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http://sleep.alleninstitute.org

Collection of gene expression data in mouse brain for five different conditions of sleep and wakefulness to understand sleep deprivation and dynamic changes underlying sleep and wake cycles. Platform to generate cellular resolution expression data.

Proper citation: Allen Institute for Brain Science Sleep Study (RRID:SCR_002983) Copy   

•   Source: SciCrunch Registry

http://www.virtualflybrain.org

An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the adult Drosophila melanogaster brain.

Proper citation: Virtual Fly Brain (RRID:SCR_004229) Copy   

•   Source: SciCrunch Registry

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

Human brain atlases for adult, pediatric and elderly populations, by iterative joint deformable registration of training datasets into a single unbiased average image. Atlases packages include T1-weighted images, tissue priors (WM,GM,CSF), lobar parcellation maps and subcortical structures. Current available atlases: * Adult atlas: Symmetric atlas generated from 50+ healthy adult subjects (20-59 year old). * UNC-MNI Pediatric 1-year-old atlas: Symmetric atlas generated from 104 1-year-old subjects, combining children at high familial risk of autism and controls. * Pediatric 4-year-old atlas: Symmetric atlas generated from 10 4-year-old healthy subjects. * Elderly atlas: Atlas generated from 27 healthy elderly subjects (60+ years old). Additional information and acknowledgment for their usage can be found by clicking on the release notes.

Proper citation: UNC Human Brain Atlas (RRID:SCR_002606) Copy   

•   Source: SciCrunch Registry

http://aimlab.cs.uoregon.edu/NEMO/web/

THIS RESOURCE IS NO LONGER IN SERVICE. NIH tombstone webpage lists Project Period : 2009 - 2013. NIH funded project to create EEG and MEG ontologies and ontology based tools. These resources will be used to support representation, classification, and meta-analysis of brain electromagnetic data. Three pillars of NEMO are: DATA, ONTOLOGY, and DATABASE. NEMO data consist of raw EEG, averaged EEG (ERPs), and ERP data analysis results. NEMO ontologies include concepts related to ERP data (including spatial and temporal features of ERP patterns), data provenance, and cognitive and linguistic paradigms that were used to collect data. NEMO database portal is large repository that stores NEMO consortium data, data analysis results, and data provenance. EEG and MEG ontologies and ontology-based tools to support representation, classification, and meta-analysis of brain electromagnetic data. Raw EEG and ERP data may be uploaded to the NEMO FTP site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Neural ElectroMagnetic Ontologies (NEMO) Project (RRID:SCR_002001) Copy   

•   Source: SciCrunch Registry

http://cvr.yorku.ca/home/

The Centre for Vision Research focuses on interdisciplinary research into human and machine vision and visual processes, into vision's interactions with other senses and with motor and cognitive processes, and in applications such as visually-guided robotics or clinical diagnosis and treatment. The Centre for Vision Research includes the following major research themes: - Human Visual Performance - Visual Human-Computer Interaction, Graphics and Virtual Reality - Visual Psychophysics - Eye Movements and Hand-Eye Coordination - Computational Modeling and Computer Vision - Electrophysiology - Clinical and Developmental Studies - Brain Imaging

Proper citation: Centre for Vision Research (RRID:SCR_002879) Copy   

•   Source: SciCrunch Registry

http://cocomac.g-node.org/main/index.php?

Online access (html or xml) to structural connectivity ("wiring") data on the Macaque brain. The database has become by far the largest of its kind, with data extracted from more than four hundred published tracing studies. The main database, contains data from tracing studies on anatomical connectivity in the macaque cerebral cortex. Also available are a variety of tools including a graphical simulation workbench, map displays and the CoCoMac-Paxinos-3D viewer. Submissions are welcome. To overcome the problem of divergent brain maps ORT (Objective Relational Transformation) was developed, an algorithmic method to convert data in a coordinate- independent way based on logical relations between areas in different brain maps. CoCoMac data is used to analyze the organization of the cerebral cortex, and to establish its structure- function relationships. This includes multi-variate statistics and computer simulation of models that take into account the real anatomy of the primate cerebral cortex. This site * Provides full, scriptable open access to the data in CoCoMac (you must adhere to the citation policy) * Powers the graphical interface to CoCoMac provided by the Scalable Brain Atlas * Sports an extensive search/browse wizard, which automatically constructs complex search queries and lets you further explore the database from the results page. * Allows you to get your hands dirty, by using the custom SQL query service. * Displays connectivity data in tabular form, through the axonal projections service. CoCoMac 2 was initiated at the Donders Institute for Brain, Cognition and Behaviour, and is currently supported by the German neuroinformatics node and the Computational and Systems Neuroscience group at the Juelich research institute.

Proper citation: CoCoMac (RRID:SCR_007277) Copy   

•   Source: SciCrunch Registry

http://www.oasis-brains.org/

Project aimed at making neuroimaging data sets of brain freely available to scientific community. By compiling and freely distributing neuroimaging data sets, future discoveries in basic and clinical neuroscience are facilitated.

Proper citation: Open Access Series of Imaging Studies (RRID:SCR_007385) 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

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://www.brainnav.com

THIS RESOURCE IS NO LONGER IN SERVICE, documented December 31, 2013. An interactive atlas and 3D brain software for research, structure analysis, and education, it offers six atlases representing four species: the mouse, rat, monkey and human. The stereotaxic coordinates atlases are available for all four species and the rodent models have additional chemoarchitectonic atlases. BrainNavigator helps locate specific areas of the brain, making visualizing and experimental planning in the brain easier. *Plan: Browse 6 Atlases, Visualize with 3D models, Search Literature, Analyze gene expression, Identify connections *Publish: Access reference tools, Use and print images for publication, Search literature *Propose: Use and print images for proposals, Search literature, Locate gene expression in 2D and 3D, Identify connections *Produce: Simulate injections, Customize new coordinates, virtually slice sections, overlay atlas maps on your own images, create personal atlas maps With BrainNavigator, you''ll gain 24/7 access to their powerful 3D brain interactive software tool that helps further research in the neurosciences. In addition, their vast library of widely respected and referenced brain publications will provide a plethora of information on the most current brain research available. As publisher of the gold standard in brain atlas publications authored by the team around the leading brain cartographers George Paxinos and Charles Watson, they are pleased to bring an advanced tool to today''s neuroscientists and educators. Combining atlas content and 3D capabilities based on technologies from the Allen Institute for Brain Science, this online workflow solution brings brain research, analysis and education tools to your fingertips.

Proper citation: BrainNavigator (RRID:SCR_008289) 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

http://www.fmri.wfubmc.edu/cms/software

Research group based in the Department of Radiology of Wake Forest University School of Medicine devoted to the application of novel image analysis methods to research studies. The ANSIR lab also maintains a fully-automated functional and structural image processing pipeline supporting the image storage and analysis needs of a variety of scientists and imaging studies at Wake Forest. Software packages and toolkits are currently available for download from the ANSIR Laboratory, including: WFU Biological Parametric Mapping Toolbox, WFU_PickAtlas, and Adaptive Staircase Procedure for E-Prime.

Proper citation: Advanced Neuroscience Imaging Research Laboratory Software Packages (RRID:SCR_002926) Copy   

•   Source: SciCrunch Registry

http://www.brainmysteries.com

A blog featuring articles on the brain, consciousness, cognitive science, psychology and neurology. This resource is in Russian.

Proper citation: Brain Mysteries (RRID:SCR_000504) Copy   

•   Source: SciCrunch Registry

http://www.brain-connectivity-toolbox.net

A large selection of complex network measures in Matlab that are increasingly used to characterize structural and functional brain connectivity datasets. Several people have contributed to the toolbox, and if you wish to contribute with a new function or set of functions, please contact Olaf Sporns. All efforts have been made to avoid errors, but users are strongly urged to independently verify the accuracy and suitability of toolbox functions for the chosen application. Please report bugs or substantial improvements.

Proper citation: Brain Connectivity Toolbox (RRID:SCR_004841) Copy   

•   Source: SciCrunch Registry

http://www.thomaskoenig.ch/Lester/ibaspm.htm

The aim of this work is to present a toolbox for structure segmentation of structural MRI images. All programs were developed in MATLAB based on a widely used fMRI, MRI software package, SPM99, SPM2, SPM5 (Wellcome Department of Cognitive Neurology, London, UK). Other previous works have developed a similar strategy for obtaining the segmentation of individual MRI image into different anatomical structures using a standardized Atlas. Have to be mentioned the one introduced by Montreal Neurological Institute (MNI) that merges the information coming from ANIMAL (algorithm that deforms one image (nonlinear registration) to match previously labelled) and INSECT (Cerebral Tissue Classification) programs for obtaining a suitable gross cortical structure segmentation (Collins et al, 1999). Here both, nonlinear registration and gray matter segmentation processes have been performed through SPM99, SPM2, SPM5 subroutines. Three principal elements for the labeling process are used: gray matter segmentation, normalization transform matrix (that maps voxels from individual space to standardized one) and MaxPro MNI Atlas. All three are combined to yield a good performance in segmenting gross cortical structures. The programs here can be used in general for any standardized Atlas and any MRI image modality. System Requirements: 1. The IBASPM graphical user interface (GUI) runs only under MATLAB 7.0 or higher. The non-graphical version runs under MATLAB 6.5 or higher. 2. Statistical Parametrical Mapping Software SPM2, SPM5 Main Functions: * Atlasing: Main function ( This file contains spm_select script from SPM5 toolbox and uigetdir script from MATLAB 7.0 ). * Auto_Labeling : Computes individual atlas. * Create_SPAMs : Constructs Statistical Probability Anatomy Maps (SPAMs). * Create_MaxProb : Creates Maximum Probability Atlas (MaxPro) using the SPAMs previously computed. * All_Brain_Vol : Computes whole brain volume masking the brain using the segmentation files (if the segmentation files does not exist it segments). * Struct_Vol : Computes the volume for different structures based on individual Atlas previously obtained by the atlasing process. * Vols_Stats : Computes mean and standard deviation for each structure in a group of individual atlases.

Proper citation: IBASPM: Individual Brain Atlases using Statistical Parametric Mapping Software (RRID:SCR_007110) Copy   

•   Source: SciCrunch Registry

http://brainhealthregistry.org/

A website aimed at recruiting and assessing subjects for all types of neuroscience studies with the internet. The hope is to accelerate various types of observational studies and clinical trials, and also reduce costs. They are interested in having people, including healthy subjects of all ages, join the registry. Joining only takes a few minutes. The web-based project is designed to speed up cures for Alzheimer's, Parkinson's and other brain disorders. It uses online questionnaires and online neuropsychological tests (which are very much like online brain games).

Proper citation: Brain Health Registry (RRID:SCR_010230) Copy   

•   Source: SciCrunch Registry

https://support.inscopix.com/search/site/Mosaic

Mosaic software features apps designed to help you derive deeper insights from videos of large scale circuit dynamics by Inscopix Inc.

Proper citation: Mosaic (RRID:SCR_017408) Copy   

•   Source: SciCrunch Registry

https://github.com/dorianps/LESYMAP

Software R package to conduct lesion-to-symptom mapping from human MRI data.Takes lesion maps and cognitive performance scores from patients with stroke, and maps brain areas responsible for cognitive deficit.

Proper citation: LESYMAP (RRID:SCR_017967) Copy   

•   Source: SciCrunch Registry

http://blog.wholebraincatalog.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. The blog of the Whole Brain Catalog.

Proper citation: Whole Brain Catalog Blog (RRID:SCR_000582) Copy   

•   Source: SciCrunch Registry