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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://www.drugabuseresearchtraining.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on November 07, 2012. Decemeber 15, 2011 - Thank you for your interest in DrugAbuseResearchTraining.org. The site, courses, and resources are no longer available. Please send an email to inquiry (at) md-inc.com if you would like to be notified if the site or courses become available again. Introduction to Clinical Drug and Substance Abuse Research Methods is an online training program intended to introduce clinicians and substance abuse professionals to basic clinical research methods. The program is divided into four modules. Each module covers an entire topic and includes self-assessment questions, references, and online resources: * The Neurobiology of Drug Addiction * Biostatistics for Drug and Substance Abuse Research * Evaluating Drug and Substance Abuse Programs * Designing and Managing Drug and Substance Abuse Clinical Trials The learning objectives of this program are to help you: * Evaluate the benefits of alternative investigative approaches for answering important questions in drug abuse evaluation and treatment. * Define the proper levels of measurement and appropriate statistical methods for a clinical study. * Address common problems in data collection and analysis. * Anticipate key human subjects and ethical issues that arise in drug abuse studies. * Interpret findings from the drug abuse research literature and prepare a clinical research proposal. * Prepare research findings for internal distribution or publication in the peer reviewed literature. * Recognize drug addiction as a cyclical, chronic disease. * Understand and describe the brain circuits that are affected by addicting drugs, and explain to others the effects of major classes of addicting drugs on brain neurotransmitters. * Utilize new pharmacologic treatments to manage persons with drug addiction. Physicians can earn AMA PRA Category 1 Credit and purchase a high resolution printable electronic CME certificate(view sample); non-physicians can purchase high resolution printable electronic certificate of course participation that references AMA PRA Category 1 credit (view sample). This program does not offer printed certificates.

Proper citation: Online Education for the International Research Community: AboutIntroduction to Clinical Drug and Substance Abuse Research Methods (RRID:SCR_000802) Copy   

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http://isc.temple.edu/neuroanatomy/lab/atlas/S5/

Sectional atlas featuring sections of the spinal cord and brain for a neuroanatomy course offered by Temple University. Labels may be turned on and off.

Proper citation: Sectional Atlas of Human Brain and Spinal Cord (RRID:SCR_000799) Copy   

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http://mbl.org

Collection of high resolution images and databases of brains from many genetically characterized strains of mice with aim to systematically map and characterize genes that modulate architecture of mammalian CNS. Includes detailed information on genomes of many strains of mice. Consists of images from approximately 800 brains and numerical data from just over 8000 mice. You can search MBL by strain, age, sex, body or brain weight. Images of slide collection are available at series of resolutions. Apple's QuickTime Plugin is required to view available MBL Movies.

Proper citation: Mouse Brain Library (RRID:SCR_001112) Copy   

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http://www.cogsci.ucsd.edu/index.php

This UCSD department, the first Cognitive Science Department in the world, provides a focus for the continued evolution of the discipline of cognitive science. Cognitive science is a diverse field unifying three broad categories: the brain, behavior and computation. It's the study of how people, animals and computers think, act and learn. In order to understand the mind/brain, cognitive science brings together the methods and discoveries from neuroscience, psychology, linguistics, anthropology, philosophy and computer science. The interdisciplinary aspects of cognitive science continue to flourish, and the participation of the broader cognitive science community on campus continues to be fundamental to cognitive science as practiced at UCSD. The interdisciplinary Ph.D. program continues to be offered as a degree option (in addition to the departmental Ph.D.), with participation by members of the Departments of Anthropology, Biology, Cognitive Science, Communication, Computer Science and Engineering, Linguistics, Music, Neuroscience, Philosophy, Psychiatry, Psychology, and Sociology. Cognitive Science is a relatively young field that focuses on conducting new research into the field or applying existing knowledge into new applications. This Department contains several research labs each specializing in different areas and the Department's faculty has also been published many times in various publications. Sponsors: This department is supported by the University of California at San Diego.

Proper citation: UCSD Cognitive Science: The Future of Cognitive Science (RRID:SCR_001926) Copy   

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http://nips.cc/

The Neural Information Processing Systems (NIPS) Foundation is a non-profit corporation whose purpose is to foster the exchange of research on neural information processing systems in their biological, technological, mathematical, and theoretical aspects. Neural information processing is a field which benefits from a combined view of biological, physical, mathematical, and computational sciences. The primary focus of the NIPS Foundation is the presentation of a continuing series of professional meetings known as the Neural Information Processing Systems Conference, held over the years at various locations in the United States and Canada.

Proper citation: NIPS - Neural Information Processing Systems Conference (RRID:SCR_001998) Copy   

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http://www.yerkes.emory.edu/

Center for advancing scientific understanding and improving the health and well-being of humans and nonhuman primates. The Center conducts research in microbiology and immunology, neurologic diseases, neuropharmacology, behavioral, cognitive and developmental neuroscience, and psychiatric disorders.

Proper citation: Yerkes National Primate Research Center (RRID:SCR_001914) Copy   

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http://hendrix.ei.dtu.dk/software/mriwarp/mriwarp.html

Warping tool for intersubject registration of brain images consisting of C functions for Unix systems plus Matlab visualization utility functions. Apart from warping there are also (command line) functions for ANALYZE header information, mirroring, translation, subsampling. The package cannot only be used as a preprocessing step in function neuroimaging but also as a step in deformation-based morphometry.

Proper citation: MRIWarp (RRID:SCR_002072) Copy   

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http://sccn.ucsd.edu/

Computational neuroscience center that observes and models how functional activities in multiple brain areas interact dynamically to support human cognition, creativity and social interaction. Center research involves development computational methods and software, experimental methods and equipment, collection and analysis of human cognitive experiments, and collaborations to analyze data collected by other groups in such experiments. The Center has a 72-channel EEG recording system customized for use in the fMRI environment, and a very-high density Biosemi Active Two active-electrode EEG system, rapidly configurable either as a 256-channel system for a single subject or as two 136-channel systems for recording from two subjects simultaneously. In addition, UCSD now has a 306-channel MEG plus 128-channel EEG system (Neuromag/Elektra). Projects in the Center include studies of human cognitive processes including attention and memory, role of the anterior/posterior cingulate, time perception and emotional expression. Data acquisition includes high-density EEG, concurrent EEG and fMRI recording and analysis, and face video processing. Current analysis approaches include independent component and time-frequency analysis.

Proper citation: Swartz Center for Computational Neuroscience (RRID:SCR_001933) Copy   

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http://www.pc.rhul.ac.uk/staff/J.Larsson/software.html

Set of programs and Tk/Tcl scripts, with a GUI wrapper, for extracting the inner and outer cortical surfaces from a T1-weighted MR image of the human brain. It is based on the TFI C++ library and is written for a Unix-based environment (specifically 64-bit and 32-bit versions of Ubuntu). As a courtesy to Apple users a version for Apple/X11 is maintained but the OS X version will always lag the Linux version; also, because some of the third-party libraries SurfRelax relies on may not be supported in or compatible with future versions of OS X, there is no guarantee that the OS X version will be supported indefinitely. Although in principle SurfRelax could be run under Windows (using Cygwin), because of the difficulties of maintaining multiple platforms and the limited support libraries available under Cygwin, there will no longer be support for SurfRelax on this platform. The surfaces are guaranteed to be topologically equivalent to a sphere, thereby obviating the need for handle removal. SurfRelax requires no user intervention, although minor manual editing is recommended for optimal results (normally less than 10 minutes per hemisphere). SurfRelax has several properties that compare favorably with other software packages for surface reconstruction: * Free software - The binaries (written in C++ and Tcl/Tk) are in the public domain. The source code will be released once legacy code issues have been resolved (i.e. replacing with GPL code). * Uses standard public file formats: Analyze file format (SPM/FSL-compatible) for volumes and OOGL OFF binary format for surfaces (see www.geomview.org (http://www.geomview.org/docs/html/geomview_26.html#OOGLRef)) * Combines advantages of volumetric and surface-based methods for surface generation * Correct topology of output surface guaranteed * Requires little or no user intervention - no need for manual handle removal * Relatively robust to noise - multi-scale method compensates for partial volume effects and intensity inhomogeneities * Relatively fast (an entire brain is segmented, extracted and unfolded in less than 2 hours of CPU time) * Powerful editing and visualization tools for volumes and surfaces * Readily extendable - for instance for use with monkey brains or children's brains * Can be used to visualize functional data from SPM or FSL * Includes tools for integration with Stanford's VISTASOFT tools for FMRI data analysis (white.stanford.edu)

Proper citation: SurfRelax (RRID:SCR_002139) Copy   

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http://www.incf.org/

Independent international facilitator catalyzing and coordinating global development of neuroinformatics aiming to advance data reuse and reproducibility in global brain research. Integrates and analyzes diverse data across scales, techniques, and species to understand brain function and positively impact the health and well being of society.

Proper citation: International Neuroinformatics Coordinating Facility (RRID:SCR_002282) Copy   

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http://www.bioon.com/bioline/neurosci/course/index.htm

An illustrated guide to the essential basics of clinical neuroscience created in conjunction with the first-year course for medical students.
Topics covered:
* Coronal and horizontal sections
* Basic visual pathway
* Basic somatosensory pathway
* Basic motor pathway
* Eye and retina
* Central visual pathways
* Auditory and vestibular systems
* Somatosensory pathways from the body
* Somatosensory pathways from the face
* Spinal motor structures
* Brainstem nuclei of cranial nerves
* Basal ganglia and cerebellum
* Hypothalamus and autonomic nervous system
* Medial temporal lobe and memory
* Sleep and language
* Where is...?

Proper citation: Washington University School of Medicine Neuroscience Tutorial (RRID:SCR_002271) Copy   

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http://connectomes.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Project mapping whole mouse brain connectivity using serial block face scanning electron microscopy (SBF-SEM) with a specially-designed whole-brain microtome (WBM). With any luck, the whole mouse brain will be mapped ultrastructurally in the near term, which will then open the door to more serious problems; reliable automated segmentation and circuit reconstruction. These will undoubtedly require advances in machine learning methods and their application. Connectomics Software and a Multiresolution Image Viewer (MIV) is also available.

Proper citation: Connectomes.org (RRID:SCR_002243) Copy   

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http://www.kumc.edu/instruction/medicine/anatomy/histoweb/nervous/nervous.htm

Histology atlas of different parts of the nervous system that corresponds with the laboratory exercises of the Cell & Tissue Biology course of the School of Medicine of the University of Kansas. Succinct explanations of the tissues to guide the first-year medical student in the use of their microscope is provided and subsequently serves as a permanent histology resource for all medical students and physicians. Sections of the brain that are included are: * Spinal Cord * Central Canal * White Matter * Gray Matter * Dorsal Root Ganglion * Cerebellum * Cerebrum * Astrocytes * Nerve * Node of Ranvier * Pacinian Corpuscle

Proper citation: HistoWeb: Nervous System (RRID:SCR_002369) Copy   

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http://www.behav.org/abcd/abcd.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 21, 2017.

Database developed for storing, retrieving and cross-referencing neuroscience information about the connectivity of the avian brain. It contains entries about the new and old terminology of the areas and their hierarchy and data on connections between brain regions, as well as a functional keyword system linked to brain regions and connections.

Proper citation: Avian Brain Circuitry Database (RRID:SCR_002401) 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.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   

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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   

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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   

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