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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version.
Proper citation: BECA (RRID:SCR_015846) Copy
Consortium for the cell census in the brain. Integrated network of data generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate brains.
Proper citation: BICCN (RRID:SCR_015820) Copy
Consortium studying the regulation and alternative splicing of gene expression in multiple tissues from human brains. The UKBEC dataset comprises of brains from individuals free of neurodegenerative disorders.
Proper citation: UK Brain Expression Consortium (RRID:SCR_015889) Copy
https://github.com/ABCD-STUDY/ABCDreport
Software application as a simple system to review study progress. Used in ABCD study.
Proper citation: ABCDreport (RRID:SCR_016030) Copy
Research project examining how biological, psychological, and environmental factors during adolescence may influence brain development and mental health. Using brain imaging and genetics, the project will help develop prevention strategies and improved therapies for mental health disorders in the future., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: IMAGEN (RRID:SCR_016045) Copy
https://www.nitrc.org/projects/normalizefov
FSoftware for field-of-view normalization to minimize mismatch in different subjects' images. It aids that streamline analysis of large-scale brain MRI datasets.
Proper citation: NeuroImage Field-of-View Normalization Tool (RRID:SCR_015957) Copy
https://github.com/ABCD-STUDY/DEAP
Web service for data exploration and analysis of the ABCD Study - the largest long-term study of brain development and child health in the United States.
Proper citation: DEAP - Data Exploration and Analysis Portal (RRID:SCR_016158) Copy
Data repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification, histone modification profiles and chromatin accessibility.
Proper citation: NeMOarchive (RRID:SCR_016152) Copy
http://ielvis.pbworks.com/w/page/116347253/FrontPage
Software toolkit consisting of MATLAB and Bash scripts for intracranial electrode localization/visualization. It maps electrodes to various anatomical and functional atlases, and overlays electrode data over functional neuroimaging data. Software for intracranial electrode localization and visualization.
Proper citation: iELVis (RRID:SCR_016109) Copy
Project whose goal is to improve health care and lessen the global burden of TBI through the discovery of causal relationships between treatments and clinically meaningful outcomes. InTBIR seeks to encourage well-designed, hypothesis-driven studies that include the collection of high quality data followed by rigorous statistical analysis.
Proper citation: International Initiative for Traumatic Brain Injury Research (RRID:SCR_016237) Copy
https://github.com/nighres/nighres
Software package for processing of high-resolution neuroimaging data. Nighres is a community-developed project that aims to make neuroscience data tools easier to install, use and extend.
Proper citation: Nighres (RRID:SCR_016287) Copy
http://www.nitrc.org/projects/vdb/
Virtual resource for neuroscience.
Proper citation: Virtual Digital Brain (RRID:SCR_016265) Copy
http://www.nitrc.org/projects/mica/
Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging.
Proper citation: masked ICA (mICA) Toolbox (RRID:SCR_016349) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.Center hosting a number of related projects concerning neural networks, functional neuroimaging, multimedia signal processing, and biomedical signal processing. Neuroinformatics is a research field rooted in classical disciplines like signal processing, biology, physics, computer science and engineering. Neuroinformatics combines learning from the brain and learning about the brain. By studying information processing in the brain neuroinformatics invents new computing paradigms (e.g., artificial neural networks) with the objective of understanding the dynamics of the conscious mind. Artificial neural networks is an active neuroinformatics research field, which combines many approaches to adaptive signal processing in solving real world problems. They began using neural networks for general nonlinear adaptive signal processing. Since 1991 the CONNECT groups have participated in the development of neural computing as an advanced, non-linear statistical tool, which has been applied to forecasting within dynamical systems, pattern recognition, and medical image analysis, particularly functional neuroimages. While neural computing has largely been viewed as a black box approach, they have initiated research aimed at opening this black box, using hypertext, multimedia, and interactivity. Their key objective is to convert abstract models into intuitive knowledge through interactive visualization.
Proper citation: THOR Center for Neuroinformatics (RRID:SCR_001400) Copy
http://www.opencolleges.edu.au/informed/learning-strategies/
Interactive infographic of a brain exploring more than 100,000 chemical reactions, highlighted by areas and explanations of what that area is known to do.
Proper citation: Open Colleges Interactive Brain (RRID:SCR_001427) Copy
http://www.brain.northwestern.edu/index.html
The Cognitive Neurology and Alzheimer's Disease Center (CNADC) is a multidisciplinary organization dedicated to conducting research to discover how the brain coordinates mental functions such as memory, language, attention, and emotion; transferring the benefits of this research to patients with brain diseases that impair cognitive function; and training researchers and clinicians who want to work in this field. The CNADC's mission is to investigate the neurological basis of cognitive function, to elucidate causes of dementia, and to ensure that the patients and their families are the beneficiaries of resultant discoveries. * Clinical Services: Neurobehavior and Memory Health Clinical Services * Annual Grant Opportunities: Annual Core Pilot Project Funding Opportunities * Research Areas & Faculty: Alzheimer's Disease / Primary Progressive Aphasia / Frontal Dementia, Brain Endowment (Brains are permanently stored, and requests for tissue for research purposes are submitted to Dr. Bigio for review by the Northwestern Alzheimer's Disease Center); Cognitive Brain Mapping Group, Volunteer For A Study * Fellowships: Neuropathology Fellowship, Behavioral Neurology & Neuropsychiatry Fellowship * Training Programs: Mechanisms of Aging and Dementia (M.A.D.) Training Program; Training Program in the Neuroscience of Human Cognition
Proper citation: Northwestern University Cognitive Neurology and Alzheimers Disease Center (RRID:SCR_012747) Copy
https://www.nia.nih.gov/alzheimers
Portal for Alzheimer's disease that compiles, archives and disseminates information about current treatments, diagnostic tools and ongoing research for health professions, people with AD, their families and the public. The Center provides informational services and referrals for AD symptoms, diagnosis and treatment for patients; clinical trial information and literature searches for researchers; training materials and guidelines for caregivers; and Spanish language resources.
Proper citation: Alzheimer's Disease Education and Referral Center (RRID:SCR_012787) Copy
http://umcd.humanconnectomeproject.org
Web-based repository and analysis site for connectivity matrices that have been derived from neuroimaging data including different imaging modalities, subject groups, and studies. Users can analyze connectivity matrices that have been shared publicly and upload their own matrices to share or analyze privately.
Proper citation: USC Multimodal Connectivity Database (RRID:SCR_012809) Copy
http://www.zebrafinchatlas.org
Expression atlas of in situ hybridization images from large collection of genes expressed in brain of adult male zebra finches. Goal of ZEBrA project is to develop publicly available on-line digital atlas that documents expression of large collection of genes within brain of adult male zebra finches.
Proper citation: Zebra Finch Expression Brain Atlas (RRID:SCR_012988) Copy
https://itunes.apple.com/be/app/3d-brain/id331399332?mt=8
iPhone and iPad app that provides a good overview of the brain and its structures allowing you to rotate and zoom around 29 interactive structures with your touch screen. Discover how each brain region functions, what happens when it is injured, and how it is involved in mental illness. Each detailed structure comes with information on functions, disorders, brain damage, case studies, and links to modern research. Compatible with iPhone, iPod touch and iPad. Requires iOS 3.0 or later.
Proper citation: 3D Brain (RRID:SCR_013138) Copy
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