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http://nif.nimh.nih.gov/

Neurophysiology imaging core facility that provides anatomical and functional MRI scanning for researchers in the National Institute of Mental Health (NIMH), the National Eye Institute (NEI), and the National Institute for Neurological Disorders and Stroke (NINDS). The shared intramural resource centers on a cutting-edge 4.7T vertical bore scanner dedicated to imaging of nonhuman primates.

Proper citation: Neurophysiology Imaging Facility (RRID:SCR_004080) Copy   

•   Source: SciCrunch Registry

http://www.mri-resource.kennedykrieger.org/

Biomedical technology research center that provides expertise for the design of quantitative magnetic resonance imaging (MRI) and spectroscopy (MRS) data acquisition and processing technologies that facilitate the biomedical research of a large community of clinicians and neuroscientists in Maryland and throughout the USA. These methods allow noninvasive assessment of changes in brain anatomy as well as in tissue metabolite levels, physiology, and brain functioning while the brain is changing size during early development and during neurodegeneration, i.e. the changing brain throughout the life span. The Kirby Center has 3 Tesla and 7 Tesla state of the art scanners equipped with parallel imaging (8, 16, and 32-channel receive coils) and multi-transmit capabilities. CIS has an IBM supercomputer that is part of a national supercomputing infrastructure. Resources fall into the following categories: * MRI facilities, image acquisition, and processing * Computing facilities and image analysis * Novel statistical methods for functional brain imaging * Translating laboratory discoveries to patient treatment

Proper citation: National Resource for Quantitative Functional MRI (RRID:SCR_006716) Copy   

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https://scicrunch.org/scicrunch/data/source/nlx_154697-8/search?q=*

A data set of connectivity statements from BAMS, CoCoMac, BrainMaps, Connectome Wiki, the Hippocampal-Parahippocampal Table of Temporal-Lobe.com, and Avian Brain Circuitry Database. The data set lists which brain sites connectivity is to and from, the organism connectivity is mapped in, and journal references.

Proper citation: Integrated Nervous System Connectivity (RRID:SCR_006391) Copy   

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http://www.braindonors.org

An Australian brain bank which aims to collect, store, characterize and provide tissue to national and international researchers studying disorders of the brain such as alcohol-related brain damage and mental illness, like schizophrenia. The program encourages those who are medically healthy to donate.

Proper citation: Using our Brains Tissue Donor Program (RRID:SCR_000705) Copy   

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https://neuropsychological-assessment-tests.com/sanzen-tower-london-test

CATs Tower of London test is a free, computer-based software test originally developed by Shallice (1982) to investigate problem solving in subjects with damage to the frontal lobes. The CATs Tower of London Test comes with one preprogrammed test along with extensive normative data for that test. You can also create a test using your design. Briefly, subjects are required to move colored beads from a window on the left (working area) until they achieve the arrangement in the window on the right (goal position). Subjects are instructed to try to achieve the goal arrangement in as few moves as possible. The software contains a Tower of London test. The test contains trials with 3 beads and 3 pegs, 4 beads and 4 pegs, and 5 beads and 5 pegs. You can use the Setup screen to create a test using your design. A test can contain 3, 4, and 5 bead problems with varying number of moves required for the optimal solution. In Shallice's initial investigation using the Tower of London, patients with damage to the left anterior frontal lobe demonstrated impaired planning (i.e., greater number of moves required for solution). Patients with damage to the right anterior, and left or right posterior areas of the frontal lobes were not impaired. Thus, results from this initial study provided support for the view that the left anterior frontal lobe area is involved in the planning required for solving the Tower of London test. Recent studies using neuroimaging techniques support this notion. Studies using regional cerebral blood flow (rCBF) imaging indicate an involvement of the left frontal lobes in the planning required for successfully completing the Tower of London puzzle. Studies of patients with damage to the frontal lobes indicate less cortical specificity, but are consistent with the view that the frontal lobes are involved in the planning required for solving this puzzle.

Proper citation: Colorado Assessment Tests - Tower of London (RRID:SCR_003507) Copy   

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http://www.bcgsc.ca/project/pleiades-promoter-project

Project to generate human DNA promoters of less than 4 kb (MiniPromoters) to drive gene expression in defined brain regions of therapeutic interest for diseases such as Alzheimer, Parkinson, Huntington, Amyotrophic Lateral Sclerosis, Multiple Sclerosis, Spinocerebellar Ataxia, Depression, Autism, and Cancer. Project develops and shares tools like human MiniPromoters that drive region- and cell-specific gene expression in the mouse brain, expression constructs, mouse embryonic stem cell lines, and knock-in mice all of which carry brain-specific MiniPromoters. Project is daughter of Genome Canada Project, Atlas of Gene Expression in Mouse Development, within which mouse brain gene expression data have already been gathered. Project team has collaborated with International BioPharma Solutions Ltd., management and communications consulting company specializing in product development and commercialization advice. Project will explore challenging interface between science and journalism with focus on genomics and gene therapy.

Proper citation: Pleiades Promoter Project: Genomic Resources Advancing Therapies for Brain Disorders (RRID:SCR_003282) Copy   

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http://biomed.brown.edu/rhode-island-biobank/

Cryogenic facility for human tissue and fluid samples under management of Brown University Division of Biology and Medicine and supports biomedical research on Brown campus and across affiliated hospitals of Warren Alpert Medical School.

Proper citation: Brown University Rhode Island Biobank Core Facility (RRID:SCR_004289) Copy   

•   Source: SciCrunch Registry

http://banyanbio.com/

Banyan Biomarkers was founded in 2002 by Ron Hayes, PhD , Kevin Wang, PhD, and Nancy Denslow, PhD to create the first Point of Care (POC) Blood Test to diagnose traumatic brain injury (TBI) and to diagnose neurological diseases. Initially inspired by research conducted at the University of Florida and The Evelyn F. and William McKnight Brain Institute, Banyan Biomarkers has made significant progress in developing and clinically validating novel enzyme linked immunosorbent assays (ELISAs) for traumatic brain injury (TBI). Banyan scientists have created an extensive pipeline of potential biomarkers and the company has a robust intellectual property portfolio. Jackson Streeter, Banyan''s CEO, has extensive experience in development of medical devices for acute brain injury. Currently no blood test exists for use by physicians to detect the presence and severity of brain trauma. Banyan Biomarkers'' research has identified unique and proprietary biomarkers present in the patient''s blood following injury to the brain. The detection and quantification of these biomarkers may provide early indications of brain trauma essential for earlier intervention and management. Banyan Biomarkers, Inc. offers preclinical and clinical sample analyses with a proven panel of neurological, psychiatric, neurodegenerative disease, and organ toxicity biomarker assays. The company provides analytical services to a wide range of customers including pharmaceutical companies, biotechnology companies and investigators at academic research institutes.

Proper citation: Banyan Biomarkers (RRID:SCR_004515) Copy   

•   Source: SciCrunch Registry

http://zfishbook.org/

Collection of revertible protein trap gene-breaking transposon (GBT) insertional mutants in zebrafish with active or cryopreserved lines from initially identified lines. Open to community-wide contributions including expression and functional annotation and represents world-wide central hub for information on how to obtain these lines from diverse members of International Zebrafish Protein Trap Consortium (IZPTC) and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information. Registration allows users to save their favorite lines for easy access, request lines from Mayo Clinic catalog, contribute to line annotation with appropriate credit, and puts them on optional mailing list for future zfishbook newletters and updates.

Proper citation: zfishbook (RRID:SCR_006896) Copy   

•   Source: SciCrunch Registry

http://www.pymvpa.org

A Python package intended to ease statistical learning analyses of large datasets. It offers an extensible framework with a high-level interface to a broad range of algorithms for classification, regression, feature selection, data import and export. While it is not limited to the neuroimaging domain, it is eminently suited for such datasets. PyMVPA is truly free software (in every respect) and additionally requires nothing but free-software to run. Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. This Python-based, cross-platform, open-source software toolbox software toolbox for the application of classifier-based analysis techniques to fMRI datasets makes use of Python's ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine learning packages.

Proper citation: PyMVPA (RRID:SCR_006099) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3520032/

Algorithm for computational imaging of MRI data that detects and quantifies ischemic core–penumbra using only a single MRI modality (T2- or diffusion-weighted imaging, T2WI/DWI). It can be used with 3D data on lesions and normal-appearing brain matter (NABM) volumes.

Proper citation: Hierarchical Region Splitting (RRID:SCR_016398) Copy   

•   Source: SciCrunch Registry

https://github.com/jefferis/elmr

Software tool as support for working with light and electron microscopy fly brain data. Part of suite of R packages based on NeuroAnatomy Toolbox. Provides tools to move between adult brain EM and light level data, emphasising interaction between CATMAID web application and R Neuroanatomy Toolbox package.

Proper citation: elmr (RRID:SCR_017249) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/neurolucida-explorer

Companion analytical software for Neurolucida and Neurolucida 360, designed to perform extensive morphometric analysis on neuron reconstructions, serial section reconstructions, and brain maps.

Proper citation: Neurolucida Explorer (RRID:SCR_017348) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/bva-io/

Software package for interfacing the Brain Vision Analyser data files (load/save) for ongoing development of Matlab routines . This package is also compatible with the EEGLAB software, and may be uncompressed in the plugin folder of this software.

Proper citation: BVA import/export EEGLAB plugin (RRID:SCR_016333) Copy   

•   Source: SciCrunch Registry

https://github.com/DiedrichsenLab/DCBC/tree/v1.0.0

Software Python toolbox for brain parcellation evaluation.

Proper citation: DCBC toolbox (RRID:SCR_022176) Copy   

•   Source: SciCrunch Registry

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

Software toolbox for resting state HRF estimation and deconvolution analysis. Matlab and Python toolbox that implements HRF estimation and deconvolution from resting state BOLD signal. Used to retrieve optimal lag between events and HRF onset, as well as HRF shape. Once that HRF has been retrieved for each voxel/vertex, it can be deconvolved from time series or one can map shape parameters everywhere in brain and use it as pathophysiological indicator. Input can be 2D GIfTI, 3D or 4D NIfTI images, but also on time series matrices/vectors. Output are three HRF shape parameters for each voxel/vertex, plus deconvolved time series, and number of retrieved pseudo events. All can be written back to GIfTI or NIfTI images.

Proper citation: Resting State Hemodynamic Response Function Retrieval and Deconvolution (RRID:SCR_023663) Copy   

•   Source: SciCrunch Registry

http://www.kcl.ac.uk/ioppn/depts/cn/research/MRC-London-Neurodegenerative-Diseases-Brain-Bank/MRC-London-Neurodegenerative-Diseases-Brain-Bank.aspx

A biomaterial supply resource which provides high quality, clinically and neuropathologically well-characterised human brain and spinal cord tissue. The Brain Bank focuses on neurodegenerative diseases such as Alzheimer’s Disease (AD), Frontotemperal dementias (FTD) and Motor Neurone Disease (MND). However, it also contains tissues for the study of HIV, Autism and Schizophrenia, and movement disorders.

Proper citation: MRC London Neurodegenerative Diseases Brain Bank (RRID:SCR_013839) Copy   

•   Source: SciCrunch Registry

http://semmelweis.hu/hbtb/

A biomaterial resource which stores and distributes dissected human brain samples and topographically oriented tissue blocks. Most brains were removed from the skull and frozen within 2-6 hours after death. The microdissection of 260 different brain nuclei is performed on frozen brains and the samples are kept in -70ºC. Materials must be studied in the course of an approved research project, which has scientific aims and is devoid of any commercial profit for the researches involved and for their respective institutions.

Proper citation: Human Brain Tissue Bank (RRID:SCR_013837) Copy   

•   Source: SciCrunch Registry

http://www.stritch.luc.edu/depts/path/residency/anatomic_pathology.htm#Neuropathology

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. A medical center with a neuropathology research program focused on the normal and abnormal aging process of the central nervous system and a funding source for research. The center serves as a collection site for brains in order to study normal aging and neurodegenerative diseases like Alzheimer's.

Proper citation: Loyola University Medical Center / Hines VA Brain Bank (RRID:SCR_013277) Copy   

•   Source: SciCrunch Registry

http://www.uzh.ch/keyinst/loreta

Software application which computes cortical three-dimensional distribution of current density of the brain based on the scalp-recorded electric potential distribution. The exact low resolution brain electromagnetic tomography method has the property of exact localization to test point sources, yielding images of current density with exact localization, albeit with low spatial resolution. eLORETA has no localization bias even in the presence of structured noise. Deep structures, such as the anterior cingulate cortex and mesial temporal lobes, can be correctly localized with these methods.

Proper citation: exact Low Resolution Electromagnetic Tomography (RRID:SCR_013830) Copy   

•   Source: SciCrunch Registry