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http://conp.ca/

Web interface that facilitates open science for neuroscience community by simplifying global access to and sharing of datasets and tools. Portal internalizes typical data cycle of research project, beginning with data acquisition, followed by data processing with published tools, and ultimately publication of results with link to original dataset. Platform to form interactive network of collaborations in brain research, interdisciplinary student training, international partnerships, clinical translation and open publishing. Provides unified interface to Canadian neuroscience research community. Open neuroscience research with sharing of both data and methods, to create large-scale databases, development of standards for sharing, facilitation of advanced analytic strategies, open dissemination to global community of neuroscience data and methods, and establishment of training programs for next generation of computational neuroscience researchers.

Proper citation: Canadian Open Neuroscience Platform (RRID:SCR_016433) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/uf2c/

Software tool to standardize and facilitate connectivity studies through a graphical user interface and validated preset parameters.

Proper citation: User Friendly Functional Connectivity - UF²C (RRID:SCR_016550) Copy   

•   Source: SciCrunch Registry

https://doi.org/10.1016/j.neuroimage.2018.07.046

Software package for simulation framework and codes for estimating nonparametric Granger causality. Used to study brain functions.

Proper citation: nonparametricGGC_toolbox (RRID:SCR_016539) Copy   

•   Source: SciCrunch Registry

https://bican.mccarrolllab.org/app/bican?_inputs_&geneList=%22XIST%20PDE10A%20%20PENK%20PDYN%22&navbarPage=%22panelGeneExpr%22&plotExpressionButton=0&exprPlotUseCommonYScale=true&cellTypeSelector=%5B%22MSN%22%2C%22MSN_D1%22%2C%22MSN_D2%22%2C%22MSN_D1_matrix%22%2C%22MSN_D2_matrix%22%2C%22MSN_D1_striosome%22%2C%22MSN_D2_striosome%22%5D&exprPlotRegionSelector=%22Pu%22&GeneExprPlot_hover=null

Project provides data currently generated with support from the NIH Brain Initiative Cell Atlas Network (BICAN). Broad Institute collaboration supported by the NIH BRAIN Initiative, to create comprehensive atlas of cellular variation in the healthy human brain. It maps data from millions of cells across diverse individuals to understand how brain biology differs, helping researchers distinguish healthy variation from disease states.

Proper citation: Human Brain Variation Project (RRID:SCR_028065) Copy   

•   Source: SciCrunch Registry

https://github.com/SCANDAN-Team/SCANDAN-DICOM-labelling

Software tool for rules for DICOM tag based labelling. Regular expression used during the SCANDAN project to label MRI scans based on DICOM tag.

Proper citation: SCANDAN-DICOM-labelling (RRID:SCR_028365) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/verbena

Software tool for quantification of perfusion and other haemodynamic parameters from Dynamic Susceptibility Contrast perfusion MRI of the brain.

Proper citation: VERBENA (RRID:SCR_024919) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT

Sotware automated robust and accurate tool for linear (affine) intra- and inter-modal brain image registration.

Proper citation: FMRIB's Linear Image Registration Tool (RRID:SCR_024922) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/XTRACT

Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain.

Proper citation: XTRACT (RRID:SCR_024933) Copy   

•   Source: SciCrunch Registry

https://marmotgraph.org

Knowledge graph system developed for managing and organizing rich metadata objects, initially for the Human Brain Project (HBP) and now extended to be a more generic, domain-agnostic solution. It is associated with CSCS (Swiss National Supercomputing Centre) and aims to provide a comprehensive toolset and API for working with knowledge graphs.

Proper citation: MarmotGraph (RRID:SCR_027452) Copy   

•   Source: SciCrunch Registry

https://imaging.uci.edu/fibre/

Facility for Imaging and Brain Research houses 3T Siemens Prisma scanner, mock scanner, and data analysis facilities. Research dedicated MRI scanning facility designed to suit wide range of basic and translational research programs by researchers across the UCI campus and beyond.

Proper citation: University of California at Irvine FIBRE Core Facility (RRID:SCR_027777) Copy   

•   Source: SciCrunch Registry

https://www.uni.lu/lcsb-en/

Research institute in Esch-sur-Alzette, Luxembourg to study brain and its diseases. Collaboration between biologists, medical and computer scientists, physicists, engineers as well as mathematicians offers new insights into complex biological mechanisms and disease processes, with the aim of developing new tools for diagnostics, prevention, and therapy. LCSB has established strategic partnerships with scientific partners worldwide and with all major biomedical research units in Luxembourg. Carries out collaborative projects with hospitals and research-oriented companies, accelerating translation of fundamental research results into clinical applications.

Proper citation: Luxembourg Centre for Systems Biomedicine (RRID:SCR_026168) Copy   

•   Source: SciCrunch Registry

http://clarityresourcecenter.org/

Protocols and other training materials related to the CLARITY protocol, a technique for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable.

Proper citation: Clarity resources (RRID:SCR_001387) Copy   

•   Source: SciCrunch Registry

http://kesm.cs.tamu.edu

A web-based, light-weight 3D volume viewer that serves large volumes (typically the whole brain) of high-resolution mouse brain images (~1.5 TB per brain, ~1 um resolution) from the Knife-Edge Scanning Microscope (KESM), invented by Bruce H. McCormick. Currently, KESMBA serves the following data sets: * Mouse: Whole-brain-scale Golgi (acquired 2008 spring): neuronal morphology: Choe et al. (2009) * Mouse: Whole-brain India Ink (acquired 2008 spring): vascular network: Choe et al. (2009); Mayerich et al. (2011); * Mouse: Whole-brain Golgi (acquired 2011 summer): neuronal morphology: Choe et al. (2011); Chung et al. (2011); * Mouse: Whole-brain Nissl (acquired 2009-2010 winter): somata (Choe et al. 2010) (Coming soon) They will ship you the full data set on a hard drive if you provide them with the hard drive and shipping cost.

Proper citation: KESM brain atlas (RRID:SCR_001559) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry