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http://narc.wustl.edu/narc/default.aspx

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. The Neurologic AIDS Research Consortium (NARC) is supported by the National Institutes of Health to design and carry out clinical trials to improve the therapy for HIV induced neurologic disease, and neurologic conditions associated with the AIDS virus. This consortium was established in 1993 when the NARC grant submitted by David B. Clifford, M.D. of Washington University School of Medicine was funded by the National Institute of Neurologic Disorders and Stroke (NINDS) to establish the consortium. Since that time the grant has supported studies of the natural history of neurologic performance in advanced AIDS, treatment of HIV associated peripheral neuropathy, progressive multifocal leukoencephalopathy, and cytomegalovirus.

Proper citation: Neurologic AIDS Research Consortium (RRID:SCR_005019) Copy   

•   Source: SciCrunch Registry

http://krasnow1.gmu.edu/cn3/hippocampus3d/

Data files for a high resolution three dimensional (3D) structure of the rat hippocampus reconstructed from histological sections. The data files (supplementary data for Ropireddy et al., Neurosci., 2012 Mar 15;205:91-111) are being shared on the Windows Live cloud space provided by Microsoft. Downloadable data files include the Nissl histological images, the hippocampus layer tracings that can be visualized alone or superimposed to the corresponding Nissl images, the voxel database coordinates, and the surface rendering VRML files. * Hippocampus Nissl Images: The high resolution histological Nissl images obtained at 16 micrometer inter-slice distance for the Long-Evans rat hippocampus can be downloaded or directly viewed in a browser. This dataset consists of 230 jpeg images that cover the hippocampus from rostral to caudal poles. This image dataset is uploaded in seven parts as rar files. * Hippocampus Layer Tracings: The seven hippocampus layers ''ML, ''GC'', ''HILUS'' in DG and ''LM'', ''RAD'', ''PC'', ''OR'' in CA were segmented (traced) using the Reconstruct tool which can be downloaded from Synapse web. This tool outputs all the tracings for each image in XML format. The XML tracing files for all these seven layers for each of the above Nissl images are zipped into one file and can be downloaded. * Hippocampus VoxelDB: The 3D hippocampus reconstructed is volumetrically transformed into 16 micrometer sized voxels for all the seven layers. Each voxel is reported according to multiple coordinate systems, namely in Cartesian, along the natural hippocampal dimensions, and in reference to the canonical brain planes. The voxel database file is created in ascii format. The single voxel database file was split into three rar archive files. Please note that the three rar archive files should be downloaded and decompressed in a single directory in order to obtain the single voxel data file (Hippocampus-VoxelDB.txt). * 3D Surface Renderings: This is a rar archive file with a single VRML file containing the surface rendering of DG and CA layers. This VRML file can be opened and visualized in any VRML viewer, e.g. the open source software view3dscene. * 3D Hippocampus Movie: This movie contains visualization of the 3D surface renderings of CA (blue) and DG (red) inner and outer boundaries; neuronal embeddings of DG granule and CA pyramidal dendritic arbors; potential synapses between CA3b interneuron axon and pyramidal dendrite, and between CA2 pyramidal axon and CA pyramidal dendrites.

Proper citation: Hippocampus 3D Model (RRID:SCR_005083) Copy   

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http://www.musicianbrain.com/#index

The human brain has the remarkable ability to adapt in response to changes in the environment over the course of a lifetime. This is the mechanism for learning, growth, and normal development. Similar changes or adaptations can also occur in response to focal brain injuries, e.g., partially-adapted neighboring brain regions or functionally-related brain systems can either substitute for some of the lost function or develop alternative strategies to overcome a disability. Through ongoing research, the Music and Neuroimaging Laboratory''s mission is to: * Reveal the perceptual and cognitive aspects of music processing including the perception and memory for pitch, rhythmic, harmonic, and melodic stimuli. * Investigate the use of music and musical stimuli as an interventional tool for educational and therapeutic purposes. * Reveal the behavioral and neural correlates of learning, skill acquisition, and brain adaptation in response to changes in the environment or brain injury in the developing and adult brain. * Reveal the determinants and facilitators for recovery from brain injury. Project topics include: Aphasia Therapy, Singing and Speaking, Tone Deafness / Congenital Amusia, Motor Recovery Studies, Music and Emotions, Music and Autism, Children and Music Making, Brain Stimulation, Adult Musician Studies, Absolute Pitch Studies, Acute Stroke Studies

Proper citation: Music and Neuroimaging Laboratory (RRID:SCR_005447) Copy   

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http://www.bri.ucla.edu/research/resources

Brain bank resources which include postmortem human frozen brain tissue and matched cerebrospinal fluid (CSF) and blood available for scientists to search for etiopathogeneses of human disease. The National Neurological Research Specimen Bank and the Multiple Sclerosis Human Neurospecimen Bank maintains a collection of quick frozen and formalin fixed postmortem human brain tissue and frozen cerebrospinal fluid from patients with neurological diseases, including Alzheimer's Disease, amyotrophic lateral sclerosis, depressive disorder/suicide, and epilepsy, among others. Diagnoses are documented by clinical medical records and gross/microscopic neuropathology. The Neuropathology Laboratory at the UCLA Medical Center maintains a bank of frozen, formalin and paraformaldehyde-fixed and paraffin-embedded postmortem human brain tissues and frozen cerebrospinal fluid (CSF) from patients who die with Alzheimer's disease and other dementing and degenerative illnesses, as well as control materials removed in a similar fashion from patients who are neurologically normal.

Proper citation: Brain Research Institute Biobank Resources (RRID:SCR_008756) Copy   

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http://mayoresearch.mayo.edu/mayo/research/dickson_lab/

A brain bank and laboratory focused on memory and motor disorders. Brains are sent to the laboratory for diagnosis and research for the State of Florida Alzheimer Disease Initiative and for the Society for Progressive Supranuclear Palsy. As part of this brain banking function, fixed and frozen brain samples are obtained at autopsy and sent to the laboratory for diagnostic evaluation and for various types of research studies. The major types of analyses performed on the brain samples include neuro-histology, immunohistochemistry, confocal microscopy, electron microscopy and image analysis, as well as immunoassays. The latter are based upon Western blotting and enzyme linked immunoassays. The laboratory has a specific interest in the interface between normal aging and Alzheimer's disease, as well as in non-Alzheimer's degenerative disorders such as Lewy body dementia, corticobasal degeneration, progressive supranuclear palsy and frontotemporal dementia. The primary focus of research on aging is neuropathologic characterization of brains of individuals who had been prospectively and longitudinally evaluated during life. These studies aim to determine differences in a range of biologic parameters in brains of people with normal cognitive, mild cognitive impairment and dementia. Their focus on Parkinson's disease is to identify preclinical Parkinson's disease in order to develop means for early diagnosis.

Proper citation: Mayo Clinic Jacksonville: Neuropathology and Microscopy (RRID:SCR_008753) Copy   

•   Source: SciCrunch Registry

http://trans.nih.gov/bmap/index.htm

The Brain Molecular Anatomy Project is a trans-NIH project aimed at understanding gene expression and function in the nervous system. BMAP has two major scientific goals: # Gene discovery: to catalog of all the genes expressed in the nervous system, under both normal and abnormal conditions. # Gene expression analysis: to monitor gene expression patterns in the nervous system as a function of cell type, anatomical location, developmental stage, and physiological state, and thus gain insight into gene function. In pursuit of these goals, BMAP has launched several initiatives to provide resources and funding opportunities for the scientific community. These include several Requests for Applications and Requests for Proposals, descriptions of which can be found in this Web site. BMAP is also in the process of establishing physical and electronic resources for the community, including repositories of cDNA clones for nervous system genes, and databases of gene expression information for the nervous system. Most of the BMAP initiatives so far have focused on the mouse as a model species because of the ease of experimental and genetic manipulation of this organism, and because many models of human disease are available in the mouse. However, research in humans, other mammalian species, non-mammalian vertebrates, and invertebrates is also being funded through BMAP. For the convenience of interested investigators, we have established this Web site as a central information resource, focusing on major NIH-sponsored funding opportunities, initiatives, genomic resources available to the research community, courses and scientific meetings related to BMAP initiatives, and selected reports and publications. When appropriate, we will also post initiatives not directly sponsored by BMAP, but which are deemed relevant to its goals. Posting decisions are made by the Trans-NIH BMAP Committee

Proper citation: BMAP - Brain Molecular Anatomy Project (RRID:SCR_008852) Copy   

•   Source: SciCrunch Registry

https://github.com/BRAINSia/BRAINSTools/tree/master/BRAINSDemonWarp

A command line program for image registration by using different methods including Thirion and diffeomorphic demons algorithms. The function takes in a template image and a target image along with other optional parameters and registers the template image onto the target image. The resultant deformation fields and metric values can be written to a file. The program uses the Insight Toolkit (www.ITK.org) for all the computations, and can operate on any of the image types supported by that library. This a an ITK based implementation of various forms of Thirion Demons based registration (including diffeomorphic demons registration originating from Tom Vercauteren at INRIA ).

Proper citation: BRAINSDemonWarp (RRID:SCR_009524) Copy   

•   Source: SciCrunch Registry

http://www.gensat.org/

Gene expression data and maps of mouse central nervous system. Gene expression atlas of developing adult central nervous system in mouse, using in situ hybridization and transgenic mouse techniques. Collection of pictorial gene expression maps of brain and spinal cord of mouse. Provides tools to catalog, map, and electrophysiologically record individual cells. Application of Cre recombinase technologies allows for cell-specific gene manipulation. Transgenic mice created by this project are available to scientific community.

Proper citation: Gene Expression Nervous System Atlas (RRID:SCR_002721) Copy   

•   Source: SciCrunch Registry

http://rsb.info.nih.gov/nih-image/index.html

Public image processing and analysis program for Macintosh.

Proper citation: NIH Image (RRID:SCR_003073) Copy   

•   Source: SciCrunch Registry

http://trans.nih.gov/bmap/resources/resources.htm

As part of BMAP gene discovery efforts, mouse brain cDNA libraries and Expressed Sequence Tags (ESTs) have been generated. Through this project a BMAP mouse brain UniGene set consisting of over 24,000 non-redundant members of unique clusters has been developed from EST sequencing of more than 50,000 cDNA clones from 10 regions of adult mouse brain, spinal cord, and retina (http://brainEST.eng.uiowa.edu/). In 2001, NIMH along with NICHD, NIDDK, and NIDA, awarded a contract to the University of Iowa ( M.B. Soares, PI) to isolate full-length cDNA clones corresponding to genes expressed in the developing mouse nervous system and determine their full-coding sequences. The BMAP mouse brain EST sequences can be accessed at NCBI's dbEST database (http://www.ncbi.nlm.nih.gov/dbEST/). Arrayed sets of BMAP mouse brain UniGenes and cDNA libraries, and individual BMAP cDNA clones can be purchased from Open Biosystems, Huntsville, AL (http://www.openbiosystems.com

Proper citation: BMAP cDNA Resources (RRID:SCR_002973) Copy   

•   Source: SciCrunch Registry

https://neurobiobank.nih.gov/

National resource for investigators utilizing human post-mortem brain tissue and related biospecimens for their research to understand conditions of the nervous system. Federated network of brain and tissue repositories in the United States that collects, evaluates, stores, and makes available to researchers, brain and other tissues in a way that is consistent with the highest ethical and research standards. The NeuroBioBank ensures protection of the privacy and wishes of donors. Provides information to the public about the need for tissue donation and how to register as a donor.

Proper citation: NIH NeuroBioBank (RRID:SCR_003131) Copy   

•   Source: SciCrunch Registry

https://fmriprep.org

Software tool as robust preprocessing pipeline for functional MRI.Used for preprocessing of diverse fMRI data.

Proper citation: fMRIPrep (RRID:SCR_016216) Copy   

•   Source: SciCrunch Registry

https://www.rarediseasesnetwork.org/cms/create/researchers/biorepository

Biorepository of samples collected from patients with ALS, ALS-frontotemporal dementia (ALS-FTD), primary lateral sclerosis (PLS), progressive muscular atrophy (PMA), hereditary spastic paraplegia (HSP) and multisystem proteinopathy (MSP). Used by Consortium members and the scientific community to advance therapeutic development through study of the relationship between clinical phenotype and underlying genotype, and also through the discovery and development of biomarkers.

Proper citation: CReATE (RRID:SCR_016436) Copy   

•   Source: SciCrunch Registry

http://www.lincsproject.org/

Project to create network based understanding of biology by cataloging changes in gene expression and other cellular processes when cells are exposed to genetic and environmental stressors. Program to develop therapies that might restore pathways and networks to their normal states. Has LINCS Data Coordination and Integration Center and six Data and Signature Generation Centers: Drug Toxicity Signature Generation Center, HMS LINCS Center, LINCS Center for Transcriptomics, LINCS Proteomic Characterization Center for Signaling and Epigenetics, MEP LINCS Center, and NeuroLINCS Center.

Proper citation: LINCS Project (RRID:SCR_016486) Copy   

•   Source: SciCrunch Registry

http://marrvel.org/

Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research.

Proper citation: MARRVEL (RRID:SCR_016871) Copy   

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http://pklab.med.harvard.edu/scde/pagoda.links.html

Software tool for analyzing transcriptional heterogeneity to detect statistically significant ways in which measured cells can be classified. Used to resolve multiple, potentially overlapping aspects of transcriptional heterogeneity by testing gene sets for coordinated variability among measured cells.

Proper citation: PAGODA (RRID:SCR_017099) Copy   

•   Source: SciCrunch Registry

https://github.com/FeeLab/seqNMF

Software tool for unsupervised discovery of sequential structure. Used to detect sequences in neural data generated by internal behaviors, such as animal thinking or sleeping. Used for unsupervised discovery of temporal sequences in high dimensional datasets in neuroscience without reference to external markers.

Proper citation: seqNMF (RRID:SCR_017068) Copy   

•   Source: SciCrunch Registry

http://www.tbi-impact.org/

Project focused on advancing knowledge of prognosis, trial design and treatment in Traumatic Brain Injury. IMPACT has developed and validated prognostic models for classification and characterization of TBI series, and participated in development of standardization of data collection in TBI studies.

Proper citation: IMPACT: International Mission for Prognosis and Analysis of Clinical Trials in TBI (RRID:SCR_000539) Copy   

•   Source: SciCrunch Registry

http://neuromorpho.org/index.jsp

Centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications that contains some of the most complete axonal arborizations digitally available in the community. Each neuron is represented by a unique identifier, general information (metadata), the original and standardized ASCII files of the digital morphological reconstruction, and a set of morphometric features. It contains contributions from over 100 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared. Users may browse by species, brain region, cell type or lab name. Users can also download morphological reconstructions for research and analysis. Deposition and distribution of reconstruction files ultimately prevents data loss. Centralized curation and annotation aims at minimizing the effort required by data owners while ensuring a unified format. It also provides a one-stop entry point for all available reconstructions, thus maximizing data visibility and impact.

Proper citation: NeuroMorpho.Org (RRID:SCR_002145) 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