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http://www.jsmf.org/

Supports research and scholarship to improve the quality of life by providing funding for grants in three program areas: studying complex systems, understanding human cognition, and mathematical and complex systems approaches for brain cancer. Types of awards include Fellowship Awards, Scholar Awards, and Collaborative Awards. * Studying Complex Systems: This program supports scholarship and research directed toward the development of theoretical and mathematical tools that can be applied to the study of complex, adaptive, nonlinear systems. It is anticipated that research funded in this program will address issues in fields such as biology, biodiversity, climate, demography, epidemiology, technological change, economic development, governance, or computation. * Understanding Human Cognition: This program supports research studying how neural systems are linked to and support cognitive functions and how cognitive systems are related to an organism's (preferably human) observable behavior. Studies with model organisms should justify why such models were selected and how data obtained from models advances our understanding of human cognition. * Mathematical & Complex Systems Approaches for Brain Cancer: (Collaborative Activity Awards grant type only.) Despite some recent cause for optimism for advancing the clinical treatment of brain cancers, for many patients brain tumor remains a devastating diagnosis. Progress against this disease has been stymied by limited understandings of the molecular, metabolic, and physiological characteristics of human brain cancers across multiple temporal and spatial scales and by the failure of many preclinical models to predict patient responses.

Proper citation: James S. McDonnell Foundation (RRID:SCR_006341) Copy   

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http://www.callisto-science.org/NSI/Neuroscience_Image_Database/Images%20of%20the%20Human%20Nervous%20System%20-%20Neuroanatomy.html

Data set of images of the human nervous system focusing on neuroanatomy.

Proper citation: Human Nervous System Neuroanatomy (RRID:SCR_006371) Copy   

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http://vinovia.ncl.ac.uk/emagewebapp/pages/eadhb_home.jsf

Database of a set of standard 3D virtual models at different stages of development from Carnegie Stages (CS) 12-23 (approximately 26-56 days post conception) in which various anatomical regions have been defined with a set of anatomical terms at various stages of development (known as an ontology). Experimental data is captured and converted to digital format and then mapped to the appropriate 3D model. The ontology is used to define sites of gene expression using a set of standard descriptions and to link the expression data to an ''''anatomical tree''''. Human data from stages CS12 to CS23 can be submitted to the HUDSEN Gene Expression Database. The anatomy ontology currently being used is based on the Edinburgh Human Developmental Anatomy Database which encompasses all developing structures from CS1 to CS20 but is not detailed for developing brain structures. The ontology is being extended and refined (by Prof Luis Puelles, University of Murcia, Spain) and will be incorporated into the HUDSEN database as it is developed. Expression data is annotated using two methods to denote sites of expression in the embryo: spatial annotation and text annotation. Additionally, many aspects of the detection reagent and specimen are also annotated during this process (assignment of IDs, nucleotide sequences for probes etc). There are currently two main ways to search HUDSEN - using a gene/protein name or a named anatomical structure as the query term. The entire contents of the database can be browsed using the data browser. Results may be saved. The data in HUDSEN is generated from both from researchers within the HUDSEN project, and from the wider scientific community. The HUDSEN human gene expression spatial database is a collaboration between the Institute of Human Genetics in Newcastle, UK, and the MRC Human Genetics Unit in Edinburgh, UK, and was developed as part of the Electronic Atlas of the Developing Human Brain (EADHB) project (funded by the NIH Human Brain Project). The database is based on the Edinburgh Mouse Atlas gene expression database (EMAGE), and is designed to be an openly available resource to the research community holding gene expression patterns during early human development.

Proper citation: HUDSEN Human Gene Expression Spatial Database (RRID:SCR_006325) Copy   

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https://sites.google.com/site/functionalconnectivitytoolbox/

MATLAB toolbox for performing functional connectivity analyses includes many of the most commonly-used approaches researchers have utilized to date for the identification of condition-dependent functional interactions between fMRI time-series obtained from two or more brain regions. The approaches are either bivariate or multivariate methods defined in time or frequency domains that emphasize distinct features of relationships among the time-series.

Proper citation: Functional Connectivity Toolbox (RRID:SCR_006394) Copy   

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http://www.medschool.lsuhsc.edu/epilepsy_center/

The LSU Epilepsy Center of Excellence is dedicated to providing state-of-the-art, comprehensive epilepsy treatment, enhancing access to epilepsy education for patients and physicians, and promoting multidisciplinary epilepsy research in pharmacology, neuroelectrophysiology, neuroimaging, neurosurgery, neuropsychology, biomedical engineering and public health. The center''s team of professionals offers diagnostic and presurgical monitoring, the strategic use of antiepileptic medications, specialized epilepsy neuroimaging, vagus nerve stimulator implantation, ketogenic diet management, neuropsychological testing, psychiatric support and epilepsy surgery for adults and children. The Center also hosts several clinical research trials each year for investigational medications and devices. The following are the treatment methods currently available at this center: - Epilepsy Brain Implants - Responsive Neurostimulator (RNS) - Medications - Medication blood level monitoring - Vagus Nerve Stimulators (VNS) - Epilepsy Surgery - Ketogenic Diet - Psychiatric Services - Radiosurgery Epilepsy Center Sections: *Electrophysiology *Neuroimaging *Neuropsychology *Neuroscience *Neurosurgery *Pharmacology *Psychiatry *Research

Proper citation: Louisiana State University School of Medicine, Health Sciences Center: Epilepsy Center (RRID:SCR_006519) Copy   

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http://www.mitre.org/news/digest/archives/2002/neuroinformatics.html

This resource''s long-term goal is to develop informatics methodologies and tools that will increase the creativity and productivity of neuroscience investigators, as they work together to use shared human brain mapping data to generate and test ideas far beyond those pursued by the data''s originators. This resource currently has four major projects supporting this goal: * Database tools: The goal of the NeuroServ project is to provide neuroscience researchers with automated information management tools that reduce the effort required to manage, analyze, query, view, and share their imaging data. It currently manages both structural magnetic resonance image (MRI) datasets and diffusion tensor image (DTI) datasets. NeuroServ is fully web-enabled: data entry, query, processing, reporting, and administrative functions are performed by qualified users through a web browser. It can be used as a local laboratory repository, to share data on the web, or to support a large distributed consortium. NeuroServ is based on an industrial-quality query middleware engine MRALD. NeuroServ includes a specialized neuroimaging schema and over 40 custom Java Server Pages supporting data entry, query, and reporting to help manage and explore stored images. NeuroServ is written in Java for platform independence; it also utilizes several open source components * Data sharing: DataQuest is a collaborative forum to facilitate the sharing of neuroimaging data within the neuroscience community. By publishing summaries of existing datasets, DataQuest enables researchers to: # Discover what data is available for collaborative research # Advertise your data to other researchers for potential collaborations # Discover which researchers may have the data you need # Discover which researchers are interested in your data. * Image quality: The approach to assessing the inherent quality of an image is to measure how distorted the image is. Using what are referred to as no-reference or blind metrics, one can measure the degree to which an image is distorted. * Content-based image retrieval: NIRV (NeuroImagery Retrieval & Visualization) is a work environment for advanced querying over imagery. NIRV will have a Java-based front-end for users to issue queries, run processing algorithms, review results, visualize imagery and assess image quality. NIRV interacts with an image repository such as NeuroServ. Users can also register images and will soon be able to filter searches based on image quality.

Proper citation: MITRE Neuroinformatics (RRID:SCR_006508) Copy   

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http://www.neuroinf.jp/

The Japan Node of the INCF coordinates neuroinformatics activities within Japan and represents Japanese efforts in INCF. This site provides information about Japanese neuroinformatics platforms (NI Platforms) and the techniques and tools available from the International Neuroinformatics Coordinating Facility (INCF). The Neuroinformatics Japan Center (NIJC) will also supply techniques and tools developed at RIKEN BSI and at other research groups in Japan. INCF expects each national node to: 1. Actively formulate and implement the INCF Work Programs, 2. Coordinate and facilitate local neuroinformatics research activities at the national level, 3. Encourage neuroinformatics data sharing that conforms with INCF standards, and 4. Promote neuroinformatics development that supports the goals of INCF. The Neuroinformatics Japan Center (NIJC) represents the Japan Node. Together with the Japan Node Committee and the Platform Subcommittees, we promote domestic activities of neuroinformatics. Platform Subcommittee members collaborate to develop databases that are available for use on the website. Standing at the intersection of neuroscience and information science, the field of neuroinformatics develops the tools to house, share and analyze neuroscientific data, and to create computational models of brain. NIJC supports researchers developing and maintaining neuroscience databases, provides a portal for these databases and Neuroinformatics, and is designing the infrastructure for Neuroinformatics. It is also developing database technologies, and facilitates cooperation and distribution of the information stored in those databases. The activities of the Japan Node * Shaping domestic neuroinformatics research and directions (Japan Node Committee) * Advising on Intellectual Property Rights and protecting experimental subjects (Japan Node Committee) * Developing and publishing brain science databases (Platform Subcommittee) * Coordinating database management (Platform Subcommittee) * Disseminating neuroinformatics information via the web portal * Developing the infrastructure for brain science information and neuroinformatics * Supporting the development and diffusion of neuroinformatics technology

Proper citation: INCF Japan Node (RRID:SCR_006569) Copy   

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http://learn.genetics.utah.edu/content/addiction/drugs/mouse.html

Mouse Party is an interactive website that teaches how various drugs disrupt the synapse by taking a look inside the brains of mice on drugs! Every drug of abuse has its own unique molecular mechanism. Where applicable, this presentation primarily depicts how drugs interact with dopamine neurotransmitters because this website focuses on the brain''s reward pathway. Mouse Party is designed to provide a small glimpse into the chemical interactions at the synaptic level that cause the drug user to feel ''high''. The simplified mechanisms of drug action presented here are just a small part of the story. When drugs enter the body they elicit very complex effects in many different regions of the brain. Often they interact with many different types of neurotransmitters and may bind with a variety of receptor types in a variety of different locations. For example, THC in marijuana can bind with cannabinoid receptors located on the presynaptic and/or postsynaptic cell in a synapse.

Proper citation: Mouse Party (RRID:SCR_006438) Copy   

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

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

Proper citation: BrainSuite (RRID:SCR_006623) Copy   

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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry