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http://www.emouseatlas.org/emap/home.html

Detailed multidimensional digital multimodal atlas of the C57BL/6J mouse nervous system with a high-throughput data and informatics pipeline that can automatically register, annotate, and visualize large scale neuroanatomical and connectivity data produced in commonly used methodologies including histology, neuronal tract tracing, MR imaging, and genetic labeling. Using multimodal imaging methods on adult mouse brains, this high-resolution atlas forms the basis of a useful interchange reference system for the mouse. MAP2.0 interoperates with commonly used publicly available databases to bring together brain architecture, gene expression, and imaging information into a single, simple interface. The project enables scientists to leverage the results of brain atlasing efforts in their investigations of gene function, connectomics, and detailed mouse neuroanatomy. The MAP atlas is comprised of a magnetic resonance microscopy (MRM) and an anatomic delineation volume, and a set of software tools for visualization, navigation, and registration of image volumes. The software tools bundled with the atlas volumes are SHIVA (visualization and analysis), BrainGraph (navigation and connectivity), and GEMporter (registration and importation). A database of ancillary volumes is available online, a supplement to the Mouse Atlas Project core volumes. They represent different developmental time points and methods of preparation. To facilitate the process of selecting and analyzing image data from this collection, we have developed a relational database application to manage and catalog the images and related data. Attributes of the subject such as age, strain, weight and anatomical structure are recorded, as are image volume properties such as modality, resolution and anatomical structure. The ongoing partnership with the Brain Architecture Center has led to the development of a robust and flexible nomenclature and anatomical ontology for MAP2.0. This collaboration extends both Mouse Atlas Project and the Brain Architecture Management System.

Proper citation: Mouse Atlas Project (RRID:SCR_007281) Copy   

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http://fmri.wfubmc.edu/software/PickAtlas

A software toolbox that provides a method for generating Region of Interest (ROI) masks based on the Talairach Daemon database. The atlases include Brodmann area, Lobar, Hemisphere, Anatomic Label (gyral anatomy), and Tissue type. The atlases have been extended to the vertex in MNI space, and corrected for the precentral gyrus anomaly. Additional atlases (including non-human atlases) can be added without difficulty., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: WFU PickAtlas (RRID:SCR_007378) Copy   

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http://mousediversity.alleninstitute.org/

A database, and associated atlas, that characterizes gene expression across genetic backgrounds and sex, expanding beyond the adult male C57BL/6J reference brain comprising the Allen Mouse Brain Atlas to include seven strains of male mice and female C57BL/6J mice. Gene expression was detected using colorimetric RNA in situ hybridization (ISH) that provides cellular level anatomic resolution. ISH data are searchable and organized by gene, strain, or sex.

Proper citation: Allen Institute Mouse Diversity Study (RRID:SCR_008009) Copy   

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http://aidb.crbs.ucsd.edu

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented October 4, 2017.

A sub-project of the Cell Centered Database (http://ccdb.ucsd.edu) providing a public repository for animal imaging data sets from MRI and related techniques. The public AIDB website provides the ability for browsing, visualizing and downloading the animal subjected MRI data. The AIDB is a pilot project to serve the current need for public imaging repositories for animal imaging data. The Cell Centered Database (CCDB) is a web accessible database for high resolution 2D, 3D and 4D data from light and electron microscopy. The AIDB data model is modified from the basic model of the CCDB where microscopic images are combined to make 2D, 3D and 4D reconstructions. The CCDB has made available over 40 segmented datasets from high resolution magnetic resonance imaging of inbred mouse strains through the prototype AIDB. These data were acquired as part of the Mouse BIRN project by Drs. G. Allan Johnson and Robert Williams. More information about these data can be found in Badea et al. (2009) (Genetic dissection of the mouse CNS using magnetic resonance microscopy - Pubmed: 19542887)

Proper citation: Animal Imaging Database (RRID:SCR_008002) Copy   

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http://www.dana.org/resources/brainweb/

BrainWeb provides information and links to validated sites about brain diseases and disorders. These include outside resources reviewed by scientific advisers, as well as articles in Dana publications. Sites listed in BrainWeb detail common brain diseases and disorders, and include general neuroscience and health resources. They offer descriptions of conditions, frequently asked questions, organization contacts, and sources for more information. BrainWeb and its links are suitable for lay readers, including students and educators, as well as people with brain disorders, their families, and caregivers.

Proper citation: Dana Foundation: BrainWeb (RRID:SCR_007996) Copy   

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http://archive.cnbc.cmu.edu/Resources/disordermodels/index.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This site aims to provide a discussion and source list for connectionist and neural network models of disorders associated with mental or brain conditions. Recent connectionist and neural network models of behavior, information processing patterns, and brain activity present in people with cognitive, affective, brain, and behavioral disorders are reviewed on this web site. Ways that assumptions regarding normal and disordered behavior may be represented in connectionist models are discussed for features of various disorders. Similarities and differences between the models and criteria for their evaluation are presented, and suggestions for inclusion of information which may help to make these models more directly comparable in the future are considered. References to Connectionist Models of Cognitive, Affective, Brain, and Behavioral Disorders include: General Neural Network Information Reviews, General Introductions, and Calls for More Connectionist Models of Mental Disorders Models of Psychopathologies and Psychiatric Disorders Models of Cognitive, Affective, Brain, and Behavioral Disorders Not Associated with Psychopathology Additionally, Web Sites for Neural Network Modelers of Disorder are provided.

Proper citation: Connectionist Models of Cognitive, Affective, Brain, and Behavioral Disorders (RRID:SCR_008088) Copy   

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http://brainspan.org/

Atlas of developing human brain for studying transcriptional mechanisms involved in human brain development. Consists of RNA sequencing and exon microarray data profiling up to sixteen cortical and subcortical structures across full course of human brain development, high resolution neuroanatomical transcriptional profiles of about 300 distinct structures spanning entire brain for four midgestional prenatal specimens, in situ hybridization image data covering selected genes and brain regions in developing and adult human brain, reference atlas in full color with high resolution anatomic reference atlases of prenatal (two stages) and adult human brain along with supporting histology, magnetic resonance imaging (MRI) and diffusion weighted imaging (DWI) data.

Proper citation: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) (RRID:SCR_008083) Copy   

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http://neuroinformatics.usc.edu/

The USC Brain Project is engaged in the effort to develop new tools and methodologies for neuroinformatics in modeling neural mechanisms of visuomotor coordination and exploring the evolution of the human language-ready brain, as well as conducting work in both neural modeling and database construction in relation to rehabilitation after stroke. Sponsors: USCBP is funded by the University of Southern California.

Proper citation: University of Southern California Brain Project (RRID:SCR_008044) Copy   

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http://www.scripps.edu/np/inia/index.html

Consortium set out to identify the molecular, cellular, and behavioral neuroadaptations that occur in the brain reward circuits associated with the extended amygdala and its connections. It is hypothesized that genetic differences and/or neuroadaptations in this circuitry are responsible for the individual differences in vulnerability to the excessive consumption of alcohol. Chronic exposure to alcohol results in neuroadaptive phenomena, including tolerance, sensitization, dependence, withdrawal, loss of control of drinking, and relapse that contribute to the development of excessive alcohol consumption. The INIA has the following goals: 1) To establish animal models to study specific neurobiological targets for vulnerability that lead to excessive consumption of alcohol at the molecular, cellular and neural circuit level of analysis, 2) To identify specific clusters of genes whose expression is regulated by alcohol and which are responsible for any given model of excessive alcohol consumption using gene expression arrays, differential display, mutagenesis directed at specific brain areas, and the development of new informatics tools to analyze and interpret gene expression, cellular circuitry and brain circuitry data with the use of transgenic and knockout approaches, and 3) To attract new and innovative investigators to the field of alcohol research by recruiting individuals for development of U01 grants and pilot projects and by developing online interactive capacity among INIA scientists and others, and by making the neuroinformatics integrated data sets accessible, searchable and interactive with other databases for all scientists interested in alcoholism research. The structure of INIA is envisioned as two domains, Dependence-induced drinking and Binge drinking, comprised of multiple U01 research grants. The flow of information within each domain moves from molecular, to cellular, to neurocircuitry levels of analysis. These U01s share information with the core facilities, which act as data depositories. The Administrative Core coordinates the flow of information among the Domains and Cores and disseminates the information back to the U01s. A Pilot Project program will identify exciting new areas for research and the continual recruitment of new investigators to the alcohol field. The INIA program is directed by an Administrative Core in close cooperation with the Animal Models, Gene Array and Neurocircuitry Cores via a Steering Committee and with the continual advice of the Scientific Advisory Committee.

Proper citation: Integrative Neuroscience Initiative on Alcoholism (RRID:SCR_008042) Copy   

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http://www.nia.nih.gov/research/dn

A funding resource that supports the research and training for understanding the structure and function of the aging nervous system, with an emphasis on studies involving Alzheimer's disease and age-related dementia. There is an emphasis on brain-behavior relationships. This program is composed of three branches: Neurobiology, Neuropsychology, and Dementias of Aging. The overall aim of this program is to understand the aging nervous system to minimize mental decline and improve the lives of older patients. This resource also includes links to sites for Alzheimer's disease (AD) studies that include: specimen repositories, genetic materials, bio-markers, data, policies on NIA and AD genetics sharing plans, and additional aging or other AD related links.

Proper citation: National Institute on Aging, Division of Neuroscience (RRID:SCR_008257) Copy   

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http://brainconnection.positscience.com/

An educational site providing accessible information about how the brain works and how people learn

Proper citation: Brain Connection (RRID:SCR_008315) Copy   

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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   

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http://www.ohsu.edu/xd/research/centers-institutes/onprc/

Center that aims to develop biomedical technologies using nonhuman primate (NHP) models. Its goal is to uncover the root causes of various disease and disorders, unlock secrets of the brain, and unleash new methods of diagnostics and treatment.

Proper citation: Oregon National Primate Research Center (RRID:SCR_008291) Copy   

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http://www.alivelearn.net/xjview8/

A viewing program for Statistical Parametric Mapping (SPM2, SPM5 and SPM8). p-value slider, displays multiple images at a time and can be used to build Region of Interest (ROI) masks. For a given region you can find the anatomical name and search the selected region in online database (wiki, Google scholar and PubMed).

Proper citation: xjView: A Viewing Program For SPM (RRID:SCR_008642) Copy   

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http://www.rad.upenn.edu/sbia/braid/braid_web/index.html

Large-scale archive of normalized digital spatial and functional data with an analytical query mechanism. One of its many applications is the elucidation of brain structure-function relationships. BRAID stores spatially defined data from digital brain images which have been mapped into normalized Cartesian coordinates, allowing image data from large populations of patients to be combined and compared. The database also contains neurological data from each patient and a query mechanism that can perform statistical structure-function correlations. The project is developing database technology for the manipulation and analysis of 3-dimensional brain images derived from MRI, PET, CT, etc. BRAID is based on the PostgreSQL server, an object/relational DBMS, which allows a standard relational DBMS to be augmented with application-specific datatypes and operators. The BRAID project is adding operations and datatypes to support querying, manipulation and analysis of 3D medical images, including: * Image Datatypes: BRAID supports a family of 3D image datatypes, each having an abstract type and an implementation type. Abstract types include boolean (for regions of interest), integer, float, vector (for representing morphological changes), tensor (for representing derivatives and standard deviations of vector images) and color. Implementation types at present include line-segment format and voxel array. * Image Operators: BRAID supports addition of images, multiplication (which is interpreted as intersection for boolean images), coercion of an image''s abstract or implementation type to another value, and determination of volumes of regions of interest. * Statistical Operators: A chi-squared test has been added to SQL as an aggregate operator on pairs of boolean values. * Web Interface: A general-purpose Web gateway allows the results of queries that return computed images to be displayed. You can download the BRAID source code 2.0. This version is developed under postgreSQL 7.3.4., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BRAID (RRID:SCR_008702) Copy   

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http://brainbank.med.miami.edu/

A biomaterial supply resource which collects and disseminates over 1500 brains and links tissue specimens to patient data. The Brain Endowment Bank distributes brain tissue specimens to scientists worldwide who are investigating neurodegenerative and neuropsychiatric diseases, as well as to scientists involved in ongoing studies on the affects of aging. Its overall objective is to support basic and clinical research activities by providing a systematic method for obtaining detailed pre-mortem clinical information, developing procedures for optimizing brain autopsies, cryopreserving neuropathological specimens, and obtaining neuropathological diagnoses after death.

Proper citation: UM Brain Endowment Bank (RRID:SCR_008721) Copy   

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http://brainu.org/

A neuroscience training program for Minnesota students and teachers. It provides teachers with three years of neuroscience training, materials, and staff support to bring brain science to their students. In these professional workshops, participants receive updates on the latest in neuroscience research -- discussion is complemented with hands-on activities and lab work. Teachers also receive curriculum materials to aid them in using neuroscience topics in support of Minnesota Intermediate and Middle Level standards. The program was expanded in 2008 to include high school teachers.

Proper citation: BrainU: The Neuroscience Teacher Institute (RRID:SCR_008677) Copy   

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http://www.alzresearch.org/index.cfm

A Alzheimer's Disease Research Center (ADRC) whose goal is to conduct basic and clinical research aimed at understanding Alzheimer's disease. The Center enrolls a variety of individuals for clinical trials, evaluation and follow-up, including: normal control subjects, individuals with mild memory problems, and patients diagnosed with Alzheimer's Disease or related dementias. Researchers can request data and specimens obtained from ADRC subjects. These include blood or DNA, brain specimens, and cross-sectional or longitudinal clinical and cognitive data, all from ADRC subjects.

Proper citation: Johns Hopkins Alzheimer's Disease Research Center (RRID:SCR_008757) Copy   

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http://www.bri.ucla.edu/research/resources

Brain bank resources which include postmortem human frozen brain tissue and matched cerebrospinal fluid (CSF) and blood available for scientists to search for etiopathogeneses of human disease. The National Neurological Research Specimen Bank and the Multiple Sclerosis Human Neurospecimen Bank maintains a collection of quick frozen and formalin fixed postmortem human brain tissue and frozen cerebrospinal fluid from patients with neurological diseases, including Alzheimer's Disease, amyotrophic lateral sclerosis, depressive disorder/suicide, and epilepsy, among others. Diagnoses are documented by clinical medical records and gross/microscopic neuropathology. The Neuropathology Laboratory at the UCLA Medical Center maintains a bank of frozen, formalin and paraformaldehyde-fixed and paraffin-embedded postmortem human brain tissues and frozen cerebrospinal fluid (CSF) from patients who die with Alzheimer's disease and other dementing and degenerative illnesses, as well as control materials removed in a similar fashion from patients who are neurologically normal.

Proper citation: Brain Research Institute Biobank Resources (RRID:SCR_008756) Copy   

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http://mayoresearch.mayo.edu/mayo/research/dickson_lab/

A brain bank and laboratory focused on memory and motor disorders. Brains are sent to the laboratory for diagnosis and research for the State of Florida Alzheimer Disease Initiative and for the Society for Progressive Supranuclear Palsy. As part of this brain banking function, fixed and frozen brain samples are obtained at autopsy and sent to the laboratory for diagnostic evaluation and for various types of research studies. The major types of analyses performed on the brain samples include neuro-histology, immunohistochemistry, confocal microscopy, electron microscopy and image analysis, as well as immunoassays. The latter are based upon Western blotting and enzyme linked immunoassays. The laboratory has a specific interest in the interface between normal aging and Alzheimer's disease, as well as in non-Alzheimer's degenerative disorders such as Lewy body dementia, corticobasal degeneration, progressive supranuclear palsy and frontotemporal dementia. The primary focus of research on aging is neuropathologic characterization of brains of individuals who had been prospectively and longitudinally evaluated during life. These studies aim to determine differences in a range of biologic parameters in brains of people with normal cognitive, mild cognitive impairment and dementia. Their focus on Parkinson's disease is to identify preclinical Parkinson's disease in order to develop means for early diagnosis.

Proper citation: Mayo Clinic Jacksonville: Neuropathology and Microscopy (RRID:SCR_008753) Copy   

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