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http://www.loni.usc.edu/Software/MultiPhase-SEG

A segmentation software that employs the implementation of the active contours without edges level set based segmentation model. Its features include: segmentation of three-dimensional brain volumes into two or more regions (for example, regions could be WM, GM, and CSF), visualization of surfaces representing boundaries of different brain regions, and being written in Matlab with the ability to run on any platform with Matlab installed.

Proper citation: MultiPhase-SEG (RRID:SCR_008275) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/DSM

The DualSurfaceMin is a C++ implementation of the fully automatic dual surface minimization (DSM) algorithm for the optimization of deformable surfaces. The method is developed for automatic surface extraction from noisy volumetric images. Its features include: global DSM, DSM-OS, and DSM-IS algorithms for automatic surface extraction from volumetric images using deformable simplex meshes; support for the VRML and OFF formats; output pf both triangulated and simplex meshes; and support for the raw and Analyze 7.5 image formats.

Proper citation: DualSurfaceMin (RRID:SCR_008278) Copy   

•   Source: SciCrunch Registry

http://loni.usc.edu/Software/SVT

Software tool for determining the statistically significant regions of activation in single or multi-subject human brain functional studies. It can be also applied to structural brain data for analyzing developmental, dementia and other changes of anatomy over time. This package was originally developed to work on Sun SPARC and SGI stations using the "C" language compiler provided by Sun/SGI as part of the standard system software.

Proper citation: Sub-Volume Thresholding Analysis (RRID:SCR_008272) Copy   

•   Source: SciCrunch Registry

http://www.hms.harvard.edu/NEPRC/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. A center that focuses on performing bio-medical research on nonhuman primates to aid in human health research. The center also focuses on training young scientists for professional careers in bio-medical research and primate biology. One of the New England Primate Research School's main accomplishments was the creation of an animal model for AIDS that first demonstrated that vaccine protection could be possible. Recent research has led to the development of novel agents for brain imaging that will aid in the diagnosis and treatment of Parkinson's disease.

Proper citation: New England Primate Research School (RRID:SCR_008290) Copy   

•   Source: SciCrunch Registry

http://users.loni.ucla.edu/~shattuck/brainsuite/

Suite of image analysis tools designed to process magnetic resonance images (MRI) of the human head. BrainSuite provides an automatic sequence to extract genus-zero cortical surface mesh models from the MRI. It also provides a set of viewing tools for exploring image and surface data. The latest release includes graphical user interface and command line versions of the tools. BrainSuite was specifically designed to guide its users through the process of cortical surface extraction. NITRC has written the software to require minimal user interaction and with the goal of completing the entire process of extracting a topologically spherical cortical surface from a raw MR volume within several minutes on a modern workstation. The individual components of BrainSuite may also be used for soft tissue, skull and scalp segmentation and for surface analysis and visualization. BrainSuite was written in Microsoft Visual C using the Microsoft Foundation Classes for its graphical user interface and the OpenGL library for rendering. BrainSuite runs under the Windows 2000 and Windows XP Professional operating systems. BrainSuite features include: * Sophisticated visualization tools, such as MRI visualization in 3 orthogonal views (either separately or in 3D view), and overlayed surface visualization of cortex, skull, and scalp * Cortical surface extraction, using a multi-stage user friendly approach. * Tools including brain surface extraction, bias field correction, voxel classification, cerebellum removal, and surface generation * Topological correction of cortical surfaces, which uses a graph-based approach to remove topological defects (handles and holes) and ensure a tessellation with spherical topology * Parameterization of generated cortical surfaces, minimizing a harmonic energy functional in the p-norm * Skull and scalp surface extraction

Proper citation: BrainSuite (RRID:SCR_006623) Copy   

•   Source: SciCrunch Registry

http://www.ncrr.nih.gov/comparative_medicine/resource_directory/primates.asp

THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 16, 2013. NCRR has been absorbed into other parts of the National Institutes of Health. This organizational structure is no longer available. Provides laboratory scientists and clinical researchers with the resources and tools they need to understand, detect, treat and prevent a wide range of diseases. Animal models, such as nonhuman primates, are a critical component of biomedical research, having profound implications for public health. Scientists depend on laboratory animals and other nonhuman models for investigating biological processes, studying the causes of diseases and testing promising new therapies. Nonhuman primates, in particular, are important for translational research because of their close physiological similarities to humans. They enable discoveries that have direct application to human studies, bridging the gap between basic science and human medicine. Discoveries in animal models are helping scientists test treatments for human conditions such as drug addiction, obesity, malaria, HIV/AIDS and neurodegenerative diseases, accelerating the pace at which these research advances can be translated into treatments for patients. Through its Division of Comparative Medicine, NCRR offers a wide variety of primate resources for NIH-funded scientists across the nation. Additionally, funding opportunities are available to National Primate Research Centers. Eight National Primate Research Centers (NPRCs) located throughout the country provide animals, facilities and expertise in all aspects of nonhuman primate biology and husbandry. These facilities and resources enable collaborative research among NPRC staff scientists, investigators from the NPRC host institution and other NIH-funded researchers. Major areas of research benefiting from the primate centers include AIDS, avian flu, Alzheimer''s disease, Parkinson''s disease, diabetes, asthma and endo-metriosis. The centers????????????????? specialized resources are intended to support investigators who receive their primary research project funding from NIH, but they also may be used by investigators who are funded by other federal, state and local agencies, as well as by research foundations and the private sector. Together the primate centers have more than 28,000 nonhuman primates of 20 different species. This portal covers the following topics: * National Primate Research Centers * Monkey Research Resources * Chimpanzee Research Resources * Chimpanzee Management Program * Specific-Pathogen-Free Macaque Resources * Nonhuman Primate Research Reagents

Proper citation: National Center for Research Resources - Primate Resources (RRID:SCR_006863) Copy   

•   Source: SciCrunch Registry

http://brainatlas.mbi.ufl.edu/Database/

Comprehensive three-dimensional digital atlas database of the C57BL/6J mouse brain based on magnetic resonance microscopy images acquired on a 17.6-T superconducting magnet. This database consists of: Individual MRI images of mouse brains; three types of atlases: individual atlases, minimum deformation atlases and probabilistic atlases; the associated quantitative structural information, such as structural volumes and surface areas. Quantitative group information, such as variations in structural volume, surface area, magnetic resonance microscopy image intensity and local geometry, have been computed and stored as an integral part of the database. The database augments ongoing efforts with other high priority strains as defined by the Mouse Phenome Database focused on providing a quantitative framework for accurate mapping of functional, genetic and protein expression patterns acquired by a myriad of technologies and imaging modalities. You must register First (Mandatory) and then you may Download Images and Data.

Proper citation: MRM NeAt (Neurological Atlas) Mouse Brain Database (RRID:SCR_007053) Copy   

•   Source: SciCrunch Registry

http://ncmir.ucsd.edu/downloads/manual_align_rts2000.shtm

Software program to adjust the alignment of two adjacent images. Allows to correct for any misalignment that may occur during auto-alignment step. Serves as a bootstrap to get the images in approximately the right place.

Proper citation: Manual Align RTS2000 (RRID:SCR_007107) Copy   

•   Source: SciCrunch Registry

http://www.birncommunity.org/collaborators/function-birn/

The FBIRN Federated Informatics Research Environment (FIRE) includes tools and methods for multi-site functional neuroimaging. This includes resources for data collection, storage, sharing and management, tracking, and analysis of large fMRI datasets. fBIRN is a national initiative to advance biomedical research through data sharing and online collaboration. BIRN provides data-sharing infrastructure, software tools, strategies and advisory services - all from a single source.

Proper citation: Function BIRN (RRID:SCR_007291) Copy   

•   Source: SciCrunch Registry

http://www.nbirn.net/research/bcc/index.shtm

THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 06, 2013. It was established to develop, implement and support the information infrastructure necessary to achieve large-scale data sharing among the test bed participants (function, morphometry and mouse birn). The BIRN-CC consists of a unique and well-established partnership between computer scientists, neuroscientists and engineers. This partnership addresses a large array of technical, policy, and architectural issues to fundamentally enable a new suite of information technology supported database and analysis tools that allow scientists to analyze and interpret significantly larger sets of data than is possible in the traditional single-institution study paradigm.

Proper citation: BIRN Coordinating Center (RRID:SCR_007290) Copy   

•   Source: SciCrunch Registry

http://www.cmrr.umn.edu/stimulate

An fMRI analysis software package with a GUI (Graphical User Interface) front end. Stimulate offers a comprehensive set of fMRI analysis tools integrated into a single package for convenient and flexible data processing. Users can point and click with the mouse to modify analysis or display variables. Activation maps can be calculated from the fMRI data and overlaid onto structural MRI image displays.

Proper citation: Stimulate (RRID:SCR_007375) Copy   

•   Source: SciCrunch Registry

http://mmcd.nmrfam.wisc.edu/

A database which supports high-throughput NMR and MS approaches to the identification and quantification of metabolites present in biological samples. MMCD serves as a hub for information on small molecules of biological interest gathered from electronic databases and the scientific literature. Each metabolite entry in the MMCD is supported by information in separate data fields, which provide the chemical formula, names and synonyms, structure, physical and chemical properties, NMR and MS data on pure compounds under defined conditions where available, NMR chemical shifts determined by empirical and/or theoretical approaches, calculated isotopomer masses, information on the presence of the metabolite in different biological species, and links to images, references, and other public databases. The MMCD search engine supports versatile data mining and allows users to make individual or bulk queries on the basis of experimental NMR and/or MS data plus other criteria.

Proper citation: Madison Metabolomics Consortium Database (RRID:SCR_007803) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/eagle-i/

Ontology that models research resources such as instruments, protocols, reagents, animal models and biospecimens. It has been developed in the context of the eagle-i project (http://eagle-i.net/) and consists of over 3451 classes of which over 1200 were created within the ERO namespace, while the rest come from existent ontologies such as the Ontology for Biomedical Investigation (OBI), the uber-anatomy ontology (Uberon), VIVO, the Ontology for Clinical Research (OCRe), the Sequence Ontology (SO), the Software Ontology (SWO) and we include terms from the NCBI Taxonomy as well. The main ontology can be browsed in OntoBee. All purls resolve to OntoBee.

Proper citation: eagle-i research resource ontology (RRID:SCR_008784) Copy   

•   Source: SciCrunch Registry

http://www.slicer.org/slicerWiki/index.php/Slicer3:Module:Rician_Noise_Removal

Two Slicer3 modules removing rician noise in diffusion tensor MRI

Proper citation: Slicer3 Module Rician noise filter (RRID:SCR_009614) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/BrainParser

Software that uses a novel statistical-learning technique to segment brain regions of interest (ROIs) based on a training set of data and generates 3D MRI volumes. The software comes pre-trained on a provided data set but can be retrained to work with your desired regions of interest.

Proper citation: LONI Brain Parser (RRID:SCR_009572) Copy   

•   Source: SciCrunch Registry

http://www.sci.utah.edu/cibc/software/map3d.html

A scientific visualization application written to display and edit complex, three-dimensional geometric models and scalar, time-based data associated with those models such as high resolution EEG, MEG, and ECG.

Proper citation: map3d (RRID:SCR_009628) Copy   

•   Source: SciCrunch Registry

http://proteogenomics.musc.edu/ma/musc_madb.php?page=home&act=manage

Database that is a repository for DNA microarray data generated by MUSC investigators as well as researchers in the global research community.

Proper citation: MUSC DNA Microarray Database (RRID:SCR_010977) Copy   

•   Source: SciCrunch Registry

https://www.cgl.ucsf.edu/chimera/

Software tool for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials.

Proper citation: UCSF Chimera (RRID:SCR_004097) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/MBAT

Workflow environment bringing together heterogenous, online biological image resources, a user's image data and biological atlases in a concise, unified and intuitive workspace. The MBAT viewer displays multiple images on a single virtual canvas allowing easy side-by-side comparisons and image compositing. MBAT is written in Java so it is platform independent and is highly extensible through it's plugin architecture. MBAT integrates three distinct workspaces for online search, image alignment (registration) and image display: * Search Workspace: able to submit a query to multiple databases simultaneously and online literature searches. * Registration Workspace: performs 2D landmark based registration. * Viewer Workspace: displays & composites images and image volumes using high performance graphics hardware. * Atlas Viewer: allows navigation and interrogation of volumetric atlases. * Hierarchy Editor: create logical groupings of atlas labels.

Proper citation: Mouse BIRN Atlasing Toolkit (RRID:SCR_002814) Copy   

•   Source: SciCrunch Registry

http://www.umc.edu/Administration/Centers_and_Institutes/Center_for_Psychiatric_Neuroscience/Core_Research_Resources.aspx

Core facility that provides access to psychiatrically characterized post-mortem brain specimens, state-of-the-art equipment, cutting-edge technologies and the technical advice of highly trained faculty members who serve as Core Directors. The sophisticated imaging systems and biotechnologically advanced molecular core resources are provided on a shared-use basis to CPN and UMMC researchers. The CPN Research Resources Cores include the Human Brain Collection Core, Animal Core, Imaging Core, Molecular Biology Core, and Information Technologies Core.

Proper citation: UMMC Center for Psychiatric Neuroscience Labs and Facilities (RRID:SCR_002688) Copy   

•   Source: SciCrunch Registry