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http://brain.ubc.ca/

Research facility for research on neurological and psychiatric disorders on the learning brain and the aging brain. The Centre utilizes a multidisciplinary approach to explore the causes and potential treatments of disorders like Alzheimer's disease, mental health and addiction, stroke and neurotrauma. The Centre focuses on translating research into patient care and therapies.

Proper citation: Djavad Mowafaghian Centre for Brain Health (RRID:SCR_013149) Copy   

•   Source: SciCrunch Registry

http://www.fz-juelich.de/ime/spm_anatomy_toolbox

A MATLAB toolbox which uses three dimensional probabilistic cytoarchitechtonic maps to correlate microscopic, anatomic and functional data of the cerebral cortex. Correlating the activation foci identified in functional imaging studies of the human brain with structural (e.g., cytoarchitectonic) information on the activated areas is a major methodological challenge for neuroscience research. We here present a new approach to make use of three-dimensional probabilistic cytoarchitectonic maps, as obtained from the analysis of human post-mortem brains, for correlating microscopical, anatomical and functional imaging data of the cerebral cortex. We introduce a new, MATLAB based toolbox for the SPM2 software package which enables the integration of probabilistic cytoarchitectonic maps and results of functional imaging studies. The toolbox includes the functionality for the construction of summary maps combining probability of several cortical areas by finding the most probable assignment of each voxel to one of these areas. Its main feature is to provide several measures defining the degree of correspondence between architectonic areas and functional foci. The software, together with the presently available probability maps, is available as open source software to the neuroimaging community. This new toolbox provides an easy-to-use tool for the integrated analysis of functional and anatomical data in a common reference space.

Proper citation: SPM Anatomy Toolbox (RRID:SCR_013273) Copy   

•   Source: SciCrunch Registry

http://www.hedtags.org/

Strategy guide for HED Annotation. Framework for systematically describing laboratory and real world events.HED tags are comma separated path strings. Organized in forest of groups with roots Event, Item, Sensory presentation, Attribute, Action, Participant, Experiment context, and Paradigm. Used for preparing brain imaging data for automated analysis and meta analysis. Applied to brain imaging EEG, MEG, fNIRS, multimodal mobile brain or body imaging, ECG, EMG, GSR, or behavioral data. Part of Brain Imaging Data Structure standard for brain imaging.

Proper citation: HED Tags (RRID:SCR_014074) Copy   

•   Source: SciCrunch Registry

http://projectreporter.nih.gov/project_info_description.cfm?aid=8662111&icde=19363315&ddparam=&ddvalue=&ddsub=&cr=2&csb=default&cs=ASC

A multi-center and multi-disciplinary study designed to dramatically increase understanding of chronic traumatic encephalopathy (CTE) and other late effects of traumatic brain injury (TBI). Overlapping clinical features, postmortem pathologies and patterns of involvement exist in TBI, CTE, and Alzheimer''s disease pose challenges to accurate diagnosis. Premortem diagnosis of CTE is currently impossible. The neuropathological consequences of single mild or moderate-severe TBI and its relationship with CTE and known dementias are unclear. The proposed project will leverage extensive resources from an ongoing population-based prospective cohort study of brain aging (Adult Changes in Thought; ACT, n=2,305) which includes excellent medical, behavioral, and genetic characterization of a cohort (20% of whom have a history of mild-moderate TBI) in addition to state-of-the-art neuropathology workup upon death. Neuropathological study of TBI effects can begin immediately in the existing ACT autopsy sample (n=489, 20% with TBI exposure). Additional cohorts of TBI- exposed individuals will come from the Brain Injury Research Center at Mount Sinai (n=150 individuals with moderate-severe TBI), the University of Texas Southwestern (n=50 retired boxers with repetitive TBI exposure), and the National Football League (n=76 retired players with repetitive TBI exposure). All participants in the proposed study (ACT and other sites) will undergo uniform harmonized neurobehavioral assessment (chosen to maximize correspondence with existing large-scale TBI and dementia studies), MRI scan, and genomic analysis. Those individuals who expire during the course of the study will undergo ex-vivo neuroimaging and extensive neuropathological exam using state-of-the-art techniques (such as Histelide) designed to quantify tau and A�� in whole brain specimens. Only by examining postmortem pathology in a sample of individuals with varying levels of TBI exposure who are well characterized during life (as proposed herein) can postmortem pathology facilitate identification of in-vivo biomarkers that can act as diagnostic tools. This project represents the most systematic and scientifically rigorous effort to date to develop a more complete understanding of the long-term clinical and neuropathological sequelae of single and multiple TBI.

Proper citation: Neuropathology of CTE and Delayed Effects of TBI: Toward In-Vivo Diagnostics (RRID:SCR_012951) Copy   

•   Source: SciCrunch Registry

http://www.sci.utah.edu/software/fluorender.html

Interactive rendering tool for confocal microscopy data visualization. Combines rendering of multi-channel volume data and polygon mesh data, where properties of each dataset can be adjusted independently and quickly. Designed for neurobiologists, allowing them to better visualize confocal data from fluorescently-stained brains, but it is also useful for other biological samples. Features include feature tracking, 3D measurement tools, multiple render modes for multi-channel confocal data, and volume paint selection and segmentation.

Proper citation: FluoRender (RRID:SCR_014303) Copy   

•   Source: SciCrunch Registry

http://knowledge-space.org/

A community encyclopaedia that links brain research concepts with data, models and literature from around the world. It is an open project where users can participate and contribute to the global research community.

Proper citation: KnowledgeSpace (RRID:SCR_014539) Copy   

•   Source: SciCrunch Registry

http://www.linkrbrain.eu

An online tool for managing and viewing datasets. Data can be viewed in 2D or 3D with activation points as points clouds or projections on the cortex surface. Data can be imported as a NIfTI file or a list of activation peaks and results can be exported as a PDF file.

Proper citation: linkRbrain (RRID:SCR_014562) Copy   

•   Source: SciCrunch Registry

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

Graphical user interface that has been implemented as a 3D Slicer plugin (scripted module). It serves to display a corresponding set of cortical regions from functional connectivity matrix in an explorable 3D scene that represents brain anatomical environment. In addition to grey matter regions, MultiXplore automatically finds and extracts deterministic fiber bundles which exist between selected region(s) and adds them to the 3D environment. This feature helps in generating region-based fiber bundles given a desired whole-brain tractography data.

Proper citation: MultiXplore (RRID:SCR_014814) Copy   

•   Source: SciCrunch Registry

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

Integrated pipeline for tractography-based brain parcellation with automatic processing and massive parallel computing. ATPP offers a CLI version for parcellating multiple brain regions and a GUI version for parcellating a specific brain region. " ATPP completely follows the scientific cultural shift to open science, which aims at making scientific research including journal papers, lab notes, data, and, of course, workflow tools, accessible and transparent to all levels of society. ATPP is publicly accessible in Neuroimaging Informatics Tools and Resources Clearinghouse8 (NITRC) (https://www.nitrc.org/projects/atpp). Its source codes are hosted in GitHub9 (https://github.com/haililihai/ATPP_CLI; https://github.com/haililihai/ATPP_GUI), under the GNU generic purpose license version 310 (GPLv3), and are welcome to download and fork. The Digital Object Identifiers (DOIs) providing a persistent way to make digital data easily and uniquely citable was created from Zenodo11 platform with those GitHub repositories (ATPP CLI v2.0.0, doi: https://doi.org/10.5281/zenodo.239702; ATPP GUI v2.0.0, doi: https://doi.org/10.5281/zenodo.239705). "

Proper citation: Automatic Tractography-based Parcellation Pipeline (RRID:SCR_014815) Copy   

•   Source: SciCrunch Registry

https://github.com/BlueBrain/BluePyOpt

An extensible framework for data-driven model parameter optimization that wraps and standardizes several existing open-source tools. BluePyOpt abstracts the optimization and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. It also provides methods for setting up both small- and large-scale optimizations on a variety of platforms.

Proper citation: BluePyOpt (RRID:SCR_014753) Copy   

•   Source: SciCrunch Registry

http://brainmap.org/software.html#GingerALE

Software available from brainmap.org to perform meta-analyses via the activation likelihood estimation (ALE) method. It also includes the transforms for icbm2tal conversions.

Proper citation: GingerALE (RRID:SCR_014921) Copy   

•   Source: SciCrunch Registry

https://bams1.org/cells/list.php, https://bams1.org/cells/search_bams_ref.php, https://bams1.org/cells/search_by_brain_region.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023.BAMS is an online resource for information about neural circuitry. The BAMS Cell view focuses on the major brain regions and which cells are contained therein.

Proper citation: BAMS Cells (RRID:SCR_003531) Copy   

•   Source: SciCrunch Registry

http://www.emouseatlas.org

Detailed multidimensional digital multimodal atlas of C57BL/6J mouse nervous system with data and informatics pipeline that can automatically register, annotate, and visualize large scale neuroanatomical and connectivity data produced in histology, neuronal tract tracing, MR imaging, and genetic labeling. MAP2.0 interoperates with commonly used publicly available databases to bring together brain architecture, gene expression, and imaging information into single, simple interface.Resource to visualise mouse development, identify anatomical structures, determine developmental stage, and investigate gene expression in mouse embryo. eMouseAtlas portal page allows access to EMA Anatomy Atlas of Mouse Development and EMAGE database of gene expression.EMAGE is freely available, curated database of gene expression patterns generated by in situ techniques in developing mouse embryo. EMA, e-Mouse Atlas, is 3-D anatomical atlas of mouse embryo development including histology and includes EMAP ontology of anatomical structure, provides information about shape, gross anatomy and detailed histological structure of mouse, and framework into which information about gene function can be mapped.

Proper citation: eMouseAtlas (RRID:SCR_002981) Copy   

•   Source: SciCrunch Registry

https://confluence.crbs.ucsd.edu/display/NIF/DRG

Gene expression data from published journal articles that test hypotheses relevant to neuroscience of addiction and addictive behavior. Data types include effects of particular drug, strain, or knock out on particular gene, in particular anatomical region. Focuses on gene expression data and exposes data from investigations using DNA microarrays, polymerase chain reaction, immunohistochemistry and in-situ hybridizations. Data are available for query through NIF interface.Data submissions are welcome.

Proper citation: Drug Related Gene Database (RRID:SCR_003330) Copy   

•   Source: SciCrunch Registry

http://hendrix.imm.dtu.dk/services/jerne/brede/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 4th, 2023. A database of human data from functional neuroimaging scientific articles containing Talairach coordinates that provides data for novel information retrieval techniques and automated meta-analyses. Each article in this database is identified by a unique number: A WOBIB. Some of the structure of the Brede database is similar to the structure of the BrainMap database (Research Imaging Center, San Antonio). The database is inspired by the hierarchical structure of BrainMap with scientific articles (bib structures) on the highest level containing one or more experiments (exp structure, corresponding to a contrast in general linear model analyses), these in turn comprising one or more locations (loc structures). The information on the bib level (author, title, ...) is setup automatically from PubMed while the rest of the information is entered manually in a Matlab graphical user interface. On the loc level this includes the 3D stereotactic coordinates in either Talairach or MNI space, the brain area (functional, anatomical or cytoarchitectonic area) and magnitude values such as Z-score and P-value. On the exp level information such as modality, scanner and behavioral domain are recorded with external components (such as face recognition or kinetic boundaries) organized in a directed graph and marked up with Medical Subject Headings (MeSH) where possible. The database is distributed as part of the Brede neuroinformatics toolbox (hendrix.imm.dtu.dk/software/brede/) which also provides the functions to manipulate and analyze the data. The Brede Toolbox is a program package primarily written in Matlab. As of 2006/11, 186 papers with 586 experiments.

Proper citation: Brede Database (RRID:SCR_003327) Copy   

•   Source: SciCrunch Registry

http://www.mknt.hu/sites/default/files/NEPSYBANK_0.doc

The Hungarian Society of Clinical Neurgenetics established a nationwide collaboration for prospective collection of human biological materials and databases from patient with neurological and psychiatric diseases. The basic triangle of the NEPSYBANK is the sample, the information and the study management. The present participants of the NEPSYBANK are the Department of Neurology and Psychiatry of the four Medical Universities (in Budapest, Debrecen, Pecs, Szeged) and the National Institute of Psychiatry and Neurology in Budapest. The NEPSYBANK is a disease based biobank collecting both phenotypical and environmental data and biological materials such as DNA/RNA, whole blood, plasma, cerebral spinal fluid, muscle / nerve / skin biopsy, brain, and fibroblast. The target of the diseases is presently (Phase I): stroke syndromes, dementias, movement disorders, motoneuron diseases, epilepsy, multiple sclerosis, schizophrenia, alcohol addiction. In the near future (Phase II.) it is planned to enlarge the scale with headaches, disorders of the peripheral nerves, disorders of neuromuscular transmission, disorders of skeletal muscle, depression, anxiety. DNA/RNA is usually extracted from whole blood, but occasionally different tissues such as muscle, brain etc. can be used as well. The extracting procedures differ among the institutes, but in all cases the concentration and the quality of the DNA/RNA must be registered in the database. Participating institutional biobanks have committed themselves to follow common quality standards, which provide access to samples after prioritization on scientific grounds only. In every case the following data are registered. 1. General data: main bank categories, age, sex, ethnicity, body height, body weight, economic stats, education, type of place of living, marital status, birth complications, alcohol, drugs, smoking. 2. Sample properties (sample ID, type of sample, date of extraction, concentration, and level of purity). General patient data as blood pressure, heart rate, internal medical status, ECG, additional diseases. Disease specific question e.g. in schizophrenia the diagnosis after DSMIV and ICD 10, detailed diagnostic questions after both classification, detailed psychiatric and neurological status, laboratory findings, rating scales, data of neuroimaging, genetic tests, applied medication (with generic name, dose, duration), adverse drug effects and other treatments. The Biobank Information Management System (BIMS) is responsible for linkage of databases containing information on the individual sample donors. If you want to have samples from the NEPSYBANK an application must be submitted containing the following information: short research plan including aims and study design, ethic application with a positive decision, specific demands regarding the right of disposition, agreements with grant organizations which regulate immaterial property, information about financing (academic grants, support from industry). All participants have the right to withdraw their samples through a simple order.

Proper citation: Hungarian Neurological-Psychiatric Biobank (RRID:SCR_003715) Copy   

•   Source: SciCrunch Registry

http://www.psychologytoday.com/blog/the-compass-pleasure

A blog written by David J. Linden, Ph.D., professor of Neuroscience at the Johns Hopkins University School of Medicine, focusing on the brain''s pleasure circuits. Topics covered include exercise, pleasure and the brain; and understanding the biology of runners high. The Compass of Pleasure: How Our Brains Make Fatty Foods, Orgasm, Exercise, Marijuana, Generosity, Vodka, Learning, and Gambling Feel So Good is also a book and available for purchase. David J. Linden, Ph.D., is a professor in the Department of Neuroscience at the Johns Hopkins University School of Medicine. His laboratory has worked for many years on the cellular substrates of memory storage in the brain and a few other topics. He has a longstanding interest in scientific communication and serves as the Chief Editor of the Journal of Neurophysiology. He has written two books for a general audience about the biological basis of mental function: The Compass of Pleasure (Viking Press, 2011) and The Accidental Mind (Harvard/Belknap, 2007).

Proper citation: Compass of Pleasure (RRID:SCR_004756) Copy   

•   Source: SciCrunch Registry

http://www.brainbankforautism.org.uk/

Encourages and facilitates brain tissue donation for use in the best scientific studies to better understand the biological basis of autism down to the cellular and molecular levels and through that understanding bring about the development of effective interventions for those affected by autism spectrum disorders. To ensure the best co-ordinated use of brain tissue, the UK Brain Bank for Autism works in collaboration with the Autism Tissue Program in the US and shares the same Tissue Advisory board. The Brain Bank for Autism & Related Developmental Research was established in 2009. It is an initiative to develop a similar program in the UK to the Autism Tissue Program, which has been developed in the US since 1998. Our Brain Bank is the first extension outside the US of the Autism Tissue Program and is integrated with it. The Brain Bank is based at Oxford University, where it forms part of the Thomas Willis Oxford Brain Collection. It operates in accordance with all UK legal and ethical requirements. The donation of post-mortem brain tissue for this research program is of fundamental importance to our understanding of the causes of autism and to help us develop more effective diagnostic measures and interventions. A separate brain bank for autism is necessary because we need to understand how, in autism, the brain develops over time and how the brain functions as a whole. However, our Brain Bank will promote close cooperation across all relevant brain banks in order to take the research forward. Our research focuses on: * people within the autism spectrum or their family members * people not affected by autism but who are affected by epilepsy * individuals without autism or epilepsy.

Proper citation: Brain Bank for Autism (RRID:SCR_004664) Copy   

•   Source: SciCrunch Registry

http://www.tmf-ev.de/BiobankenRegisterEN/Registry.aspx?udt_2021_param_detail=84

A brain bank which collects brain tissue from patients who died from various neurological and psychiatric diseases. These tissues are available for biochemical, molecular biological, and other work groups with the aim of supporting research on the pathogenesis, diagnosis, and therapy of these diseases. Collected brains are clinically and neuropathologically well-characterized. The collection and distribution of brain tissue samples is an ongoing process. NeuroBiobank Munich offers help with the organization and implementation of autopsies as well as with the neuropathologic diagnostics. The thematic emphasis of the NeuroBiobank Munich is Parkinson's disease and demential degenerative disorders such as Alzheimer's disease or Creutzfeldt-Jakob disease. NeuroBiobank Munich coordinates the German national brain tissue bank (BrainNet) and the European brain tissue bank (BrainNet Europe).

Proper citation: NeuroBiobank Munich (RRID:SCR_005014) Copy   

•   Source: SciCrunch Registry

http://udn.nichd.nih.gov/brainatlas_home.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 1, 2019. The first brain atlas for the common marmoset to be made available since a printed atlas by Stephan, Baron and Schwerdtfeger published in 1980. It is a combined histological and magnetic resonance imaging (MRI) atlas constructed from the brains of two adult female marmosets. Histological sections were processed from Nissl staining and digitized to produce an atlas in a large format that facilitates visualization of structures with significant detail. Naming of identifiable brain structures was performed utilizing current terminology. For the present atlas, an adult female was perfused through the heart with PBS followed by 10% formalin. The brain was then sent to Neuroscience Associates of Knoxville, TN, who prepared the brain for histological analysis. The brain was cut in the coronal (frontal) plane at 40 microns, every sixth section stained for Nissl granules with thionine and every seventh section stained for myelinated fibers with the Weil technique. The mounted sections were photographed at the NIH (Medical Arts and Photography Branch). The equipment used was a Nikon Multiphot optical bench with Zeiss Luminar 100 mm lens, and scanned with a Better Light 6100 scan back driven by Better Light Viewfinder 5.3 software. The final images were saved as arrays of 6000x8000 pixels in Adobe Photoshop 6.0. A scale in mm provided with these images permitted construction of the final Nissl atlas files with a horizontal and vertical scale. Some additional re-touching (brightness and contrast) was done with Adobe Photoshop Elements 2.0. The schematic (labeled) atlas plates were created from the Nissl images. The nomenclature came almost exclusively from brainmaps.org, where a rhesus monkey brain with structures labeled can be found. The labels for the MRI images were placed by M. R. Zametkin, under supervision from Dr. Newman.

Proper citation: Brain atlas of the common marmoset (RRID:SCR_005135) Copy   

•   Source: SciCrunch Registry