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http://connectivity.brain-map.org/transgenic

Data detailing transgene expression in Cre and other driver lines for adult and developing brain. Experiments include colorimetric in situ hybridization, fluorescent in situ hybridization and other histological methods. Expression maps of transgenic Cre and other driver lines in mice.

Proper citation: Allen Brain Atlas expression map of Cre and other drivers (RRID:SCR_017510) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.istge.it/cldb/indexes.html

Hypertext on cell culture availability extracted from the Cell Line Data Base of the Interlab Project. HyperCLDB includes links to records of OMIM, the Online Mendelian Inheritance in Man Catalogue, and now also links to the PubMed, database of bibliographic biomedical references, which are drawn primarily from MEDLINE and PREMEDLINE.

Proper citation: Hyper Cell Line Database (RRID:SCR_007730) Copy   

•   Source: SciCrunch Registry

http://pubanatomy.org

An integrated exploration of biomedical literature and data. An anatomy viewer can be accessed and searches of PubMed literature are visualized as to the anatomical regions that they effect. PubAnatomy takes advantage of the 25-micron voxel level mouse brain structure annotation generated by the Allen Brain Institute and integrates Allen Brain Atlas gene expression data, relationships between brain regions and diseases for more efficient exploration of Medline database and gene expression data.

Proper citation: PubAnatomy (RRID:SCR_007999) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/asd/aedb/index.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 27, 2013. A manual generated database for alternative exons and their properties from numerous species - the data is gathered from literature where these exons have been experimentally verified. Most alternative exons are cassette exons and are expressed in more than two tissues. Of all exons whose expression was reported to be specific for a certain tissue, the majority were expressed in the brain. At the moment, AEdb products that are available are sequence (a database of alternative exons), function (a database of functions attributed to constitutive and alternative exon), regulatory sequence (a database of transcript regulatory motifs), minigenes (a table of minigenes and their associations to splicing events), and diseases (a table of diseases associated with splicing and their associations to AltSplice). Alternative splicing is an important regulatory mechanism of mammalian gene expression. The alternative splicing database (ASD) consortium is systematically collecting and annotating data on alternative splicing. The continuation and upgrade of the ASD consists of computationally and manually generated data. Its largest parts are AltSplice, a value-added database of computationally delineated alternative splicing events. Its data include alternatively spliced introns/exons, events, isoform splicing patterns and isoform peptide sequences. AltSplice data are generated by examining gene-transcript alignments. The data are annotated for various biological features including splicing signals, expression states, (SNP)-mediated splicing and cross-species conservation. AEdb forms the manually curated component of ASD. It is a literature-based data set containing sequence and properties of alternatively spliced exons, functional enumeration of observed splicing events, characterization of observed splicing regulatory elements, and a collection of experimentally clarified minigene constructs.

Proper citation: Alternative Exon Database (RRID:SCR_008157) Copy   

•   Source: SciCrunch Registry

https://epilepsy.uni-freiburg.de/freiburg-seizure-prediction-project

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 29,2025. Electroencephalogram (EEG) data recorded from invasive and scalp electrodes. The EEG database contains invasive EEG recordings of 21 patients suffering from medically intractable focal epilepsy. The data were recorded during an invasive pre-surgical epilepsy monitoring at the Epilepsy Center of the University Hospital of Freiburg, Germany. In eleven patients, the epileptic focus was located in neocortical brain structures, in eight patients in the hippocampus, and in two patients in both. In order to obtain a high signal-to-noise ratio, fewer artifacts, and to record directly from focal areas, intracranial grid-, strip-, and depth-electrodes were utilized. The EEG data were acquired using a Neurofile NT digital video EEG system with 128 channels, 256 Hz sampling rate, and a 16 bit analogue-to-digital converter. Notch or band pass filters have not been applied. For each of the patients, there are datasets called ictal and interictal, the former containing files with epileptic seizures and at least 50 min pre-ictal data. the latter containing approximately 24 hours of EEG-recordings without seizure activity. At least 24 h of continuous interictal recordings are available for 13 patients. For the remaining patients interictal invasive EEG data consisting of less than 24 h were joined together, to end up with at least 24 h per patient. An interdisciplinary project between: * Epilepsy Center, University Hospital Freiburg * Bernstein Center for Computational Neuroscience (BCCN), Freiburg * Freiburg Center for Data Analysis and Modeling (FDM).

Proper citation: Electroencephalogram Database: Prediction of Epileptic Seizures (RRID:SCR_008032) Copy   

•   Source: SciCrunch Registry

http://fcon_1000.projects.nitrc.org/indi/pro/nyu.html

Datasets including a collection of scans from 49 psychiatrically evaluated neurotypical adults, ranging in age from 6 to 55 years old, with age, gender and intelligence quotient (IQ) information provided. Future releases will include more comprehensive phenotypic information, and child and adolescent datasets, as well as individuals from clinical populations. The following data are released for every participant: * At least one 6-minute resting state fMRI scan (R-fMRI) * * One high-resolution T1-weighted mprage, defaced to protect patient confidentiality * Two 64-direction diffusion tensor imaging scans * Demographic information (age, gender) and IQ-measures (Verbal, Performance, and Composite; Weschler Abbreviated Scale of Intelligence - WASI) * Most participants have 2 R-fMRI scans, collected less than 1 hour apart in the same scanning session. Rest_1 is always collected first.

Proper citation: NYU Institute for Pediatric Neuroscience Sample (RRID:SCR_010458) Copy   

•   Source: SciCrunch Registry

http://fcon_1000.projects.nitrc.org/indi/pro/VirginiaTech.html

Dataset including a T1 weighted anatomical image as well as two 10-minute resting state scans acquired during the same session from 25 psychiatrically screened healthy adults (community sample) ranging in age from 18 to 65 years old, with age, sex, education level, and ethnicity provided. Some subjects also returned several weeks after the first scan for a second scanning session. The number of days between scan sessions, for subjects that had two sessions, is indicated in the demographics spreadsheet. The study scanning protocol included: # 13 sec localizer # 4 minute 38 second T1 weighted anatomical # Subject given instructions for resting state scan #1 # 10 minute 4 second resting state scan #1 # Subject given instructions for resting state scan #2 # 10 minute 4 second resting state scan #2 Scanning was performed on one of three different 3T Siemens TIM TRIOs at the Human Neuroimaging Lab at Baylor College of Medicine in Houston, Texas. All scans were acquired using the standard Siemen''s TIM 12-channel head matrix. The resting state scans were acquired with a custom sequence that is a slight modification to the standard Siemen''s EPI sequence that supports real-time fMRI. Images were acquired slightly oblique to minimize dephasing in the orbito-frontal cortex. Detailed scanning parameters are included in separate .pdf files.

Proper citation: Virginia Tech Carilion Research Institute Sample (RRID:SCR_010459) Copy   

•   Source: SciCrunch Registry

https://marmotgraph.org

Knowledge graph system developed for managing and organizing rich metadata objects, initially for the Human Brain Project (HBP) and now extended to be a more generic, domain-agnostic solution. It is associated with CSCS (Swiss National Supercomputing Centre) and aims to provide a comprehensive toolset and API for working with knowledge graphs.

Proper citation: MarmotGraph (RRID:SCR_027452) Copy   

•   Source: SciCrunch Registry

https://imaging.uci.edu/fibre/

Facility for Imaging and Brain Research houses 3T Siemens Prisma scanner, mock scanner, and data analysis facilities. Research dedicated MRI scanning facility designed to suit wide range of basic and translational research programs by researchers across the UCI campus and beyond.

Proper citation: University of California at Irvine FIBRE Core Facility (RRID:SCR_027777) Copy   

•   Source: SciCrunch Registry

https://bican.mccarrolllab.org/app/bican?_inputs_&geneList=%22XIST%20PDE10A%20%20PENK%20PDYN%22&navbarPage=%22panelGeneExpr%22&plotExpressionButton=0&exprPlotUseCommonYScale=true&cellTypeSelector=%5B%22MSN%22%2C%22MSN_D1%22%2C%22MSN_D2%22%2C%22MSN_D1_matrix%22%2C%22MSN_D2_matrix%22%2C%22MSN_D1_striosome%22%2C%22MSN_D2_striosome%22%5D&exprPlotRegionSelector=%22Pu%22&GeneExprPlot_hover=null

Project provides data currently generated with support from the NIH Brain Initiative Cell Atlas Network (BICAN). Broad Institute collaboration supported by the NIH BRAIN Initiative, to create comprehensive atlas of cellular variation in the healthy human brain. It maps data from millions of cells across diverse individuals to understand how brain biology differs, helping researchers distinguish healthy variation from disease states.

Proper citation: Human Brain Variation Project (RRID:SCR_028065) Copy   

•   Source: SciCrunch Registry

https://github.com/SCANDAN-Team/SCANDAN-DICOM-labelling

Software tool for rules for DICOM tag based labelling. Regular expression used during the SCANDAN project to label MRI scans based on DICOM tag.

Proper citation: SCANDAN-DICOM-labelling (RRID:SCR_028365) Copy   

•   Source: SciCrunch Registry

http://www.ohsu.edu/xd/research/centers-institutes/onprc/

Center that aims to develop biomedical technologies using nonhuman primate (NHP) models. Its goal is to uncover the root causes of various disease and disorders, unlock secrets of the brain, and unleash new methods of diagnostics and treatment.

Proper citation: Oregon National Primate Research Center (RRID:SCR_008291) 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

https://kinarm.com/solutions/kinarm-end-point-lab/

Robotics research tool designed to make quantitative neurological assessments of sensorimotor, proprioception, and cognitive brain function by BKIN Technologies. Robotic manipulandum with display for studying arm movements. Allows to assess coordination of limbs at multiple joints while measuring joint specific force.

Proper citation: Kinarm: End-Point Lab (RRID:SCR_017060) Copy   

•   Source: SciCrunch Registry

http://www.incf.org/

Independent international facilitator catalyzing and coordinating global development of neuroinformatics aiming to advance data reuse and reproducibility in global brain research. Integrates and analyzes diverse data across scales, techniques, and species to understand brain function and positively impact the health and well being of society.

Proper citation: International Neuroinformatics Coordinating Facility (RRID:SCR_002282) Copy   

•   Source: SciCrunch Registry

http://www.sbtf.org/home.html

Founded in 1995, the Southeastern Brain Tumor Foundation (SBTF), a 501c3 not-for-profit charitable foundation, is devoted to improve the quality of life for brain tumor patients and their families. By offering information, education and support services, we aspire to instill hope, knowledge and comfort to all involved. The Southeastern Brain Tumor Foundation also raises funds for research and medical personnel so that a cure can be found. For over a decade, the SBTF has become a well-known fundraising entity supporting critical, cutting edge brain tumor research at major medical centers in the Southeast. Our annual Race for Research held in Atlanta, Georgia each summer, is our main fundraising event popular throughout Atlanta and the surrounding metropolitan area and has funded over $1.2 million dollars in research grants to leading researchers at major medical centers throughout the Southeast over the past decade. We are proud of our dedicated, all volunteer Board of Directors who meet monthly. Our Board is a diverse group comprised of individuals who''ve been touched by brain tumors in many different ways. Ranging from patients and family members to healthcare professionals; we are all committed to promoting the awareness of brain tumors in the community, communicating with patients and families and raising critical funds for research grants furthering advancements in the treatment of brain tumors. Our monthly support group, lead by a nurse practitioner, welcomes patients and their families to sit side by side with each other, share their experiences, communicate and receive support. As a neurosurgeon-scientist focused on the treatment of patients with brain tumors, I am committed to advancing the mission of SBTF forward in the fight against brain tumors. Our ability to serve the brain tumor community is dependent on each of you. Whether you support us with a financial donation in our fundraising efforts or with your time as a volunteer, each of you are a vital and integral part of our success and we thank you.

Proper citation: Southeastern Brain Tumor Foundation (RRID:SCR_004768) Copy   

•   Source: SciCrunch Registry

http://www.meduniwien.ac.at/kin/index.html

The (Clinical) Institute of Neurology (IN) of the Medical University Vienna was founded in 1882 by Heinrich Obersteiner. It is the oldest institution embracing the multidisciplinarity of neurosciences and has served as model for the establishment of similarly designed institutions in many countries. The original location of the then Neurological Institute in Vienna was at Schwarzspanierstrasse. Since 1993, IN is located in the Vienna General Hospital in top-class laboratory facilities. IN is committed to its proud tradition as Obersteiner Institute and to a promising future of a nationally and internationally leading institution in the clinical neurosciences. Our work aims to translate the understanding of nervous diseases to the development of novel therapeutics and diagnostics. IN''''s tasks include diagnostic patient service, research and graduate / postgraduate teaching in neuropathology, neurochemistry, and neuro-molecular biology in an integrated way. Neuropathology is a recognized medical specialty in Austria. It analyzes structural changes of nervous tissues in disease. Diagnostic neuropathology makes use of most modern morphological techniques applied to diseased central, peripheral and vegetative nervous tissues and fluids, and muscle. Neuropathological diagnoses are a basis for disease classification and rational therapies. Neurodegenerative disorders, in particular prion diseases, virus diseases affecting the nervous system, and brain tumors (neuro-oncology) are research priorities. In the highly publicized area of prion diseases, IN has developed into a national and international center of excellence and expertise that leads several European, EU-funded networks in prion research. As an indispensable asset, the IN possesses a large brain bank that has systematically collected neuropathological specimens since 1948. Most samples are fixed and paraffin-embedded tissue only, but in a part of neurosurgical, nerve and muscle biopsies and autopsies, also fresh tissue is obtained, frozen and stored at -80 degrees C. Occasionally blood and CSF are also available. The unique neuropathological collection of histological slides, paraffin blocks and formol-fixed nervous tissues now comprises about 16.000 brain autopsies, 30.000 neurosurgical and 7.500 nerve/muscle biopsies. Also a number of cell cultures have been stored, mainly fibroblasts from patients with rare neurometabolic diseases, and primary cultures of brain tumors. IN participates in the EU-supported European Network of Brain Banks BrainNet Europe.

Proper citation: Medical University of Vienna Institute of Neurology (RRID:SCR_005030) Copy   

•   Source: SciCrunch Registry

http://www.braintumorfunders.org/

The Brain Tumor Funders'' Collaborative is a partnership among five private philanthropic and advocacy organizations: American Brain Tumor Association, Brain Tumour Foundation of Canada, Children''s Brain Tumor Foundation, James S. McDonnell Foundation, and Sontag Foundation. This Collaborative promotes research directly relating to brain tumors and offers grants to professors and institutions to conduct research.

Proper citation: Brain Tumor Funders Collaborative (RRID:SCR_005104) Copy   

•   Source: SciCrunch Registry

https://alleninstitute.org/

Non profit bioscience research organization in Seattle, Washington dedicated to accelerating research globally and sharing that data within the science community. Allen Institute for Brain Science, Allen Institute for Cell Science, Allen Institute for Immunology, and The Paul G. Allen Frontiers Group are four divisions of this Institute with commitment to open science model within its research institutes.

Proper citation: Allen Institute (RRID:SCR_005435) Copy   

•   Source: SciCrunch Registry

http://gnif.org/

The GNIF is a non-profit charity organization for the advancement of neurological and mental health patient welfare, education, and research. We aim to further brain related studies, end mental health stigmatization and discrimination, improve the well-being of afflicted individuals, promote the free and open-access distribution of brain related information, and institute universal and multidisciplinary distance educational programs. The paramount GNIF mission is the betterment of neurological and mental health patient welfare, education, and research. With the development of novel free and open-access Therapeutic Recreational Centers, health promotion campaigns, and other charitable activities throughout the world, this organization can aid diagnosed individuals and their advocates. By presenting free and open-access information and educational courses via a distance, the GNIF aims to educate clinicians, teachers, scientists, patients, and the general public on neuroscience, medicine, psychology, biotechnology, and computer science. Moreover, the GNIF supports a variety of sound research programs ranging from biomedical to spiritual studies on the nature of the mind-body connection, biopsychosocial model of health and disease, and health psychology/behavioral medicine practices. The Global Neuroscience Initiative Foundation (GNIF) offers several projects and partnerships adherent to its missions. The following is an alphabetical listing of the GNIF Project Directory: * Brain Blogger * Brain Sciences & Neuropsychiatry * Distance Education Division * Ethics in Mental Health * Knowledge Center * Living with a Brain Disorder * Neuropsychiatry for Kids * Surgical Webcasts * Therapeutic Recreational Centers * Visual Brain Application

Proper citation: Global Neuroscience Initiative Foundation (RRID:SCR_005468) Copy   

•   Source: SciCrunch Registry