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http://cibsr.stanford.edu/

The Center for Interdisciplinary Brain Sciences Research (CIBSR) at the Stanford University School of Medicine is dedicated to research that will improve the lives and well-being of individuals with disorders of the brain and improve knowledge of healthy brain and behavioral development. CIBSR research staff are dedicated to identifying biological and environmental risk factors, understanding disease pathophysiology and developmental outcomes, and developing new treatments for neurodevelopmental, neurogenetic and neuropsychiatric disorders of childhood onset. Our research studies are truly multi/interdisciplinary as they bring together experts from the fields of psychiatry, neurology, psychology, computer science, biostatistics and genetics to explore and seek answers for complex questions related to brain-behavior relationships. Active research at CIBSR includes: * Mutlimodal imaging of the brain utilizing anatomical and functional magnetic resonance imaging (MRI), diffusion tensor imaging (DTI) and magnetic resonance spectroscopy (MRS). * Behavioral, cognitive, and physiological assessment to address questions concerning the influence of biological and environmental factors on outcome. * The development of new biological and cognitive-behavioral treatments. * Development of brain image analysis methods and software.

Proper citation: Stanford University, Center for Interdisciplinary Brain Sciences Research (RRID:SCR_004134) Copy   

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http://www.caneucre.org

Cre expressing mice under the control of promoters with a design focus on the brain. Each promoter is derived from human sequence, but the resulting expression is assessed in the mouse for the activation of a LacZ reporter gene by the Cre activity. Promoters tested as large MaxiPromoters (BACs inserted into the mouse genome) and MiniPromoters (plasmid-based sequences inserted either into the mouse genome or introduced within AAV viruses). The Cre-related project continues from the Pleiades Promoter Project. Here is the list of genes for which icre/ERT2 mice are currently in development: AGTR1, CARTPT, CLDN5, CLVS2, CRH, GABRA6, HTR1A, HTR1B, KCNA4, KDM5C, MKI67, NEUROD6, NKX6-1, NOV, NPY2R, NR2E1, OLIG2, POU4F2, SLITRK6, SOX1, SOX3, SOX9,, SPRY1, VSX2

Proper citation: CanEuCre (RRID:SCR_004159) Copy   

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https://www.uab.edu/medicine/alzheimers/

The UAB Alzheimer's Disease Center provides comprehensive treatment for Alzheimer's patients while also promoting research for the prevention and cure of Alzheimer's disease and related disorders. The ADC is an interdisciplinary program of scientists working in areas including neurology, psychiatry, genetics, and psychology. The Center provides comprehensive treatment and promotes research for the prevention and/or cure of Alzheimer's disease and other related disorders with memory loss and impaired cognition. A major emphasis of research is the maintenance of a clinical research database comprised of neurological, medical, and neuropsychological test data from participants seen in the ADRC Clinical study since 1999, many of whom have been followed for several years in the study.

Proper citation: UAB Alzheimer's Disease Center (RRID:SCR_004305) Copy   

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http://brainspan.org/rnaseq/downloads.html?format=html

BrainSpan, an atlas of the developing human brain, is designed as a foundational resource for studying transcriptional mechanisms involved in human brain development. One of the BrainSpan datasets, RNA-Seq exons, is presented. It is a downloadable archive of files containing normalized RNA-Seq expression values for analysis.

Proper citation: BrainSpan: RNA-Seq exons (RRID:SCR_004344) Copy   

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http://www.brainnet-europe.org/

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 7, 2022. Consortium of 19 brain banks across Europe with an aim to harmonize neuropathological diagnostic criteria and develop gold standards for quality, safety and ethics standards for brain banking. BrainNet Europe also contributes to research on rare diseases, such as: Pick''s disease or other rare forms of dementia, as well as to questions after the events in the aging brain. Anyone can be a donor - irrespective of disease of the central nervous system or not, because for research purposes, one does not only need tissue samples from ill donors, but also from healthy ones for comparison.

Proper citation: BrainNet Europe (RRID:SCR_004461) Copy   

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http://www.epilepsy.ie/index.cfm/spKey/research.html

Epilepsy Research Ireland is a non-profit organization (Charity CHY17527), run by a group of volunteers, who are dedicated to find cure for epilepsy by raising awareness and money for research. We can say cure now with much more confidence than we could even 10 years ago because recent advances in genetics, brain imaging and drug therapy, all hold out the promise of that holy grail the cure. We can also say with confidence that you can be part of that push by participating in this new foundation since we have collaborations with doctors and scientists all over Europe, the US and Australia, all of whom share the same goal. Epilepsy research, conducted by Epilepsy Research Ireland, is essential and will deliver benefits across the board. Research planned and already underway by Epilepsy Research Ireland will help develop and improve clinical skills; it will provide a knowledge base to develop new ways to manage and treat epilepsy; it will help in the evaluation of new medical advances. Ultimately we can improve the quality of care and provide greater understanding, better and more accurate diagnosis and more tailored treatments. Ireland is uniquely well-positioned, given its relatively homogenous population to make the goal, of making real discoveries in epilepsy research that will directly improve the lives of people with epilepsy, a realistic one.

Proper citation: Epilepsy Research Ireland (RRID:SCR_004448) Copy   

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http://www.cbtf.org/

Children''s Brain Tumor Foundation, a non-profit organization, was founded in 1988 by dedicated parents, physicians and friends. Our mission is to improve the treatment, quality of life and the long term outlook for children with brain and spinal cord tumors through research, support, education, and advocacy to families and survivors. Knowledge is critical for families to access expert care and ensure quality of life. Our free publication A Resource Guide for Parents of Children with Brain and Spinal Cord Tumors is now in its fourth edition, and is full of practical information to sort out the complexities of medical procedures, interruptions in school and social life, and uncertainty about the future. CBTF co-sponsors conferences for families, survivors and health care professionals, offering the latest information about research, treatments and strategies for living. Only scientific research will identify the causes and lead to effective treatments for brain tumors in children. CBTF funds cutting-edge research by scientists at top academic medical centers. Their discoveries hold the promise of improving the lives of affected children today and discovering the means of prevention for future generations. CBTF has awarded over $5 million in grants for basic and clinical research related to pediatric brain and spinal cord tumors. Also, over $625,000 has been given out in Quality of Life Grants.

Proper citation: Childrens Brain Tumor Foundation (RRID:SCR_004422) Copy   

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http://www.nature.com/jcbfm/index.html

The Journal of Cerebral Blood Flow & Metabolism stands at the interface between basic and clinical neurovascular research, and features timely and relevant research highlighting experimental, theoretical, and clinical aspects of brain circulation, metabolism and imaging. The journal is relevant to any physician or scientist with an interest in brain function, cerebrovascular disease, cerebral vascular regulation and brain metabolism, including neurologists, neurochemists, physiologists, pharmacologists, anesthesiologists, neuroradiologists, neurosurgeons, neuropathologists and neuroscientists. On this website, you will find the full text of articles published online weekly, in advance of print, the current issue and an archive of previous issues. You can also find general information about the journal, and more detailed information for readers, authors, referees, librarians, advertisers, and journalists. Most articles are published online before they appear in print. New papers are uploaded weekly to the Advance online publication (AOP) page. The online publication date is specified for each paper; these versions are identical to the printed version in every respect and may be cited using the digital object identifier (DOI).

Proper citation: Journal of Cerebral Blood Flow and Metabolism (RRID:SCR_001769) Copy   

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http://neuroscience.ucdavis.edu/

Recognizing the importance of research in Neuroscience and its great promise, as well as the importance of educating the neuroscientists of the future, the University of California, Davis, in 1990, established The Center for Neuroscience. The Center has now become the focus of interdisciplinary studies in Cellular, Molecular, Systems, Cognitive and Translational Neuroscience, with a Faculty made up of world leaders in brain research. The Center occupies facilities especially designed to promote and foster interactions among the resident faculty, associated faculty, postdoctoral fellows, and graduate students, with state-of-the-art lab space and associated facilities such as cellular and molecular imaging, functional imaging of the human brain and extensive databasing facilities. The Center provides an attractive setting for seminar series that feature distinguished National and International guest speakers as well as speakers from the UC Davis community of scientists. The Center is home to a number of visiting scholars each year and enjoys a lively intellectual atmosphere.

Proper citation: University of California Davis Center for Neuroscience (RRID:SCR_001640) Copy   

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http://neuroimage.usc.edu/brainstorm/

Software as collaborative, open source application dedicated to analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and animal invasive neurophysiology. User-Friendly Application for MEG/EEG Analysis.

Proper citation: Brainstorm (RRID:SCR_001761) Copy   

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http://dynamicbrain.neuroinf.jp/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19. 2022. Platform to promote studies on dynamic principles of brain functions through unifying experimental and computational approaches in cellular, local circuit, global network and behavioral levels. Provides services such as data sets, popular research findings and articles and current developments in field. This site has been archived since FY2019 and is no longer updated.

Proper citation: Dynamic Brain Platform (RRID:SCR_001754) Copy   

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http://cmbn-approd01.uio.no/nesys/

Public neuroscience database providing a collection of published data describing structure and structure-function relationships in one of the largest projection systems of the brain: the cerebro-cerebellar system. It also gives access to a suite of tools that allow the user to visualize and analyze any selected combination of data sets. Contact them if you are interested in contributing data. The overall goal is to improve communication of results and permit re-use of previously published data in new contexts. FACCS is a part of the Rat Brain WorkBench, a new research and development project funded by The Research Council of Norway, the Centre for Molecular Biology and Neuroscience, and the European Union. The project is directed by Jan G. Bjaalie, Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.

Proper citation: Functional Anatomy of the Cerebro-Cerebellar System (FACCS) (RRID:SCR_001661) Copy   

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https://lcn.salk.edu/WSMain.html

The Salk Institute's Laboratory for Cognitive Neuroscience (LCN) is dedicated to the study of the neural and genetic underpinnings of language and cognition. The LCN organizes its resources into two research foci: Linking Gene, Brain, and Cognition, and Language, Modality and the Brain. Linking Gene, Brain, and Cognition: Behavioral Neurogenetics: - This research is designed to increase the understanding of genetically based disorders, to investigate the consequences of genetic alterations on the development of the brain, and to explore the resulting alteration of cognitive capabilities. Language, Modality, and the Brain: - The focus of this research is to obtain a greater understanding of how language and cognition are represented in the brain. Sponsors: This resource is supported by LCN.

Proper citation: Salk Institute for Medical Research: Laboratory for Cognitive Neuroscience (RRID:SCR_001851) Copy   

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http://qnl.bu.edu/obart

Tool that provides an interactive method to examine quantitative relationships between brain regions defined by different digital atlases or parcellation methods. Its current focus is for human brain imaging, though the techniques generalize to other domains. The method offers a quantitative answer to the nomenclature problem in neuroscience by comparing brain parts on the basis of their geometrical definitions rather than on the basis of name alone. Thus far these tools have been used to quantitatively compare eight distinct parcellations of the International Consortium for Brain Mapping (ICBM) single-subject template brain, each created using existing atlasing methods. This resources provides measures of global and regional similarity, and offers visualization techniques that allow users to quickly identify the correspondences (or lack of correspondences) between regions defined by different atlases.

Proper citation: OBART (RRID:SCR_001903) Copy   

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http://flybrain.stanford.edu/

Project content including raw image data, neuronal tracings, image registration tools and analysis scripts covering three manuscripts: Comprehensive Maps of DrosophilaHigher Olfactory Centres : Spatially Segregated Fruit and Pheromone Representation which uses single cell labeling and image registration to describe the organization of the higher olfactory centers of Drosophila; Diversity and wiring variability of olfactory local interneurons in the Drosophila antennal lobe which uses single cell labeling to describe the organization of the antennal lobe local interneurons; and Sexual Dimorphism in the Fly Brain which uses clonal analysis and image registration to identify a large number of sex differences in the brain and VNC of Drosophila. Data * Raw Data of Reference Brain (pic, amira) (both seed and average) * Label field of LH and MB calyx and surfaces for these structures * Label field of neuropil of Reference Brain * Traces (before and after registration). Neurolucida, SWC and AmiraMesh lineset. * MB and LH Density Data for different classes of neuron. In R format and as separate amira files. * Registration files for all brains used in the study * MBLH confocal images for all brains actually used in the study (Biorad pic format) * Sample confocal images for antennal lobe of every PN class * Confocal stacks of GABA stained ventral PNs Programs * ImageJ plugins (Biorad reader /writer/Amira reader/writer/IGS raw Reader) * Binary of registration, warp and gregxform (macosx only, others on request) * Simple GUI for registration tools (macosx only at present) * R analysis/visualization functions * Amira Script to show examples of neuronal classes The website is a collaboration between the labs of Greg Jefferis and Liqun Luo and has been built by Chris Potter and Greg Jefferis. The core Image Registration tools were created by Torsten Rohlfing and Calvin Maurer.

Proper citation: Flybrain at Stanford (RRID:SCR_001877) Copy   

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http://bmi.neuroinf.jp/

Databases of accumulating BMI (Brain Machine Interfaces)-related experimental data, mathematical models, and tools generated in neuroscience, computational theory, and robotics. Databases include: # Database of BMI (Brain Machine Interfaces)-related papers: More than 3500 BMI-related papers are registered. Each paper has original tags, for example, recording method and subject, for easy searching. # Database of original contents: BMI-related materials (Movie, Picture, Data, Program) provided by scientists. # Database of BMI-related research sites: 185 BMI-related research sites in the world (university, institute and company) are registered. The research site can be searched either by the location using clickable map or by the field of interest. # Database of BMI-related materials: Links to BMI-related materials (Movie, Picture, Document, Data, Program) are listed. You can easily find materials of your interest since each material is classified into research field. # BMI-related column: The columns are written by researchers specialized in BMI. Original contents include: * Neuronal activity during performance of a memory-guided movement * Reconstructed visual images from human fMRI activity * fMRI data and program for visual image reconstruction * Brain sections of monkeys, stained for several gene markers * Cortical Box Method: The Cortical box method is an analytical method that standardizes the serial coronal sections of rodent cortex for quantitative analysis. * Multineuron activity in monkey prefrontal cortex * Monkey Atlas: **Brain sections of monkeys, stained for AChE, ER81 mRNA and Sema3E mRNA - These pictures are low-resolution photos of serial brain sections of monkeys, stained for AChE as well as for ER81 and Sema3E mRNAs. The compressed file contains JPEG photos and html files for web browser navigation. Other materials are available at our website BraInSitu dedicated for in situ hybridization resources for brains. BraInSitu http://www.nibb.ac.jp/brish/indexE.html ** MRI Brain Atlas of Japanese Snow Monkey (Macaca Fuscata) at different ages - MRI Brain Atlas of Japanese Snow Monkey (Macaca Fuscata) at different ages ** The Stereotaxic MRI Brain Atlas of Japanese Snow Monkey - The Stereotaxic MRI Brain Atlas of Japanese Snow Monkey * Monkey M1 BMI ** m-file for checking the results of wrist angle estimation- This program is m-file to train the relationship between joint angles and EMG signals using artificial neural network. The input signals are four EMG signals and the output signals are joint angles of wrist, such as flexion/extension, radial deviation/uln ** m-file for training of wrist angle estimation -This program is m-file to train the relationship between joint angles and EMG signals using artificial neural network. The input signals are four EMG signals and the output signals are joint angles of wrist, such as flexion/extension, radial deviation/ulnar deviation.ar deviation. ** M1 Neuronal Activity during monkey performing a motor task - video/x-ms-wmv ** Muscle tension - To estimate muscle tension from raw emg signal ** raw EMG signal - Raw EMG signal for 5 seconds ** training data of wrist angle and emg signal - This program is m-file to train the relationship between joint angles and EMG signals using artificial neural network. The input signals are four EMG signals and the output signals are joint angles of wrist, such as flexion/extension, radial deviation/ulnar deviation. ** Weight file of neural network - This program is m-file to train the relationship between joint angles and EMG signals using artificial neural network. The input signals are four EMG signals and the output signals are joint angles of wrist, such as flexion/extension, radial deviation/ulnar deviation. * Multineuron activity in monkey prefrontal cortex: Multineuron activity in monkey prefrontal cortex recorded by 3 tetrodes. Vertical 4 lines indicate one tetrode. Adjacent tetrodes are around 500 micron apart to each other.

Proper citation: Brain Machine Interface Platform (RRID:SCR_001813) 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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