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http://www.parkinsons.org.uk/content/parkinsons-uk-brain-bank

A brain bank of the United Kingdom which collects human brains for Parkinsons disease research. The collection is comprised of brain, spinal cord and a sample of cerebrospinal fluid from people with and without Parkinson's after death. Researchers can fill out a brain tissue request form to order samples from the bank.

Proper citation: Parkinsons UK Brain Bank (RRID:SCR_007030) Copy   

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http://med.stanford.edu/narcolepsy.html

The Stanford Center for Narcolepsy was established in the 1980s as part of the Department of Psychiatry and Behavioral Sciences. Today, it is the world leader in narcolepsy research with more than 100 articles on narcolepsy to its name. The Stanford Center for Narcolepsy was the first to report that narcolepsy-cataplexy is caused by hypocretin (orexin) abnormalities in both animal models and humans. Under the direction of Drs. Emmanuel Mignot and Seiji Nishino, the Stanford Center for Narcolepsy today treats several hundred patients with the disorder each year, many of whom participate in various research protocols. Other research protocols are conducted in animal models of narcolespy. We are always looking for volunteers in our narcolepsy research studies. We are presently recruiting narcoleptic patients for genetic studies, drug clinical trials, hypocretin measurement studies in the CSF and functional MRI studies. Monetary gifts to the Center for Narcolepsy are welcome. If you wish to make the ultimate gift, please consider participating in our Brain Donation Program. To advance our understanding of the cause, course, and treatment of narcolepsy, in 2001 Stanford University started a program to obtain human brain tissue for use in narcolepsy research. Donated brains provide an invaluable resource and we have already used previously donated brains to demonstrate that narcolepsy is caused by a lack of a very specific type of cell in the brain, the hypocretin (orexin) neuron. While the brain donations do not directly help the donor, they provide an invaluable resource and a gift to others. The real answers as to what causes or occurrs in the brain when one has narcolepsy will only be definitively understood through the study of brain tissue. Through these precious donations, narcolepsy may eventually be prevented or reversible. We currently are seeking brains from people with narcolepsy (with cataplexy and without), idiopathic hypersomnia and controls or people without a diagnosed sleep disorder of excessive sleepiness. Control brains are quite important to research, as findings must always be compared to tissue of a non-affected person. Friends and loved ones of people who suffer with narcoleps may wish to donate to our program to help fill this very important need. Refer to the Movies tab for movies of Narcolepsy / Cataplexy.

Proper citation: Stanford Center for Narcolepsy (RRID:SCR_007021) Copy   

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http://openccdb-dev-web.crbs.ucsd.edu/software/index.shtm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Software to support registering brain images to the stereotaxic coordinate system of a brain atlas. It was specifically designed to work with the large scale brain mosaics. When data are uploaded to the CCDB, users may launch Jibber, a custom tool for defining correspondence points between the image and an atlas overlay. Jibber automatically downsamples the data, so that users can define the warping and scaling parameters with good interactive performance on the smaller copy. Once the warping transformation is computed, the original image and the transformation matrix are sent to a cluster of computers for warping. The current version of Jetsam is running on a 30 Sun V20 nodes and the execution time is roughly about 20 minutes per GB. The warped images are then automatically registered with an image web server that supports spatial queries based on stereotaxic coordinates. These servers generate optimized downsampled images, which can be displayed by standard online clients regardless of the size of the original image.

Proper citation: Image Workflow (RRID:SCR_007017) Copy   

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http://www.nervenet.org/main/dictionary.html

A mouse-related portal of genomic databases and tables of mouse brain data. Most files are intended for you to download and use on your own personal computer. Most files are available in generic text format or as FileMaker Pro databases. The server provides data extracted and compiled from: The 2000-2001 Mouse Chromosome Committee Reports, Release 15 of the MIT microsatellite map (Oct 1997), The recombinant inbred strain database of R.W. Elliott (1997) and R. W. Williams (2001), and the Map Manager and text format chromosome maps (Apr 2001). * LXS genotype (Excel file): Updated, revised positions for 330 markers genotyped using a panel of 77 LXS strain. * MIT SNP DATABASE ONLINE: Search and sort the MIT Single Nucleotide Polymorphism (SNP) database ONLINE. These data from the MIT-Whitehead SNP release of December 1999. * INTEGRATED MIT-ROCHE SNP DATABASE in EXCEL and TEXT FORMATS (1-3 MB): Original MIT SNPs merged with the new Roche SNPs. The Excel file has been formatted to illustrate SNP haplotypes and genetic contrasts. Both files are intended for statistical analyses of SNPs and can be used to test a method outlined in a paper by Andrew Grupe, Gary Peltz, and colleagues (Science 291: 1915-1918, 2001). The Excel file includes many useful equations and formatting that will help in navigating through this large database and in testing the in silico mapping method. * Use of inbred strains for the study of individual differences in pain related phenotypes in the mouse: Elissa J. Chesler''s 2002 dissertation, discussing issues relevant to the integration of genomic and phenomic data from standard inbred strains including genetic interactions with laboratory environmental conditions and the use of various in silico inbred strain haplotype based mapping algorithms for QTL analysis. * SNP QTL MAPPER in EXCEL format (572 KB, updated January 2002 by Elissa Chesler): This Excel workbook implements the Grupe et al. mapping method and outputs correlation plots. The main spreadsheet allows you to enter your own strain data and compares them to haplotypes. Be very cautious and skeptical when using this spreadsheet and the technique. Read all of the caveates. This excel version of the method was developed by Elissa Chesler. This updated version (Jan 2002) handles missing data. * MIT SNP Database (tab-delimited text format): This file is suitable for manipulation in statistics and spreadsheet programs (752 KB, Updated June 27, 2001). Data have been formatted in a way that allows rapid acquisition of the new data from the Roche Bioscience SNP database. * MIT SNP Database (FileMaker 5 Version): This is a reformatted version of the MIT Single Nucleotide Polymorphism (SNP) database in FileMaker 5 format. You will need a copy of this application to open the file (Mac and Windows; 992 KB. Updated July 13, 2001 by RW). * Gene Mapping and Map Manager Data Sets: Genetic maps of mouse chromosomes. Now includes a 10th generation advanced intercross consisting of 500 animals genetoyped at 340 markers. Lots of older files on recombinant inbred strains. * The Portable Dictionary of the Mouse Genome, 21,039 loci, 17,912,832 bytes. Includes all 1997-98 Chromosome Committee Reports and MIT Release 15. * FullDict.FMP.sit: The Portable Dictionary of the Mouse Genome. This large FileMaker Pro 3.0/4.0 database has been compressed with StuffIt. The Dictionary of the Mouse Genome contains data from the 1997-98 chromosome committee reports and MIT Whitehead SSLP databases (Release 15). The Dictionary contains information for 21,039 loci. File size = 4846 KB. Updated March 19, 1998. * MIT Microsatellite Database ONLINE: A database of MIT microsatellite loci in the mouse. Use this FileMaker Pro database with OurPrimersDB. MITDB is a subset of the Portable Dictionary of the Mouse Genome. ONLINE. Updated July 12, 2001. * MIT Microsatellite Database: A database of MIT microsatellite loci in the mouse. Use this FileMaker Pro database with OurPrimersDB. MITDB is a subset of the Portable Dictionary of the Mouse Genome. File size = 3.0 MB. Updated March 19, 1998. * OurPrimersDB: A small database of primers. Download this database if you are using numerous MIT primers to map genes in mice. This database should be used in combination with the MITDB as one part of a relational database. File size = 149 KB. Updated March 19, 1998. * Empty copy (clone) of the Portable Dictionary in FileMaker Pro 3.0 format. Download this file and import individual chromosome text files from the table into the database. File size = 231 KB. Updated March 19, 1998. * Chromosome Text Files from the Dictionary: The table lists data on gene loci for individual chromosomes.

Proper citation: Mouse Genome Databases (RRID:SCR_007147) Copy   

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http://www.bmu.psychiatry.cam.ac.uk/software/

Suite of programs developed for fMRI analysis in a Virtual Pipeline Laboratory facilitates combining program modules from different software packages into processing pipelines to create analysis solutions which are not possible with a single software package alone. Current pipelines include fMRI analysis, statistical testing based on randomization methods and fractal spectral analysis. Pipelines are continually being added. The software is mostly written in C. This fMRI analysis package supports batch processing and comprises the following general functions at the first level of individual image analysis: movement correction (interpolation and regression), time series modeling, data resampling in the wavelet domain, hypothesis testing at voxel and cluster levels. Additionally, there is code for second level analysis - group and factorial or ANOVA mapping - after co-registration of voxel statistic maps from individual images in a standard space. The main point of difference from other fMRI analysis packages is the emphasis throughout on the use of data resampling (permutation or randomization) as a basis for inference on individual, group and factorial test statistics at voxel and cluster levels of resolution.

Proper citation: Cambridge Brain Activation (RRID:SCR_007109) Copy   

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https://www.nitrc.org/projects/fmridatacenter/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2013 Public curated repository of peer reviewed fMRI studies and their underlying data. This Web-accessible database has data mining capabilities and the means to deliver requested data to the user (via Web, CD, or digital tape). Datasets available: 107 NOTE: The fMRIDC is down temporarily while it moves to a new home at UCLA. Check back again in late Jan 2013! The goal of the Center is to help speed the progress and the understanding of cognitive processes and the neural substrates that underlie them by: * Providing a publicly accessible repository of peer-reviewed fMRI studies. * Providing all data necessary to interpret, analyze, and replicate these fMRI studies. * Provide training for both the academic and professional communities. The Center will accept data from those researchers who are publishing fMRI imaging articles in peer-reviewed journals. The goal is to serve the entire fMRI community.

Proper citation: fMRI Data Center (RRID:SCR_007278) Copy   

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http://www.ikaros-project.org/

Ikaros is an open infrastructure for system level modeling of the brain including databases of experimental data, computational models and functional brain data. The system makes heavy use of the emerging standards for Internet based information and makes all information accessible through an open web-based interface. In addition, Ikaros can be used as a control architecture for robots which in the extension will lead to the development of a brain inspired robot architecture. The main components of the Ikaros systems are: a platform independent simulation kernel; a set of computational brain models; a set of I/O modules for interfacing with data files and peripheral such as robots or video cameras; tools for building systems of interconnected models; a plug-in architecture that allows new models to be easily added to the system; and a database with data from learning experiments that can be used for validation of the computational models.

Proper citation: Ikaros Project (RRID:SCR_007391) Copy   

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http://www.nia.nih.gov/research/dab/aged-rodent-tissue-bank-handbook/tissue-arrays

Offer high-throughput analysis of tissue histology and protein expression for the biogerontology research community. Each array is a 4 micron section that includes tissue cores from multiple tissues at multiple ages on one slide. The arrays are made from ethanol-fixed tissue and can be used for all techniques for which conventional tissue sections can be used. Ages are chosen to span the life from young adult to very old age. (available ages: 4, 12, 18, 24 and 28 months of age) Images of H&E stained punches are available for Liver, Cardiac Muscle, and Brain. The NIA aged rodent tissue arrays were developed with assistance from the National Cancer Institute (NCI) Tissue Array Research Program (TARP), led by Dr. Stephen Hewitt, Director. NCI TARP contains more information on tissue array construction, protocols for using arrays, and references. Preparation and Product Description Tissue arrays are prepared in parallel from different sets of animals so that experiments can be conducted in duplicate, with each array using unique animals with a unique product number. The product descriptions page describes each array, including: * Strain * Gender * Ages * Tissues * Animal Identification Numbers

Proper citation: Aged Rodent Tissue Arrays (RRID:SCR_007332) Copy   

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https://ida.loni.usc.edu/login.jsp

Archive used for archiving, searching, sharing, tracking and disseminating neuroimaging and related clinical data. IDA is utilized for dozens of neuroimaging research projects across North America and Europe and accommodates MRI, PET, MRA, DTI and other imaging modalities.

Proper citation: LONI Image and Data Archive (RRID:SCR_007283) Copy   

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http://www.neurolens.org/NeuroLens/

An integrated environment for the analysis and visualization of functional neuroimages. It is intended to provide extremely fast and flexible image processing, via an intuitive user interface that encourages experimentation with analysis parameters and detailed inspection of both raw image data and processing results. All processing operations in NeuroLens are built around a Plugin architecture, making it easy to extend its functionality. NeuroLens runs on Apple computers based on the G4, G5, or Intel chipsets and running MacOSX 10.4 (Tiger) or later. It is available free for academic and non-profit research use. * Operating System: MacOS * Programming Language: Objective C * Supported Data Format: AFNI BRIK, ANALYZE, COR, DICOM, MGH/MGZ, MINC, Other Format

Proper citation: NeuroLens (RRID:SCR_007372) Copy   

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http://human.brain-map.org/static/brainexplorer

Multi modal atlas of human brain that integrates anatomic and genomic information, coupled with suite of visualization and mining tools to create open public resource for brain researchers and other scientists. Data include magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), histology and gene expression data derived from both microarray and in situ hybridization (ISH) approaches. Brain Explorer 2 is desktop software application for viewing human brain anatomy and gene expression data in 3D.

Proper citation: Allen Human Brain Atlas (RRID:SCR_007416) Copy   

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https://med.uth.edu/nrc/

The Neuroscience Research Center (NRC) is a university-wide center where diverse and multidisciplinary research is conducted to further the understanding of neural and behavioral disorders. Whether conducting cellular research in laboratories or clinical trials in patient care settings, the work of NRC researchers may someday contribute to preventing and treating such devastating disorders as: * Dementias resulting from Alzheimer''s disease and stroke * Mental retardation and other learning disabilities * Mental illnesses, including schizophrenia and manic-depressive illness * Alcoholism and other substance abuse problems * Inability to process knowledge due to factors such as aging and head trauma * Disabilities due to disorders of the developing nervous system More than 280 faculty hold NRC appointments, and are on the faculties of the Medical School, School of Public Health, School of Nursing, Dental Branch, and School of Biomedical Informatics. Departments with significant NRC research activities within the Medical School include Neurobiology and Anatomy; Neurology; Neurosurgery; Ophthalmology and Visual Science; Psychiatry and Behavioral Sciences and Radiology. NRC activities are guided by an executive committee appointed by the President of the Health Science Center. The Neuroscience Research Center (NRC) is affiliated with educational opportunities at the graduate and postdoctoral levels.

Proper citation: UTHealth at Houston Neuroscience Research Center (RRID:SCR_007486) Copy   

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http://brancusi1.usc.edu/thesaurus/list/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19,2022. The BAMS Thesaurus is a part of the larger BAMS The Foundational Model of Connectivity (FMC). The principle of constructing the resource are: 1. Systematic attempts to produce internally consistent classifications and taxonomies require theoretical frameworks for deciding between alternatives. 2. Alternate classification and taxonomy schemes are always possible and must be accommodated. 3. The FMC is based on evidence, not authority. All components are justified by reference to the best observational or experimental evidence from the literature, combined with reference to priority when possible, not by undocumented statements from textbooks, the Web, or elsewhere. 4. The FMC is based on evolving evidence and concepts, revisions are based on enforced rules, and versioning is systematic and historical. The first version of FMC and the foundation of this online version was published in Swanson & Bota (2010). Please cite this reference whenever any part of the FMC is used in any way. This online version of FMC has the following main parts: 1. Thesaurus, which includes an alphabetical list of all concepts and terms used in FMC to date. The preferred terms are in bold. Clicking on each term of the Thesaurus will retrieve its definition, reference, list of synonyms, and a comment form that can be used by registered users. 2. References, which includes an alphabetical list of the literature used to construct FMC. Listed references are associated with the definitions included in the Thesaurus, and PubMed links. 3. Search form that can be used to search for terms defined in FMC, included in their definitions, their abbreviations, and references (search by authors). We strongly recommend to read FMC rules and notations before starting to use the online version.

Proper citation: BAMS Thesaurus (RRID:SCR_008003) Copy   

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http://www.brainvoyager.de/BV2000OnlineHelp/BrainVoyagerWebHelp/Talairach_brain_atlas.htm

The Talairach brain atlas visualized via BrainVoyager (Commercial software) can be used to visualize Brodmann areas as they were defined for the Talairach brain (Talairach & Tournaux, 1988) and to compare regions of subjects with respect to the Brodmann areas. The demarcated areas are based on the Talairach demon, which is a digitized version of the Talairach atlas and which has been transferred into BrainVoyager VOI files by Matthias Ruf, Mannheim. Using the Brodman.voi file you may ask questions like the following: What is the signal time course of subject N in experiment A within Brodmann area X ?. Note, however, that the defined areal boundaries should be used only as a rough guideline for determining the location of activated regions: There is substantial variation of histologically defined areas between subjects. Since cytoarchitectonically defined Brodmann areas are not available in vivo, we advise to use the provided information with care. The TalairachBrain.vmr file is located in the same folder as your BrainVoyager executable file. It can be loaded as any VMR project by using the Open... item in the File menu (or the Open icon). The TalairachBrain.vmr file is also loaded automatically when using the glass brain visualization tool.

Proper citation: BrainVoyager: Talairach Brain Atlas (RRID:SCR_008800) Copy   

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http://www.cumc.columbia.edu/dept/taub/index.html

An institute which conducts research of Alzheimer's, Parkinson's and other age-related brain diseases. This organization also provides clinical evaluations to patients with memory problems, Alzheimer's disease or other types of dementia. Furthermore, the institute leads multi-center clinical trials for the treatment and prevention of Alzheimer's, Parkinson's and other age-related brain diseases. There is a brain donation program for enrolled/examined patients. The Education Core of the Taub Institute sponsors community events and Continuing Medical Education programs, as well as the distribution of periodic newsletters and brochures highlighting research developments and other Alzheimer's topics.

Proper citation: Taub Institute for Research on Alzheimers Disease and the Aging Brain (RRID:SCR_008802) Copy   

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http://madrc.mgh.harvard.edu/

An Alzheimer's disease research center which supports new research and enhances ongoing research by providing core support to bringing together behavioral, biomedical, and clinical scientists. The Center conducts multidisciplinary research, trains scientists, and spreads information about Alzheimer's disease and related disorders to the general public. The principal goal of the Massachusetts ADRC is to support research in aging, Alzheimer's Disease and other related disorders. Researchers work with national and international multi-disciplinary teams to understand: normal aging, the transition from normal aging to mild forms of memory problems, and the later stages of dementia. The Massachusetts ADRC has an active brain donation program at the Massachusetts General Hospital (MGH) for patients as well as subjects enrolled in research studies.

Proper citation: Massachusetts Alzheimer's Disease Research Center (RRID:SCR_008764) Copy   

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https://www.radc.rush.edu/res/ext/home.htm

An Alzheimer's disease center which researches the cause, treatment and prevention of Alzheimer's disease with a focus on four main areas of research: risk factors for Alzheimer's and related disorders, the neurological basis of the disease, diagnosis, and treatment. Data includes a number of computed variables that are available for ROS, MAP and MARS cohorts. These variables are under categories such as affect and personality, chronic medical conditions, and clinical diagnosis. Specimens include ante-mortem and post-mortem samples obtained from subjects evaluated by ROS, MAP and clinical study cores. Specimen categories include: Brain tissue (Fixed and frozen), Spinal cord, Muscles (Post-mortem), and Nerve (Post-mortem), among other types of specimens. Data sharing policies and procedures apply to obtaining ante-mortem and post-mortem specimens from participants evaluated by the selected cohorts of the RADC.

Proper citation: Rush Alzheimer's Disease Center (RRID:SCR_008763) Copy   

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http://www.ttuhsc.edu/centers/aging/giabrainbank.aspx

The Brain Bank was developed with two service-minded objectives: provide a free brain autopsy to confirm clinical diagnosis of dementia, and collect, bank and provide brain tissue to qualified scientific researchers studying diseases related to dementia. By working together, patients and researchers can help us understand the origins of neurodegenerative disease and eventually improve the treatment and care of dementia. The clinical diagnosis of Alzheimer's disease can only be confirmed by brain autopsy, or the examination of brain tissue after death. This examination will determine a patients's precise type of dementia. To confirm the diagnosis of Alzheimer's, for example, the brain tissue is examined for amyloid plaques and neurofibrillary tangles by a neuropathologist. The presence of these plaques and tangles will verify the clinical diagnosis of Alzheimer's disease. While it is important to us to enroll patients with dementia, it is equally important to enroll people with no dementia. These subjects are termed as controls and the brain tissue from controls will enable researchers to make comparisons to brain tissue from dementia patients. We are seeking donations from individuals who have had an age-related neurodegenerative disease like Alzheimer's, Parkinson's, Lewy Body or other related dementia.

Proper citation: GIA Brain Bank Program (RRID:SCR_008877) Copy   

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http://adc.med.nyu.edu/

The NYU Alzheimer's Disease Center is part of the Department of Psychiatry at New York University School of Medicine. The center's goals are to advance current knowledge and understanding of brain aging and Alzheimer's disease, to expand the numbers of scientists working in the field of aging and Alzheimer's research, to work toward better treatment options and care for patients, and to apply and share its findings with healthcare providers, researchers, and the general public. The ADC's programs and services extend to other research facilities and to healthcare professionals through the use of its core facilities. The NYU ADC is made up of seven core facilities: Administrative Core, Clinical Core, Neuropathology Core, Education Core, Data Management and Biostatistics Core, Neuroimaging Core, and Psychosocial Core.

Proper citation: NYU Alzheimer's Disease Center (RRID:SCR_008754) Copy   

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http://www.ohsu.edu/xd/research/centers-institutes/neurology/alzheimers/research/data-tissue/neuro-imaging.cfm

NeuroImaging laboratory focused on detecting early brain changes associated with cognitive decline and dementia that manages the neuroimaging component of all studies at the Layton Aging and Alzheimer's Center including acquisition and archival services, as well as volumetric analysis of anonymized MRI scans. Assistance with resulting data is also available, including statistical analysis, and preparation of materials for presentation and publication. The Layton Center also manages a library of thousands of digitized MRI scans, including what is believed to be the largest collection of longitudinal MRI scans of cognitively intact elderly subjects. The OADC Neuroimaging Lab conducts MRI studies on both 3 and 7T MRI systems using advanced sequences, employing a multimodal approach to brain imaging research.

Proper citation: Layton Center NeuroImaging Laboratory (RRID:SCR_008823) Copy   

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