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http://library.med.utah.edu/kw/hyperbrain/

An online tutorial for human neuroanatomy designed as a supplement to textbook and class learning or as a lab substitute when human specimens, slides and models are not available. HyperBrain includes thousand of images and hundreds of linked illustrated glossary terms, as well as movies, quizzes and interactive animations. Last updated 2012.

Proper citation: HyperBrain (RRID:SCR_001595) Copy   

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http://www.cognitorium.com/

THIS RESOURCE IS NO LONGER IN SERVICE, documented October 28, 2015. Interactive, informative and educational community platform dedicated to cognitive science or the multidisciplinary exploration of the mind. This online platform, will help gather and link information providing a thorough and reliable source of information for students and professionals in the field, as well as help bridge the gap between academia and the society. Due to the multidisciplinary nature of cognitive science, the work is becoming increasingly specialized. Therefore to keep an eye on the bigger picture, it seems necessary to bring the discoveries of various disciplines together in one place, look at their similarities and differences and discuss them for future directions.

Proper citation: Cognitorium (RRID:SCR_000098) Copy   

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https://www.synapse.org/

Sage Bionetworks, Mount Sinai School of Medicine (MSSM), University of Pennsylvania (Penn), the National Institute of Mental Health (NIMH), and Takeda Pharmaceuticals Company Limited (TAKEDA) have launched a Public-Private Pre-Competitive Consortium, the CommonMind Consortium, to generate and analyze large-scale genomic data from human subjects with neuropsychiatric disease and to make this data and the associated analytical results broadly available to the public. This collaboration brings together disease area expertise, large scale and well curated brain sample collections, and data management and analysis expertise from the respective institutions. As many as 450 million people worldwide are believed to be living with a mental or behavioral disorder: schizophrenia and bipolar disorder are two of the top six leading causes of years lived with disability according to the World Health Organization. The burden on the individual as well as on society is significant with estimates for the health care costs for these individuals as high as four percent GNP. This highlights a grave need for new therapies to alleviate this suffering. Researchers from MSSM including Dr. Pamela Sklar, Dr. Joseph Buxbaum and Dr. Eric Schadt will join with Dr. Raquel Gur and Dr. Chang-Gyu Hahn from Penn to combine their extensive brain bank collections for the generation of whole genome scale RNA and DNA sequence data. Dr.Pamela Sklar, Professor of Psychiatry and Neuroscience at MSSM commented this is an exciting opportunity for us to use the newest genomic methods to really expand our understanding of the molecular underpinnings of neuropsychiatric disease, while Dr Raquel Gur, Professor of Psychiatry from Penn observed this will be a great complement to some of the large-scale genetic analyses that have been carried out to date because it will give a more complete mechanistic picture. The CommonMind Consortium is committed to generating an open resource for the community and invites others with common goals to contact us at info (at) CommonMind.org.

Proper citation: CommonMind Consortium (RRID:SCR_000139) Copy   

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http://www.brainnet-europe.org/index.php?option=com_content&view=article&id=99&Itemid=99

Sampling protocols produced by the BrainNet Europe Consortium generally with five types of dissection and brain processing procedures defined in all disease related protocols. * Fresh brain dissection * Fresh brain processing * Dissection of formalin-fixed brain * Histology and immunohistochemistry * Processing fresh brain

Proper citation: BrainNet Europe Sampling Protocols (RRID:SCR_000484) Copy   

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http://www.thebrainproject.org/

The Mission of the Sarah Jane Brain Project is to create a model system of care for children and young adults suffering from all Pediatric Acquired Brain Injuries in order to advance our knowledge of the brain fifty years over the next five years! As a father of a child suffering from a Pediatric Acquired Brain Injury (PABI), I have spent countless hours searching the internet and speaking with Sarah Jane's development team (doctors, therapists and other professionals) trying to improve the development of my daughter. What I found was that while there are a countless number of wonderful and informative prevention sites for Shaken Baby Syndrome and advocacy sites for brain injuries, there is no one centralized resource for research and rehabilitation for PABI. Furthermore, many of the issues families and children face are the same whether the brain injury was caused by a car crash, a sports-related concussion, an assault or by a tumor. No one person or organization has all the answers to the questions that parents of children suffering from PABI face. Yet through my own experience, I learned that the coordination and dissemination of Sarah Jane's medical and therapy records and data in an orderly manner greatly helps her development team better help her. These wonderful individuals are constantly looking for additional ways to improve Sarah Jane's progress by speaking with their colleagues, reading literature on brain injury, and collaborating with other parents. But they all admit there is a considerable amount that still needs to be learned about the human brain, particularly the developing brain. The field of neuroscience today is similar to the computer science field of the 1950s and 1960s: you have a diverse group of very smart people working independently of one another throughout the United States and the world, yet few know what the others are doing behind closed doors. Fast- forward 50 years and many of the breakthroughs in the computer industry have been made utilizing the principles of open source a research method that promotes free and open access to the design and production of goods and knowledge. Its use was made well-known through the creation of the Linux computer operating system, in which professionals share knowledge to make corrections and fix problems. Open source is commonly used by millions of people today through the Wikipedia online free encyclopedia, a collection of public entries on established subjects that allows anyone to make additions or corrections. The National Institute of Mental Health launched The Human Brain Project in 1993 to develop and support the new science of neuro-informatics. From this initiative, it became obvious what needed to be done. That's why we created the Sarah Jane Brain Virtual Center of Excellence an ecosystem for professionals and families dealing with PABI around the world and a vehicle to help implement the PABI Plan by establishing a model system for PABI.

Proper citation: Sarah Jane Brain Project (RRID:SCR_000620) Copy   

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

A versatile 1D, 2D and 3D data viewer geared for cross-platform visualization of stereotactic brain data. It is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views. It reads Analyze, Raw-binary and NetCDF volumetric data, as well as, Multi-Contour Files (MCF), LWO/LWS surfaces, atlas hierarchical brain-region labelings ( Brain Trees). It is a portable Java-based software, which only requires a Java interpreter and a 64 MB of RAM memory to run on any computer architecture. LONI_Viz allows the user to interactively overlay and browse through several data volumes, zoom in and out in the axial, sagittal and coronal views, and reports the intensities and the stereo-tactic voxel and world coordinates of the data. Expert users can use LONI_Viz to delineate structures of interest, e.g., sulcal curves, on the 3 cardinal projections of the data. These curves then may be use to reconstruct surfaces representing the topological boundaries of cortical and sub-cortical regions of interest. The 3D features of the package include a SurfaceViewer and a full real-time VolumeRenderer. These allow the user to view the relative positions of different anatomical or functional regions which are not co-planar in any of the axial, sagittal or coronal 2D projection planes. The interactive part of LONI_Viz features a region drawing module used for manual delineation of regions of interest. A series of 2D contours describing the boundary of a region in projection planes (axial, sagittal or coronal) could be used to reconstruct the surface-representation of the 3D outer shell of the region. The latter could then be resliced in directions complementary to the drawing-direction and these complementary contours could be loaded in all tree cardinal views. In addition the surface object could be displayed using the SurfaceViewer. A pre-loading data crop and sub-sampling module allows the user to load and view practically data of any size. This is especially important when viewing cryotome, histological or stained data-sets which may reach 1GB (109 bytes) in size. The user could overlay several pre-registered volumes, change intensity colors and ranges and the inter-volume opacities to visually inspect similarities and differences between the different subjects/modalities. Several image-processing aids provide histogram plotting, image-smoothing, etc. Specific Features: * Region description DataBase * Moleculo-genetic database * Brain anatomical data viewer * BrainMapper tool * Surface (LightWave objects/scenes) and Volume rendering tools * Interactive Contour Drawing tool Implementation Issues: * Applet vs. Application - the software is available as both an applet and a standalone application. The former could be used to browse data from within the LONI database, however, it imposes restrictions on file-size, Internet connection and network-bandwidth and client/server file access. The later requires a local install and configuration of the LONI_Viz software * Extendable object-oriented code (Java), computer architecture independent * Complete online software documentation is available at http://www.loni.ucla.edu/LONI_Viz and a Java-Class documentation is available at http://www.loni.ucla.edu/~dinov/LONI_Vis.dir/doc/LONI_Viz_Java_Docs.html

Proper citation: LONI Visualization Tool (RRID:SCR_000765) Copy   

•   Source: SciCrunch Registry

http://zebrafishucl.org/zebrafishbrain#about-1

Collates and curates neuroanatomical data and information generated both in-house and by community to communicate current state of knowledge about neuroanatomical structures in developing zebrafish. Most of data come from high resolution confocal imaging of intact brains in which neuroanatomical structures are labelled by combinations of transgenes and antibodies. Community repository for image based data related to neuroanatomy of zebrafish.

Proper citation: Zebrafish Brain Atlas (RRID:SCR_000606) Copy   

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http://brainatlas.mbi.ufl.edu/ImageGallery.php

Image Gallery of a 3D MRI Atlas of an Adult C57BL/6J Mouse Brain showing Slice Animation and 3D Animation including Axial, Coronal, Sagittal views. RealPlayer or Windows Media Player needs to be installed for viewing these animations.

Proper citation: MRM NeAt (Neurological Atlas) Mouse Brain Database Image Gallery (RRID:SCR_007032) Copy   

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http://www.siumed.edu/alz/research%20Dementia.html

A brain autopsy program developed to serve the needs of Illinois families and individuals affected by dementing diseases and to advance dementia research by providing tissue to researchers studying dementing diseases. The SIU School of Medicine (SIU-SM) Dementia Brain Autopsy Program facilitates the postmortem process for families wishing to obtain an autopsy for a loved one. A brain autopsy provides family members with accurate information regarding the exact nature of their relative's dementia. This includes information about the possibility of an inherited disorder which may affect other family members. The brain autopsy also helps clinicians improve their clinical skills by identifying the precise cause of the clinical dementia.

Proper citation: SIU CADRD Dementia Brain Autopsy Program (RRID:SCR_006918) Copy   

•   Source: SciCrunch Registry

http://brainmaps.org

An interactive multiresolution brain atlas that is based on over 20 million megapixels of sub-micron resolution, annotated, scanned images of serial sections of both primate and non-primate brains and integrated with a high-speed database for querying and retrieving data about brain structure and function. Currently featured are complete brain atlas datasets for various species, including Macaca mulatta, Chlorocebus aethiops, Felis catus, Mus musculus, Rattus norvegicus, Tyto alba and many other vertebrates. BrainMaps is currently accepting histochemical, immunocytochemical, and tracer connectivity data, preferably whole-brain. In addition, they are interested in EM, MRI, and DTI data.

Proper citation: BrainMaps.org (RRID:SCR_006878) Copy   

•   Source: SciCrunch Registry

http://humanconnectome.org/consortia/

Project to map the neural pathways that underlie human brain function for several modalities of neuroimaging data including fMRI. The purpose of the Project is to acquire and share data about the structural and functional connectivity of the human brain. It will greatly advance the capabilities for imaging and analyzing brain connections, resulting in improved sensitivity, resolution, and utility, thereby accelerating progress in the emerging field of human connectomics. Altogether, the Human Connectome Project will lead to major advances in the understanding of what makes us uniquely human and will set the stage for future studies of abnormal brain circuits in many neurological and psychiatric disorders. The sixteen institutes and centers of the NIH Blueprint for Neuroscience have funded two major grants that will take complementary approaches to deciphering the brain's amazingly complex wiring diagram. An 11-institution consortium led by Washington University in St. Louis and the University of Minnesota received a 5-year grant to enable development and utilization of advanced Magnetic Resonance Imaging (MRI) methods to chart brain circuitry. A consortium led by Massachusetts General Hospital and the University of California at Los Angeles received a grant to enable building and refining a next-generation 3T MR scanner that improves the quality and spatial resolution with which brain connectivity data can be acquired at this field strength.

Proper citation: NIH Human Connectome Project (RRID:SCR_006942) Copy   

•   Source: SciCrunch Registry

http://www.wholebraincatalog.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016. An open source, downloadable, 3d atlas of the mouse brain and its cellular constituents that allows multi-scale data to be visualized in a seamless way, similar to Google earth. Data within the Catalog is marked up with annotations and can link out to additional data sources via a semantic framework. This next generation open environment has been developed to connect members of the neuroscience community to facilitate solutions for today's intractable challenges in brain research through cooperation and crowd sourcing. The client-server platform provides rich 3-D views for researchers to zoom in, out, and around structures deep in a multi-scale spatial framework of the mouse brain. An open-source, 3-D graphics engine used in graphics-intensive computer gaming generates high-resolution visualizations that bring data to life through biological simulations and animations. Within the Catalog, researchers can view and contribute a wide range of data including: * 3D meshes of subcellular scenes or brain region territories * Large 2D image datasets from both electron and light level microscopy * NeuroML and Neurolucida neuronal reconstructions * Protein Database molecular structures Users of the Whole Brain Catalog can: * Fit data of any scale into the international standard atlas coordinate system for spatial brain mapping, the Waxholm Space. * View brain slices, neurons and their animation, neuropil reconstructions, and molecules in appropriate locations * View data up close and at a high resolution * View their own data in the Whole Brain Catalog environment * View data within a semantic environment supported by vocabularies from the Neuroscience Information Framework (NIF) at http://www.neuinfo.org. * Contribute code and connect personal tools to the environment * Make new connections with related research and researchers 5 Easy Ways to Explore: * Explore the datasets across multiple scales. * View data closely at high resolution. * Observe accurately simulated neurons. * Readily search for content. * Contribute your own research.

Proper citation: Whole Brain Catalog (RRID:SCR_007011) Copy   

•   Source: SciCrunch Registry

http://www.nybb.hs.columbia.edu/

A brain bank which collects postmortem human brains to meet the needs of neuroscientists investigating specific psychiatric and neurological disorders. NYBB disburses tissue samples to investigating clinicians or scientists whose research has been approved by their Institutional Review Board. The tasks of the NYBB include: collection and processing of human postmortem brain samples for research; neuropathological evaluation and diagnosis; storage and computerized inventory of brain samples; and distribution of brain samples to investigating clinicians and scientists. Brains from individuals without neurological or psychiatric disorders are used as normal controls.

Proper citation: New York Brain Bank at Columbia University (RRID:SCR_007142) 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://www.stanleyresearch.org/dnn/BrainResearchLaboratory/tabid/195/Default.aspx

It is a widely used resource for researchers trying to find the causes of, and better treatments for, schizophrenia, bipolar disorder and major depression. Brains were collected 1994 to 2005 with the permission of the families in a standardized manner, with half of each specimen being frozen and half fixed in formalin. Currently four cohorts are available for study; the Neuropathology Consortium consisting of 60 cases (15 each schizophrenia, bipolar disorder, depression, and controls), the Array Collection consisting of 105 cases (35 each schizophrenia, bipolar disorder, and controls), the Depression Collection consisting of 36 cases (12 each depression with psychosis, depression without psychosis, and controls), and the Parietal Collection of 48 cases (fixed inferior parietal sections from 24 each schizophrenia and controls). Since 1996, the Stanley Brain Collection has sent over 200,000 sections and 10,000 blocks of brain tissue to 240 research laboratories in 23 states and 20 foreign countries. All tissue has been provided to the researchers without charge. All costs for collecting, processing, and storing the brain tissue have been borne by The Stanley Medical Research Institute as a public service. All reasonable requests for brain tissue (over 90 percent of applications) have been honored. Researchers selected to receive tissue must sign an agreement that sets forth conditions for its use. Results received from researchers become part of the Stanley brain collection data set and will be used for integrative, multivariate analyses. In addition to overseeing the brain collection, the laboratory conducts research on the neuropathology of schizophrenia and bipolar disorder and on brain development. Many studies carried out at the Stanley Brain Research Laboratory are done in cooperation with studies at the Stanley Laboratory of Developmental Neurovirology.

Proper citation: Stanley Brain Collection (RRID:SCR_007062) Copy   

•   Source: SciCrunch Registry

http://www9.biostr.washington.edu/da.html

Atlases of human brain, thoracic viscera and knee designed for teaching gross anatomy. Also provides a neuroanatomy Interactive syllabus, suitable as a laboratory guide, with an instructive caption accompanying each image and interactive quizzes. The Digital Anatomist Project is motivated by the belief that anatomy is the basis of all the biomedical sciences (including clinical medicine). Manifestations of health and disease can be regarded as attributes of anatomical structures ranging in size from molecules to body parts. Therefore DAP''s goal is to represent anatomy in a comprehensive and consistent way, which should meet the needs of all biomedical applications that require anatomical knowledge. DAP has pursued two parallel tracks for representing anatomical information: 1. The generation of graphical models derived from cadaver and clinical imaging data; and 2. Symbolic modeling of the structures and relationships that constitute the human body. It''s initial work with graphical representations of anatomy provided the impetus and motivation for the National Library of Medicine to establish the Visible Human Project, and it''s symbolic modeling has enhanced NLM''s Unified Medical Language System in order to represent deep anatomical knowledge. In collaboration with the knowledge systems group at Stanford, it has now created a very large knowledge base which provides the foundation for the machine-based intelligence needed to remotely interact with biomedical image data.

Proper citation: Digital Anatomist Interactive Atlases Project (RRID:SCR_007060) Copy   

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http://www.alz.org/

A non profit organization dedicated to providing support for patients and families with Alzheimer's disease, to educating the public about the disease, to funding a wide range of Alzheimer's disease related research and to finding ways to treat and eventually to prevent Alzheimer's disease. Resources include: the Alzheimer's Association Green-Field Library, a research grants program, and the Journal of the Alzheimer's Association.

Proper citation: Alzheimers Association (RRID:SCR_007398) Copy   

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http://www.neuropat.dote.hu/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 07, 2013. A set of human neuroanatomical resources developed at the University of Hungary. Resources include an on-line brain atlas, a neuropathology atlas, functional neuroanatomy for neurologists and an extensive series of links to other neuroanatomy and neurological resources on the web. The original resources developed by this site include a set of neuropathological slides covering many neurological conditions, e.g., Alzheimer's disease, an atlas of normal human neuroanatomy based on unstained brain slices, along with histological images of brainstem and spinal cord. On-line quizzes are also provided. This is an excellent educational site and gateway to neurological resources on the web.

Proper citation: Neuroanatomy and Neuropathology on the Internet (RRID:SCR_007272) Copy   

•   Source: SciCrunch Registry

http://www.hbpp.org/

An open international project under the patronage of the Human Proteome Organisation (HUPO) that aims: To analyze the brain proteome of human as well as mouse models in healthy, neurodiseased and aged status with focus on Alzheimer's and Parkinson's Disease; To perform quantitative proteomics as well as complementary gene expression profiling on disease-related brain areas and bodily fluids; To advance knowledge of neurodiseases and aging in order to push new diagnostic approaches and medications; To exchange knowledge and data with other HUPO projects and national / international initiatives in the neuroproteomic field; To make neuroproteomic research and its results available in the scientific community and society. Recent work has shown that standards in proteomics and especially in bioinformatics are mandatory to allow comparable analyses, but still missing. To address this challenge, the HUPO BPP is closely working together with the HUPO Proteome Standards Initiative (HUPO PSI).

Proper citation: HUPO Brain Proteome Project (RRID:SCR_007302) Copy   

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http://www.nntc.org/

Collects, stores, and distributes samples of nervous tissue, cerebrospinal fluid, blood, and other tissue from HIV-infected individuals. The NNTC mission is to bolster research on the effects of HIV infection on human brain by providing high-quality, well-characterized tissue samples from patients who died with HIV, and for whom comprehensive neuromedical and neuropsychiatric data were gathered antemortem. Researchers can request tissues from patients who have been characterized by: * degree of neurobehavioral impairment * neurological and other clinical diagnoses * history of drug use * antiretroviral treatments * blood and CSF viral load * neuropathological diagnosis The NNTC encourages external researchers to submit tissue requests for ancillary studies. The Specimen Query Tool is a web-based utility that allows researchers to quickly sort and identify appropriate NNTC specimens to support their research projects. The results generated by the tool reflect the inventory at a previous time. Actual availability at the local repositories may vary as specimens are added or distributed to other investigators.

Proper citation: National NeuroAIDS Tissue Consortium (RRID:SCR_007323) Copy   

•   Source: SciCrunch Registry