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http://crcns.org

Website for brain experimental data and other resources such as stimuli and analysis tools. Provides marketplace and discussion forum for sharing tools and data in neuroscience. Data repository and collaborative tool that supports integration of theoretical and experimental neuroscience through collaborative research projects. CRCNS offers funding for new class of proposals focused on data sharing and other resources.

Proper citation: CRCNS (RRID:SCR_005608) Copy   

•   Source: SciCrunch Registry

https://www.bminds.brain.riken.jp/

Web-accessible digital brain atlas of the common marmoset (Callithrix jacchus), prepared from histological sections of the marmoset brain using various staining techniques.

Proper citation: Digital Brain Atlas of the Common Marmoset (RRID:SCR_005069) Copy   

•   Source: SciCrunch Registry

http://penglab.janelia.org/proj/v3d/V3D/About_V3D.html

V3D is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions, is Open Source, supports a very simple and powerful plugin interface and thus can be extended & enhanced easily. V3D-Neuron is a powerful 3D neuron reconstruction, visualization, and editing software built on top of V3D. Both V3D and V3D-Neuron have recently been published in Nature Biotechnology (April, 2010), and Highlighted in Nature Methods (May, 2010), and Science News (April, 2010), etc. V3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. This makes V3D suitable for various bioimage informatics applications, and a nice platform to develop new 3D image analysis algorithms for high-throughput processing. In short, V3D streamlines the workflow of visualization-assisted analysis. In the latest V3D development, it can render 5D (spatial-temporal) data directly in 3D volume-rendering mode; it supports convenient and interactive local and global 3D views at different scales. It even has a Matlab file IO toolbox. A user can now write his/her own plugins to take advantage of the V3D platform very easily.

Proper citation: V3D (RRID:SCR_008646) Copy   

•   Source: SciCrunch Registry

http://www.nimh.nih.gov/labs-at-nimh/research-areas/research-support-services/hbcc/index.shtml

A collection of brain tissue from individuals suffering from schizophrenia, bipolar disorder, depression, anxiety disorders, and substance abuse, as well as healthy individuals. The research mission of the NIMH Brain Bank is to better understand the underlying biological mechanisms and pathways that contribute to schizophrenia and other neuropsychiatric disorders, as well as to study normal human brain development.

Proper citation: NIMH Brain Tissue Collection (RRID:SCR_008726) Copy   

•   Source: SciCrunch Registry

http://www.utsouthwestern.edu/education/medical-school/departments/neurology/programs/alzheimers-disease-center/brain-tissue-donation-program.html

Brain tissue donation program at the UT Southwestern Memory Clinic that aims to utilize these contributions for research on Alzheimer's. Diagnosis of Alzheimer's disease or other dementias are made through autopsy, the results of which are available to family members.

Proper citation: UT Southwestern ADC Brain Tissue Donation Program (RRID:SCR_008837) Copy   

•   Source: SciCrunch Registry

https://brainiak.org

Open source software package of Python modules for neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI) analysis. Used for analyzing neuroimaging data.

Proper citation: Brain Imaging Analysis Kit (RRID:SCR_014824) Copy   

•   Source: SciCrunch Registry

http://caprica.genetics.kcl.ac.uk/BRAINEAC/

Database for the UK Brain Expression Consortium (UKBEC) dataset that comprises of brains from individuals free of neurodegenerative disorders. The aim of Braineac is to release to the scientific community a valid instrument to investigate the genes and SNPs associated with neurological disorders.

Proper citation: Braineac (RRID:SCR_015888) Copy   

•   Source: SciCrunch Registry

http://www.uimcimes.es/contenidos/golink?p=1

Software toolbox for Statistical Parametric Mapping (SPM) to fit reference-region kinetic models (SRTM, SRTM2, Patlak Reference and Logan Reference Plot) are currently available in QModeling to dynamic PET studies. Used for the analysis of brain imaging data sequences.

Proper citation: QModeling (RRID:SCR_016358) Copy   

•   Source: SciCrunch Registry

http://www.geneatlas.org/gene/main.jsp

This website allows visitors to search for genes of interest based on their spatial expression patterns in the Postnatal Day 7 mouse brain. Geneatlas provides two searching tools: A graphical interface for customized spatial queries; A textual interface for querying annotated structures. Geneatlas is the product of a collaboration between researchers at Baylor College of Medicine, Rice University, and University of Houston.

Proper citation: Gene Atlas (RRID:SCR_008089) Copy   

•   Source: SciCrunch Registry

http://phm.utoronto.ca/~jeffh/surgical.htm

3D interactive atlas of two mouse brains, 129S1/SvImJ and C57Bl/6J. The aim of this resource is to enhance comparative morphometric analyses and stereotactic surgical procedures in mice. These representations of the murine brain and skull, in conjunction with the resource''s development of a new, more dynamic master coordinate system, provide improved accuracy with respect to targeting CNS structures during surgery compared with previous systems. The interactive three-dimensional nature of these atlases also provide users with stereotactic information necessary to perform accurate off-axis surgical procedures, as is commonly required for experiments such as in vivo micro-electroporation. In addition, three-dimensional analysis of the brain and skull shape in C57Bl, 129Sv, CD1, and additional murine strains, suggests that a stereotactic coordinate system based upon the lambda and rostral confluence of the sinuses at the sagittal midline, provides improved accuracy compared with the traditional lambdabregma landmark system. These findings demonstrate the utility of developing highly accurate and robust three-dimensional representations of the murine brain and skull, in which experimental outputs can be directly compared using a unified coordinate system.

Proper citation: 3D surgical atlases of the murine head (RRID:SCR_008039) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/ICBM/Downloads/Downloads_DTI-81.shtml

A stereotaxic probabilistic white matter atlas that fuses DTI-based white matter information with an anatomical template (ICBM-152). This atlas is based on probabilistic tensor maps obtained from 81 normal subjects acquired under an initiative of the International Consortium of Brain Mapping (ICBM). The subjects were normal right-handed adults ranging from 18 to 59 years of age. A hand-segmented white matter parcellation map was created from this averaged map. This map can be used for automated white matter parcellation. The precision of the affine-based image normalization and automated parcellation was measured for a group of normal subjects using manually defined anatomical landmarks. The raw diffusion-weighted images (DWIs) were first co-registered to one of the least diffusion-weighted images and corrected for subject motion with 6-mode rigid transformation with Automated Image Registgration (AIR). The average of all DWIs (aDWI) was calculated and used for a DTI-based anatomic image. For anatomical images to drive the normalization process, aDWIs were used. These images were normalized to the template (ICBM-152) using a 12-mode affine or 4th order polynomial non-linear transformation of AIR. The transformation matrix was then applied to the calculated diffusion tensor field. In the white matter parcellation map (WMPM), deep white matter regions were manually segmented into various anatomic structures based on fiber orientation information.

Proper citation: International Consortium of Brain Mapping DTI-81 Atlas (RRID:SCR_008066) Copy   

•   Source: SciCrunch Registry

http://vox.pharmacology.ucla.edu/home.html

Two-dimensional images of gene expression for 20,000 genes in a coronal slice of the mouse brain at the level of the striatum by using microarrays in combination with voxelation at a resolution of 1 cubic mm gene expression patterns in the brain obtained through voxelation. Voxelation employs high-throughput analysis of spatially registered voxels (cubes) to produce multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging systems.

Proper citation: Voxelation Map of Gene Expression in a Coronal Section of the Mouse Brain (RRID:SCR_008065) Copy   

•   Source: SciCrunch Registry

http://www.nesys.uio.no/Database/

This site contains the NeSys archive on structure and structure-function data about brain map transformations in the cerebellar system of the rat. This archive presents data not illustrated in the original publications, downloadable original data sets, interactive illustration sequences, including 3-D models. The repository is based on 5 original publications. The publications deal with: - organization of projections to the pontine nuclei from three cortical areas: primary and secondary somatosensory areas (SI and SII), and the primary motor cortex (MI) - organization of pontine neurons projecting to somatosensory representations in the posterior cerebellum The data are also included in the FACCS application, a relational database application with embedded analytical tools, available via the The Rodent Brain Workbench (www.rbwb.org). Sponsors: NeSys Research and Database development is supported by The Research Council of Norway, The European Community (grants QLRT-2000-02256 and QLG3-CT 1999-00763), The Norwegian Consortium for High Performance Computing, and The Jahre Foundation.

Proper citation: Database on Brain Map Transformations in Cerebellar Systems (RRID:SCR_008052) Copy   

•   Source: SciCrunch Registry

http://www.uky.edu/coa/adc/investigators-research-resources

An organization which includes a tissue bank, a database, study design consultation, clinical resources, and a community registry database. The UK-ADC shares data with the NIA national database (NACC), as well as with independent, qualified investigators both within and outside the UK-ADC. This resource's associated tissue bank is comprised of anonymized brain tissue, blood, and cerebrospinal fluid samples from patients in the clinic, as well as frozen post-mortem brain tissue samples. This organization also shares research resources with the National Alzheimer's Coordinating Center (NACC), NACC collaborative initiatives, the Alzheimer's Disease Neuroimaging Initiative (ADNI), other Alzheimer Disease Centers (ADCs), and any qualified investigators from either the University of Kentucky or the general scientific community.

Proper citation: University of Kentucky's Alzheimer's Disease Center (RRID:SCR_008766) Copy   

•   Source: SciCrunch Registry

http://experimentalman.com/blog/

Blog about how leading-edge bio-science and technology is impacting individuals and society. This blog is an outgrowth of David Ewing Duncan''s new book, Experimental Man: What one mans body reveals about youy future, your health, and our toxic world. In the book he reports taking over 250 tests in the realms of genes, environment, brain and body and explore what these tests can tell us about one persons health, past, present, and future.

Proper citation: Experimental Man Blog (RRID:SCR_008378) Copy   

•   Source: SciCrunch Registry

http://brainmap.wisc.edu/monkey.html

NO LONGER AVAILABLE. Documented on September 17, 2019. A set of multi-subject atlas templates to facilitate functional and structural imaging studies of the rhesus macaque. These atlases enable alignment of individual scans to improve localization and statistical power of the results, and allow comparison of results between studies and institutions. This population-average MRI-based atlas collection can be used with common brain mapping packages such as SPM or FSL.

Proper citation: Rhesus Macaque Atlases for Functional and Structural Imaging Studies (RRID:SCR_008650) Copy   

•   Source: SciCrunch Registry

https://bbgre.brc.iop.kcl.ac.uk

A database and associated tools for investigating the genetic basis of neurodisability. It combines phenotype information from patients with neurodevelopmental and behavioral problems with clinical genetic data, and displays this information on the human genome map. Basic access to genetic information (deletions, duplications) relating to participants with neurodevelopmental disorders is provided without an account; access to the full dataset requires an account. The genetic information that is available to view comprises potentially pathogenic copy number variation across the genome, detected by array comparative genome hybridization (aCGH) using a customized 44K oligonucleotide array.

Proper citation: Brain and Body Genetic Resource Exchange (RRID:SCR_008959) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/dublinbrainbank/home

A biomaterial supply resource that collects and distributes human brain tissue samples. The Dublin Brain Bank is a collaboration between the Neuropathology Department of Beaumont Hospital and the Royal College of Surgeons in Ireland. Investigators interested in applying for tissue samples need to complete tissue requisition forms and provide a record of the research groups'' ethical approval.

Proper citation: Dublin Brain Bank (RRID:SCR_010597) Copy   

•   Source: SciCrunch Registry

http://ccb.loni.usc.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2022. Center focused on the development of computational biological atlases of different populations, subjects, modalities, and spatio-temporal scales with 3 types of resources: (1) Stand-alone computational software tools (image and volume processing, analysis, visualization, graphical workflow environments). (2) Infrastructure Resources (Databases, computational Grid, services). (3) Web-services (web-accessible resources for processing, validation and exploration of multimodal/multichannel data including clinical data, imaging data, genetics data and phenotypic data). The CCB develops novel mathematical, computational, and engineering approaches to map biological form and function in health and disease. CCB computational tools integrate neuroimaging, genetic, clinical, and other relevant data to enable the detailed exploration of distinct spatial and temporal biological characteristics. Generalizable mathematical approaches are developed and deployed using Grid computing to create practical biological atlases that describe spatiotemporal change in biological systems. The efforts of CCB make possible discovery-oriented science and the accumulation of new biological knowledge. The Center has been divided into cores organized as follows: - Core 1 is focused on mathematical and computational research. Core 2 is involved in the development of tools to be used by Core 3. Core 3 is composed of the driving biological projects; Mapping Genomic Function, Mapping Biological Structure, and Mapping Brain Phenotype. - Cores 4 - 7 provide the infrastructure for joint structure within the Center as well as the development of new approaches and procedures to augment the research and development of Cores 1-3. These cores are: (4)Infrastructure and Resources, (5) Education and Training, (6) Dissemination, and (7) Administration and Management. The main focus of the CCB is on the brain, and specifically on neuroimaging. This area has a long tradition of sophisticated mathematical and computational techniques. Nevertheless, new developments in related areas of mathematics and computational science have emerged in recent years, some from related application areas such as Computer Graphics, Computer Vision, and Image Processing, as well as from Computational Mathematics and the Computational Sciences. We are confident that many of these ideas can be applied beneficially to neuroimaging.

Proper citation: Center for Computational Biology at UCLA (RRID:SCR_000334) Copy   

•   Source: SciCrunch Registry

http://www.ibro.info/

A central organization that develops, supports, co-ordinates and promotes scientific research in all fields concerning the brain; promotes international collaboration and interchange of scientific information on brain research throughout the world; and provides for and to assist in education and the dissemination of information relating to brain research by all available means. IBRO represents the interests of more than 50,000 neuroscientists around the globe. Over the years, IBRO has set up a number of program to stimulate international contacts in brain research. Symposia and workshops are sponsored on the basis of competitive applications. Under its Publications Programme, IBRO publishes the journal Neuroscience and the annual newsletter IBRO News. IBRO offers post-doctoral fellowships and travel grants to students from less-developed countries. It has run a Neuroscience Schools Programme, organized by the committees of IBROs six Regions, aimed at forming interactive networks among students and teachers during training courses in Africa, Asia, Central and Eastern Europe, Latin America, Western Europe, and the US and Canada. With just three schools in 1999, expansion has been rapid - in 2007 there were 22 schools around the world.

Proper citation: International Brain Research Organization (RRID:SCR_007406) Copy   

•   Source: SciCrunch Registry