in specifying system requirements and giving an overview of the features and necessary hardware. The Function reference goes into more detail about how to write experiments using NIMH CORTEX. The Demos reference is a good place for new and experienced users to start to get an idea of what NIMH CORTEX can do these days.

Proper citation: NIMH CORTEX (RRID:SCR_006837) Copy   

•   Source: SciCrunch Registry

http://www.cognitiveatlas.org/

Knowledge base (or ontology) that characterizes the state of current thought in cognitive science that captures knowledge from users with expertise in psychology, cognitive science, and neuroscience. There are two basic kinds of knowledge in the knowledge base. Terms provide definitions and properties for individual concepts and tasks. Assertions describe relations between terms in the same way that a sentence describes relations between parts of speech. The goal is to develop a knowledge base that will support annotation of data in databases, as well as supporting improved discourse in the community. It is open to all interested researchers. A fundamental feature of the knowledge base is the desire and ability to capture not just agreement but also disagreement regarding definitions and assertions. Thus, if you see a definition or assertion that you disagree with, then you can assert and describe your disagreement. The project is led by Russell Poldrack, Professor of Psychology and Neurobiology at the University of Texas at Austin in collaboration with the UCLA Center for Computational Biology (A. Toga, PI) and UCLA Consortium for Neuropsychiatric Phenomics (R. Bilder, PI). Most tasks used in cognitive psychology research are not identical across different laboratories or even within the same laboratory over time. A major advantage of anchoring cognitive ontologies to the measurement level is that the strategy for determining changes in task properties is easier than tracking changes in concept definitions and usage. The process is easier because task parameters are usually (if not always) operationalized objectively, offering a clear basis to judge divergence in methods. The process is also easier because most tasks are based on prior tasks, and thus can more readily be considered descendants in a phylogenetic sense.

Proper citation: Cognitive Atlas (RRID:SCR_002793) Copy   

•   Source: SciCrunch Registry

http://sumsdb.wustl.edu/sums/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures

Proper citation: SumsDB (RRID:SCR_002759) Copy   

•   Source: SciCrunch Registry

http://www.neurogems.org/neosim/

Simulation software that includes a parallel discrete event simulation kernel for running models of spiking neurons on a cluster of workstations. Models are specified using NeuroML, and visualized using Java2D. Simulation components are distributed across a parallel machine or network and communicate using timestamped events. The successor NEOSIM2 project under the NeuroGems umbrella at Edinburgh University (http://www.neurogems.org) continues to distribute the software, http://www.neurogems.org/neosim2/ The NEOSIM project includes: * a parallel discrete event simulation kernel for running models of spiking neural networks on clusters of machines. * a modules kit for extending the behavior of neurons and connectivity patterns. * a user interface for building and running simulations. OS: Linux, MS-Windows

Proper citation: Neural Open Simulation (RRID:SCR_002916) Copy   

•   Source: SciCrunch Registry

http://brainmap.org/

A community database of published functional and structural neuroimaging experiments with both metadata descriptions of experimental design and activation locations in the form of stereotactic coordinates (x,y,z) in Talairach or MNI space. BrainMap provides not only data for meta-analyses and data mining, but also distributes software and concepts for quantitative integration of neuroimaging data. The goal of BrainMap is to develop software and tools to share neuroimaging results and enable meta-analysis of studies of human brain function and structure in healthy and diseased subjects. It is a tool to rapidly retrieve and understand studies in specific research domains, such as language, memory, attention, reasoning, emotion, and perception, and to perform meta-analyses of like studies. Brainmap contains the following software: # Sleuth: database searches and Talairach coordinate plotting (this application requires a username and password) # GingerALE: performs meta-analyses via the activation likelihood estimation (ALE) method; also converts coordinates between MNI and Talairach spaces using icbm2tal # Scribe: database entry of published functional neuroimaging papers with coordinate results

Proper citation: brainmap.org (RRID:SCR_003069) Copy   

•   Source: SciCrunch Registry

http://braininfo.rprc.washington.edu

Portal to neuroanatomical information on the Web that helps you identify structures in the brain and provides a variety of information about each structure by porting you to the best of 1500 web pages at 100 other neuroscience sites. BrainInfo consists of three basic components: NeuroNames, a developing database of definitions of neuroanatomic structures in four species, their most common acronyms and their names in eight languages; NeuroMaps, a digital atlas system based on 3-D canonical stereotaxic atlases of rhesus macaque and mouse brains and programs that enable one to map data to standard surface and cross-sectional views of the brains for presentation and publication; and the NeuroMaps precursor: Template Atlas of the Primate Brain, a 2-D stereotaxic atlas of the longtailed (fascicularis) macaque brain that shows the locations of some 250 architectonic areas of macaque cortex. The NeuroMaps atlases will soon include a number of overlays showing the locations of cortical areas and other neuroscientific data in the standard frameworks of the macaque and mouse atlases. Viewers are encouraged to use NeuroNames as a stable source of unique standard terms and acronyms for brain structures in publications, illustrations and indexing systems; to use templates extracted from the NeuroMaps macaque and mouse brain atlases for presenting neuroscientific information in image format; and to use the Template Atlas for warping to MRIs or PET scans of the macaque brain to estimate the stereotaxic locations of structures.

Proper citation: BrainInfo (RRID:SCR_003142) Copy   

•   Source: SciCrunch Registry

http://phenome.jax.org/

Database enables integration of genomic and phenomic data by providing access to primary experimental data, data collection protocols and analysis tools. Data represent behavioral, morphological and physiological disease-related characteristics in naive mice and those exposed to drugs, environmental agents or other treatments. Collaborative standardized collection of measured data on laboratory mouse strains to characterize them in order to facilitate translational discoveries and to assist in selection of strains for experimental studies. Includes baseline phenotype data sets as well as studies of drug, diet, disease and aging effect., protocols, projects and publications, and SNP, variation and gene expression studies. Provides tools for online analysis. Data sets are voluntarily contributed by researchers from variety of institutions and settings, or retrieved by MPD staff from open public sources. MPD has three major types of strain-centric data sets: phenotype strain surveys, SNP and variation data, and gene expression strain surveys. MPD collects data on classical inbred strains as well as any fixed-genotype strains and derivatives that are openly acquirable by the research community. New panels include Collaborative Cross (CC) lines and Diversity Outbred (DO) populations. Phenotype data include measurements of behavior, hematology, bone mineral density, cholesterol levels, endocrine function, aging processes, addiction, neurosensory functions, and other biomedically relevant areas. Genotype data are primarily in the form of single-nucleotide polymorphisms (SNPs). MPD curates data into a common framework by standardizing mouse strain nomenclature, standardizing units (SI where feasible), evaluating data (completeness, statistical power, quality), categorizing phenotype data and linking to ontologies, conforming to internal style guides for titles, tags, and descriptions, and creating comprehensive protocol documentation including environmental parameters of the test animals. These elements are critical for experimental reproducibility.

Proper citation: Mouse Phenome Database (MPD) (RRID:SCR_003212) Copy   

•   Source: SciCrunch Registry

http://compbio.mit.edu/ChromHMM/

Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations.

Proper citation: ChromHMM (RRID:SCR_018141) Copy   

•   Source: SciCrunch Registry

https://health.uconn.edu/worm-lab/track-a-worm/

Open source system for quantitative assessment of C. Elegans locomotory and bending behavior. Used for quantitative behavioral analyses to understand circuit and gene bases of behavior. Constantly records and analyzes position and body shape of freely moving worm at high magnification.

Proper citation: Track-A-Worm (RRID:SCR_018299) Copy   

•   Source: SciCrunch Registry

https://www.epimodel.org/

Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics.

Proper citation: EpiModel (RRID:SCR_018539) Copy   

•   Source: SciCrunch Registry