rid,external_rid,resource_url,resource_name,description,scale,species,resource_type,measurement,application,area_of_study,user_support,resource_availability,parent_org,funding_agency 1,"PMC3508475 25048627",http://fcon_1000.projects.nitrc.org,1000 Functional Connectomes INDI Project,"The era of discovery science for human brain function was inaugurated by the collaborative launch of the 1000 Functional Connectomes Project (FCP) on December 11,2009,by leading members of the functional magnetic resonance imaging (fMRI) community. Following the precedent of full unrestricted data sharing, which has become the norm in molecular genetics, the FCP entailed the aggregation and public release (via www.nitrc.org) of over 1200 resting state fMRI (R-fMRI) datasets collected from 33 sites.",whole,primates,"database ontology & data mngmt.*",functional,"visualization* data analysis","cogn. & behav. neurosci. neuroinformatics*","user manual user forum citations",freeware,"ABIDE, ADHD-200 (ADHD200), INDI", 2,23943281,http://3dbar.org,3d Brain Atlas Reconstructor,3d Brain Atlas Reconstructor on-line service is a repository of three dimensional reconstructions of brain structures.,"whole* regions","rodents* primates others","atlas* software",anatomical,visualization,neuroinformatics,"user manual citations",freeware,Nencki Institute of Experimental Biology,infrastructural grant from the Polish Ministry of Regional Development POIG 3,23408326,http://people.cs.nctu.edu.tw/~percycat/4DSPA/,4D SPA,Here we present a supervised 4D Structural Plasticity Analysis (4D SPA) computer method to align and match 3-Dimensional neuronal structures across different time points on a semi-automated basis.,cellular,all,software,anatomical,"annotation data analysis*","neuroanatomy neuroinformatics*","user manual citations",freeware,"National Chiao Tung University, Hsin Chu, Taiwan","National Institutes of Health, Hahn Family Foundation, Nancy Lurie Marks Family Foundation, National Science Council" 4,nif-0000-00386,http://behav.org/abcd/abcd.php,ABCD: Avian Brain Circuitry Database,"Database developed for storing, retrieving and cross-referencing neuroscience information about the connectivity of the avian brain. It contains entries about the new and old terminology of the areas and their hierarchy, data on connections between brain regions, as well as a functional keyword system linked to brain regions and connections.",regions,others,"database* ontology & data mngmt. atlas","anatomical* functional",annotation,"neuroanatomy* neuroinformatics comput. neurosci. cogn. & behav. neurosci.","FAQs user manual citations",freeware,Szent Istvan University Faculty of Veterinary Science; Budapest; Hungary,OTKA Foundation 5,PMC3986524,http://www.irisa.fr/kerdata/abrain/,A-Brain,Joint genetic and neuroimaging data analysis on large cohorts of subjects is a new approach used to assess and understand the variability that exists between individuals. The project relies on Microsoft's Azure cloud platform and leverages the complementary expertise of KerData in the area of scalable cloud data management and Parietal team (Saclay) in the fi eld of neuroimaging.,"macromol. whole*",primates,"software instrumentation*",functional,"data analysis* modeling & simulation","cogn. & behav. neurosci.* cell., mol., & syst. neurosci.",user manual,,"KerData Team, INRIA Rennes", 6,24993814,http://diffusiontools.com/,ACID - Artefact correction in diffusion MRI,"The Artefact correction in diffusion MRI (ACID) toolbox is an academic software toolkit for pre-processing of diffusion MRI data, estimation of DTI indices and spatially normalization of DTI index maps, which fully integrates into the batch system of SPM8.",regions,primates,software,anatomical,"visualization* data analysis","comput. neurosci.* cogn. & behav. neurosci.","user manual citations",open source,"UCL Institute of Neurology, London",Wellcome Trust 7,nif-0000-11872,http://www.addgene.org,Addgene - plasmid sharing portal,"Non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. They work with laboratories to assemble a high-quality library of published and useful plasmids and their associated cloning / sequence data for use in research and discovery. By linking plasmids with articles, scientists can always find data related to the materials they request.",macromol.,"mammals* insects","database* topical portal","biochemical* functional",data analysis,"cell., mol., & syst. neurosci.","FAQs user manual citations","freeware* licensed",,Fees collected from plasmid sales support operation of the repository. 8,"24338729 PMC4058415",http://adni-info.org,ADNI,"Since 2005, the longitudinal Alzheimer's Disease Neuroimaging Initiative (ADNI) has been validating the use of biomarkers including blood tests, tests of cerebrospinal fluid, and MRI/ PET imaging for Alzheimer's disease (AD) clinical trials and diagnosis.",whole,primates,database,anatomical,visualization,clinical & dev. neurobiol.,"user manual citations",freeware,"University of California, San Francisco",National Institute on Aging; National Institute of Biomedical Imaging and Bioengineering; Alzheimer's Association and Alzheimer's Drug Discovery Foundation; U.S. Food and Drug Administration 9,PMC3578208,http://afni.nimh.nih.gov/afni/suma,AFNI/SUMA Software,SUMA is a program that adds cortical surface based functional imaging analysis to the AFNI suite of programs.,"regions* whole",primates,software,"functional* anatomical","visualization* data analysis","neuroinformatics* cogn. & behav. neurosci.","FAQs user manual user forum citations",freeware,"NIMH, NIH, DHHS", 10,nif-0000-23326,http://www.uwaging.org/genesdb/,Aging Genes Database,A database of genes and interventions connected with aging phenotypes including those with respect to their effects on life-span or age-related neurological diseases.,macromol.,all,database,functional,annotation,"neuroinformatics clinical & dev. neurobiol.*","user manual citations",freeware,University of Washington; Washington; USA,Ellison Medical Foundation 11,PMC2525865,http://brain-map.org,Allen Brain Atlas,A data portal of Allen brain institute to access the high-resolution genome wide atlases for developing and adult mouse and human brains together with neural connectivity maps.,"whole* regions","rodents* primates","atlas* database ontology & data mngmt.",anatomical,"visualization* data analysis annotation","cell., mol., & syst. neurosci.* neuroanatomy neuroinformatics clinical & dev. neurobiol.","FAQs user manual user forum blog/social networking citations",freeware,Allen institute,Allen institute 12,PMC4033128,http://www.socsci.uci.edu/~jkrichma/ABADV/,Allen Brain Atlas-Driven Visualizations (ABADV),A web-based application created for visualizing expression energy data from the Allen Brain Atlas (ABA).,macromol.,rodents,software,functional,visualization,"neuroinformatics cell., mol., & syst. neurosci.*",user manual,open source,"University of California, Irvine",Intelligence Advanced Research Projects Activity (IARPA) 13,PMC3374366,http://allmanlab.caltech.edu,Allman lab: microscopic anatomy of cerebral cortex,"In our laboratory, we are mainly concerned with brain evolution as revealed through the comparative study of brain structure and with the neural mechanisms of economic and social decision-making.","cellular* regions whole",mammals,topical portal,"anatomical* functional","visualization* annotation","neuroanatomy* cogn. & behav. neurosci. clinical & dev. neurobiol.","user manual citations",freeware,"California Institute of Technology, Pasadena, CA, USA",James S. McDonnell Foundation 14,nif-0000-20935,http://amigo.geneontology.org,AmiGO,AmiGO 2 is a project to create the next generation of AmiGO--the current official web-based set of tools for searching and browsing the Gene Ontology database.,macromol.,all,"database* ontology & data mngmt.","biochemical* physiological","annotation* visualization","neuroinformatics* cell., mol., & syst. neurosci.","user manual user forum citations",freeware,GO,National primates Genome Research Institute 15,nif-0000-07730,http://antibodyregistry.org,Antibody Registry,Public registry of antibodies with unique identifiers for commercial and non-commercial antibody reagents to give researchers a way to universally identify antibodies used in publications.,macromol.,all,"database* ontology & data mngmt. topical portal",biochemical,annotation,"neuroinformatics* cell., mol., & syst. neurosci.","user manual citations",freeware,NIF, 16,PMC4009425,http://picsl.upenn.edu/software/ants/,ANTS,Advanced Normalization Tools (ANTs) extracts information from complex datasets that include imaging. ANTs development is led by Brian Avants and supported by other researchers and developers at PICSL and other institutions.,"whole regions*",primates,"software ontology & data mngmt.*",anatomical,"data analysis annotation*","neuroinformatics clinical & dev. neurobiol.*","user manual user forum citations",open source,Penn Image Computing & Science Lab, 17,25433513,https://github.com/stnava/ANTsR,ANTsR,To interface the supervised learning capabilities of the random forest model with regularized probabilistic segmentation using the recently developed ANTsR package a comprehensive statistical and visualization interface between the popular Advanced Normalization Tools (ANTs) and the R statistical project.,"whole* regions",primates,software,anatomical,"annotation data analysis visualization*","clinical & dev. neurobiol.* cogn. & behav. neurosci. neuroinformatics",user manual,open source,University of Virginia,NIH 18,24234916,http://talkbank.org/AphasiaBank/,AphasiaBank,AphasiaBank is construction of a shared database of multimedia interactions for the study of communication in aphasia. The ultimate goal of this work is the improvement of evidence-based therapy for aphasia.,whole,primates,"database* ontology & data mngmt.",functional,"visualization* annotation","cogn. & behav. neurosci. clinical & dev. neurobiol.* neuroinformatics","user manual citations",freeware,AphasiaBank consortium,NIH-NIDCD 19,10.4249/scholarpedia.1463 ,http://iridia.ulb.ac.be/argos,ARGoS,"ARGoS is a state-of-the-art, open source robot simulator. Its main design focus is the simulation of large heterogeneous swarms of robots.",whole,all,software,functional,neurotechnology,cognitive & behavioral neuroscience,"user manual user forum citations",freeware,Swarmanoid project, ERC Advanced Grant E-SWARM 20,PMC3427544,http://www.nitrc.org/projects/artifact_detect,Artifact Detection Tools (ART),"Toolbox for post-processing fMRI data. Includes software for comprehensive analysis of sources of artifacts in timeseries data including spiking and motion. Most compatible with SPM processing, but adaptable for FSL as well.","whole regions*",primates,software,"functional* anatomical","data analysis* visualization","cogn. & behav. neurosci.* neuroinformatics","user manual user forum citations",open source,MIT,NIH 21,PMC3741535,http://www.sci.utah.edu/software/atlaswerks.html,AtlasWerks,AtlasWerks is an open-source (BSD license) software package for medical image atlas generation.,"whole regions*",primates,software,anatomical,visualization,"neuroanatomy clinical & dev. neurobiol.* neuroinformatics",user manual,open source,Scientific Computing and Imaging Institute (SCI), 22,PMC4174732,http://audacity.sourceforge.net/,Audacity,"Audacity is free, open source, cross-platform software for recording and editing sounds.",whole,primates,"software* instrumentation",functional,neurotechnology,cogn. & behav. neurosci.,"user manual user forum FAQs citations",open source,,runs on donations 23,21573886,http://cvlab.epfl.ch/research/medical/lm,Automated Reconstruction of Complex Curvilinear Structures,"A novel probabilistic approach to fully automated delineation of tree structures in noisy 2D images and 3D image stacks. Unlike earlier methods that rely mostly on local evidence, ours builds a set of candidate trees over many different subsets of points likely to belong to the optimal tree and then chooses the best one according to a global objective function that combines image evidence with geometric priors.",cellular,rodents,software,anatomical,"visualization* data analysis","neuroanatomy* comput. neurosci. neuroinformatics","user manual citations",,"Cole Polytechnique Fedarale de Lausanne, Switzerland", 24,PMC3885811,http://www.nitrc.org/projects/autoseg/,AutoSeg,AutoSeg is a novel C++ based application developped at UNC-Chapel Hill that performs automatic brain tissue classification and structural segmentation.,"regions whole*",primates,"software atlas*",anatomical,"visualization* annotation","neuroinformatics* neuroanatomy","user manual user forum citations",open source,University of north carolina chapell hill,NIH 25,nif-0000-90175,http://brancusi.usc.edu,BAMS Cells,BAMS is an online resource for information about neural circuitry.,"cellular* regions",rodents,"database* ontology & data mngmt.",anatomical,annotation,"neuroanatomy* neuroinformatics","user manual citations",freeware,Brain Architecture Management System,"NIMH, NINDS, NIBIB" 26,PMC4224204,http://www.ncbi.nlm.nih.gov/sites/batchentrez,Batch Entrez,"Allows to upload a file of GIs or accession numbers from the Nucleotide or Protein databases, or upload a list of record identifiers from other Entrez databases",macromol.,all,software,functional,data analysis,"cell., mol., & syst. neurosci. neuroinformatics*","user manual citations",freeware,NCBI,NIH 27,PMC3499764,http://www.schalklab.org/research/bci2000,BCI2000,"BCI2000 is a general-purpose system for brain-computer interface (BCI) research. It can also be used for data acquisition, stimulus presentation, and brain monitoring applications.",whole,primates,"software instrumentation*",physiological,"neurotechnology* data analysis","cell., mol., & syst. neurosci.","user manual user forum citations",freeware,Wadsworth Center of the New York State Department of Health,NIH/NIBIB 28,PMC4224204,http://insitu.fruitfly.org/cgi-bin/ex/insitu.pl,Berkeley Drosophila Genome Project (BDGP),"We use high throughput 96-well plate RNA in situ protocol to determine patterns of gene expression during embryogenesis for Drosophila genes represented in non-redundant sets of Drosophila ESTs, the DGC collections and the Drosophila Gold Collection.",macromol.,insects,"database* ontology & data mngmt.","anatomical* functional","annotation visualization data analysis*","cell., mol., & syst. neurosci.* neuroinformatics","user manual FAQs citations",freeware,"Lawrence Berkeley National Laboratory, Berkeley CA", 29,PMC3437523,http://besa.de,BESA: Brain Electrical Source Analysis,"BESA GmbH consists of three business units: BESA Research, BESA Clinical and BESA Systems. The first two business units continuously develop state-of-the-art software for researchers and clinicians in the field of EEG/MEG. Our tools provide the latest technology in a user-friendly, workflow-orientated environment. BESA Systems offers individual software solutions for customers.","whole* regions",primates,software,"physiological* anatomical","data analysis* visualization","clinical & dev. neurobiol.* cogn. & behav. neurosci.","user manual citations",licensed,, 30,nif-0000-24919,http://biocompare.com,Biocompare,A web catalog of over 1M antibodies from hundreds of different companies and other research supplies. Biocompare has made large quantities of data available to the antibodyregistry.org facilitating tagging important research reagents to literature and continues to work with the antibody registry.,"macromol.* cellular",all,"database* ontology & data mngmt.",biochemical,"annotation* visualization","neuroinformatics* cell., mol., & syst. neurosci.","FAQs user manual user forum blog/social networking citations","licensed* freeware",NA,NA 31,nif-0000-00432,http://thebiogrid.org,BioGRID,"A curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts.",macromol.,all,"database* software",biochemical,annotation,"cell., mol., & syst. neurosci. neuroinformatics*","user manual user forum citations",freeware,"Princeton University; New Jersey; USA, University of Edinburgh; Scotland; United Kingdom, Mount Sinai Hospital; Ontario; Canada, University of Montreal; Montreal; Canada","NIH, BBSRC, CIHR, IRSC" 32,23319241,http://bioimagesuite.org,BioImage Suite,BioImage Suite is an integrated image analysis software suite developed at Yale University. BioImage Suite has extensive capabilities for both neuro/cardiac and abdominal image analysis and state of the art visualization.,"whole* regions",primates,software,"anatomical* functional",visualization,"clinical & dev. neurobiol.* cogn. & behav. neurosci. neuroinformatics","user manual user forum citations",freeware,Yale University,"NIH, NIBIB" 33,10.4249/scholarpedia.3036,http://www.ebi.ac.uk/biomodels-main/,BioModels Database,BioModels Database is a repository of computational models of biological processes. Models described from literature are manually curated and enriched with cross-references.,macromol.,all,"database ontology & data mngmt.*",biochemical,"modeling & simulation* annotation","cell., mol., & syst. neurosci.* neuroinformatics comput. neurosci.","user manual FAQs citations",freeware,EMBL-EBI,EMBL-EBI 34,"PMC3338117 Nif-0000-23346",http://bioportal.bioontology.org,Bioportal,Open repository of biomedical ontologies that provides access via Web browsers and Web services to ontologies.,all,all,ontology & data mngmt.,all,annotation,"clinical & dev. neurobiol.* neuroinformatics cogn. & behav. neurosci.","user manual user forum blog/social networking citations",freeware,"National Center for Biomedical Ontology, Stanford University; California; USA","NHGRI, the NHLBI, and the NIH Common Fund" 35,PMC3437523,http://www.biosemi.com,BioSemi ActiveTwo system,"ActiveTwo: 280-channel, DC amplifier, 24-bit resolution, biopotential measurement system with Active Electrodes",whole,primates,"instrumentation* software",physiological,"data analysis* neurotechnology","cogn. & behav. neurosci.* cell., mol., & syst. neurosci.","FAQs user manual user forum citations","licensed* freeware open source",, 36,PMC3930095,http://biosig.sourceforge.net,BioSig,"BioSig is an open source software library for biomedical signal processing, featuring for example the analysis of biosignals such as the electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), respiration, and so on.",whole,primates,software,physiological,data analysis,"neuroinformatics* cogn. & behav. neurosci. clinical & dev. neurobiol.","user manual user forum citations",open source,, 37,nif-0000-00241,http://flystocks.bio.indiana.edu/bloomhome.htm,Bloomington Drosophila Stock Center,"Collects, maintains and distributes Drosophila melanogaster strains for research. Emphasis is placed on genetic tools that are useful to a broad range of investigations.","whole* cellular macromol.",insects,"database* ontology & data mngmt.","anatomical functional*",annotation,"cell., mol., & syst. neurosci.* neuroinformatics","user manual citations","licensed* freeware",Indiana University,NIH 38,nif-0000-10378,http://bmi.neuroinf.jp,BMI-Platform,Brain Machine Interface Platform (BMI PF) accumulates BMI(Brain Machine Interface)-related data that are useful for education and experiment.,whole,primates,"database* software","physiological* functional",modeling & simulation,"cogn. & behav. neurosci.* comput. neurosci.","user manual citations",freeware,"Neuroinformatics Japan Center, RIKEN Brain Science Institute", 39,PMC3539731,http://bostonretinalimplant.org,Boston Retinal Implant Project,"The Boston Retinal Implant Project is dedicated to helping patients with any form of visual impairment. Our""Smart""glasses can be used to help patients with congenital or acquired blindness. Our retinal prosthesis is designed to help patients with certain forms of acquired blindness, specifically""outer retinal blindness""like RP and AMD.","regions* whole",primates,"instrumentation* software",functional,neurotechnology,"clinical & dev. neurobiol.* cell., mol., & syst. neurosci. cogn. & behav. neurosci.","user manual citations",licensed,, 40,23893006,http://www.cbica.upenn.edu/sbia/braid/,BRAID: Brain Image Database,The BRAin Image Database (BRAID) is a large-scale archive of normalized digital spatial and functional data with an analytical query mechanism.,"whole regions*",primates,"database* software",anatomical,"visualization* data analysis","clinical & dev. neurobiol.* neuroinformatics","user manual citations",open source,"Department of Radiology University of Pennsylvania",NIH 41,20882369,https://sites.google.com/site/bctnet/,Brain Connectivity Toolbox,contains a large selection of complex network measures in Matlab. These measures are increasingly used to characterize structural and functional brain connectivity datasets.,"regions* whole","primates Others*","software* ontology & data mngmt.",anatomical,"visualization modeling & simulation data analysis*","neuroinformatics* cogn. & behav. neurosci.","user manual citations",open source,Indiana University, 42,"PMC3515865 nif-0000-00019 21789500",http://braininfo.rprc.washington.edu,Brain Info,Portal to neuroanatomical information on the Web that helps you identify structures in the brain and provides a variety of information about each structure by porting you to the best of 1500 web pages at 100 other neuroscience sites.,"regions* whole",mammals,"ontology & data mngmt.* database",anatomical,"annotation* visualization","neuroanatomy* neuroinformatics","user manual citations",freeware,"University of Washington; Washington; USA, University of California at San Diego; California; USA","NLM, NIH Office of the Director, The primates Brain Project., NCRR, NIMH, NIBIB" 43,24085487,http://bodb.usc.edu/bodb,Brain Operations Database (BODB),"An environment for documenting how a model for cognitive or systems neuroscience is linked to relevant Brain Operating Principles (BOPs), brain regions modeled, Summaries of the Experimental Data (SEDs) used to design the model, and comparisons between Summaries of Simulation Results (SSRs) and SEDs used to test the model.","whole* regions",primates,database,physiological,"modeling & simulation* visualization","cogn. & behav. neurosci.* comput. neurosci. neuroinformatics","user manual citations",freeware,University of Southern California Brain Project (USCBP),NSF 44,10.1007/s12021-014-9219-4,http://brainbase.imp.ac.at,BrainBase,"The BrainBase database, the web application BrainBaseWeb and the desktop application BrainGazer that can be used to access its content is the result of several joint projects of the Dickson Group","cellular* regions",insects,software,anatomical,"data analysis* visualization","neuroinformatics* comput. neurosci. neuroanatomy","user manual citations",freeware,"CIR Lab, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, Austria","the European Union, the Austrian Sciences Fund" 45,10.1007/s12021-012-9171-0,http://bbci.de/competition/iii,Brain-Computer Interfaces competition III,"The goal of the""BCI Competition III""is to validate signal processing and classification methods for Brain-Computer Interfaces (BCIs).",whole,primates,"ontology & data mngmt.* instrumentation topical portal",physiological,"data analysis* neurotechnology","neuroinformatics* cell., mol., & syst. neurosci. cogn. & behav. neurosci.","user manual citations",freeware,"Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands","BrainGain Smart Mix Programme of the Netherlands Ministry of Economic Affairs and the Netherlands Ministry of Education, Culture and Science" 46,"nlx_149360 21373993",http://brain-development.org,brain-development.org,"Data set of nearly 600 MR images from normal, healthy subjects, along with demographic characteristics, collected as part of the Information extraction from Images (IXI) project available for download. Tar files containing T1, T2, PD, MRA and DTI (15 directions) scans from these subjects are available.","whole* regions",primates,"software* atlas ontology & data mngmt.",anatomical,"data analysis* annotation","clinical & dev. neurobiol.* neuroinformatics","user manual citations",freeware,Imperial College London; London; United Kingdom,EPSRC 47,10.1007/s12021-010-9083-9,http://brainknowledge.ee.ntu.edu.tw,BrainKnowledge: A Human Brain Function Mapping Knowledge-Base System,We present a human brain function mapping knowledge-base (BrainKnowledge) system that integrates the fMRI results and information in the fMRI literature together.,"whole* regions",primates,"software* ontology & data mngmt.","functional* anatomical","visualization* annotation",neuroinformatics,"user manual citations",freeware,"Department of Electrical Engineering, National Taiwan University, Taiwan",National Science Council (Taiwan) 48,"10.1007/s12021-013-9182-5 nlx_91840",http://brainliner.jp,BrainLiner,Portal and tools for sharing and editing neurophysiological and behavioral data for brain-machine interface research.,"whole* regions cellular",mammals,"database* software","physiological* functional anatomical","modeling & simulation* data analysis","cogn. & behav. neurosci.* comput. neurosci.","user manual blog/social networking citations",freeware,ATR; Kyoto; Japan,Japanese Ministry of Education Culture Sports Science and Technology (MEXT) 49,10.1007/s12021-011-9125-y,http://brainmap.org,Brainmap.org,"BrainMap is a database of published functional and structural neuroimaging experiments with coordinate-based results (x,y,z) in Talairach or MNI space. The goal of BrainMap is to develop software and tools to share neuroimaging results and enable meta-analysis of studies of human brain function and structure in healthy and diseased subjects.","whole* regions",primates,"database* software ontology & data mngmt.","anatomical* functional","modeling & simulation* data analysis annotation","cogn. & behav. neurosci.* neuroinformatics","user manual user forum citations",freeware,University of Texas Health Science Center San Antonio.,NIMH 50,nif-0000-00093,http://brainmaps.org,BrainMaps.org,"An interactive multiresolution brain atlas that is based on over 20 million megapixels of sub-micron resolution, annotated, scanned images of serial sections of both primate and non-primate brains and integrated with a high-speed database for querying and retrieving data about brain structure and function. Currently featured are complete brain atlas datasets for various species, including Macaca mulatta, Chlorocebus aethiops, Felis catus, Mus musculus, Rattus norvegicus, Tyto alba and many other vertebrates. BrainMaps is currently accepting histochemical, immunocytochemical, and tracer connectivity data, preferably whole-brain. In addition, they are interested in EM, MRI, and DTI data.","whole* regions","primates* rodents others","database* atlas ontology & data mngmt.",anatomical,"visualization* annotation","neuroanatomy* neuroinformatics","user manual citations",freeware,University of California at Davis; California; USA,NIH 51,PMC3607831,http://www.nitrc.org/projects/bnv,BrainNet Viewer,"BrainNet Viewer is a brain network visualization tool, which can help researchers to visualize structural and functional connectivity patterns from different levels in a quick, easy, and flexible way.","regions whole*",primates,software,"anatomical* functional",visualization,"neuroinformatics neuroanatomy* clinical & dev. neurobiol.","user manual user forum citations",open source,Beijing Normal University,Beijing Natural Science Foundation 52,24081830,https://github.com/evl2001/brainography,Brainography,A customizable network visualization tool that creates three-dimensional brain representations based on any choice of cortical or subcortical parcellation of a brain.,regions,"primates* rodents",software,anatomical,"visualization* data analysis modeling & simulation","neuroanatomy* neuroinformatics",user manual,open source,"Weill Cornell Medical College, New York, NY","Leon Levy Foundation Neuroscience Fellowship, NIH" 53,23836390,http://www.nitrc.org/projects/brainparser,BrainParser,Brain Parser software uses a novel statistical-learning technique to segment brain regions of interest (ROIs) based on a training set of data and generates 3D MRI volumes.,"regions* whole",primates,software,anatomical,visualization,"neuroinformatics* neuroanatomy","user manual user forum citations",open source,"University of California, San Diego", 54,PMC3539731,http://brainscales.kip.uni-heidelberg.de,BrainScaleS,The BrainScaleS project aims at understanding function and interaction of multiple spatial and temporal scales in brain information processing.,regions,all,"instrumentation* software",functional,neurotechnology,"cell., mol., & syst. neurosci.* cogn. & behav. neurosci.","user manual citations","freeware* licensed",Ruprecht-Karls-Universitat Heidelberg,EU FET-Proactive FP7 55,nlx_23971,http://brainspan.org,BrainSpan: Exon microarray summarized to genes,"BrainSpan, an atlas of the developing human brain, is designed as a foundational resource for studying transcriptional mechanisms involved in human brain development. One of the BrainSpan datasets, Exon microarray summarized to genes, is presented. It is a downloadable archive of files containing normalized RNA-Seq expression values for analysis.",regions,primates,"atlas* database ontology & data mngmt.",biochemical,"visualization* data analysis annotation","clinical & dev. neurobiol.* neuroanatomy neuroinformatics","user manual blog/social networking citations",freeware,Brainspan consortium,NIMH 56,PMC4052339,http://neuroimage.usc.edu/brainstorm/,Brainstorm Toolbox,"Brainstorm is a collaborative, open-source application dedicated to MEG/EEG/sEEG/ECoG data analysis (visualization, processing and advanced source modeling).",whole,primates,"software* instrumentation ontology & data mngmt.","physiological* anatomical",data analysis,"cogn. & behav. neurosci.* cell., mol., & syst. neurosci.","user manual user forum blog/social networking citations",open source,"McGill University, Montreal, QC Canada",NIH 57,21698393,http://www.nitrc.org/projects/brainvisa_ext,BrainVisa,"It contains tools to measure global and regional gyrification, gray matter thickness and sulcal and gyral white matter spans.",regions,primates,software,anatomical,"visualization data analysis*","neuroinformatics neuroanatomy*","user manual user forum citations",open source,"Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA",National Institute of Biomedical Imaging and Bioengineering 58,nif-0000-00064,http://neuro.imm.dtu.dk/services/jerne/brede/,Brede Database,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.,whole,primates,"database* ontology & data mngmt.","functional* anatomical","annotation* data analysis","cogn. & behav. neurosci. neuroinformatics*","user manual citations",freeware,Technical University of Denmark; Lyngby; Denmark,"EU, (Project MAPAWAMO)" 59,20857234,http://briansimulator.org/,BrianSimulator.Org,"Brian is a simulator for spiking neural networks available on almost all platforms. The motivation for this project is that a simulator should not only save the time of processors, but also the time of scientists.",all,all,software,functional,modeling & simulation,"cell., mol., & syst. neurosci.* comput. neurosci.","FAQs user manual user forum blog/social networking citations",open source,"Universitat Paris Descartes, Paris, France",European Research Council 60,10.1007/s12021-014-9232-7,https://bitbucket.org/btorb/btmorph,BTMorph,Small Python library containing a data structure and tools to represent and analyze neuronal morphologies stored in the de facto standard SWC format,cellular,all,software,anatomical,"data analysis* visualization","neuroinformatics* neuroanatomy","user manual user forum citations",open source,"Computational Neuroscience Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan", 61,25129841,http://www.bigr.nl,CADDementia,"The Biomedical Imaging Group Rotterdam aims at developing and validating advanced techniques for the processing and analysis of large, complex, and heterogeneous medical and biological image data sets.","whole* regions",primates,"topical portal software*",anatomical,"data analysis modeling & simulation*","clinical & dev. neurobiol.* cogn. & behav. neurosci. neuroinformatics",user manual,freeware,Erasmus MC: University Medical Center Rotterdam,Netherlands Organization for Scientific Research 62,nif-0000-00240,http://www.cbs.umn.edu/research/resources/cgc,Caenorhabditis Genetics Center,"Acquires, maintains, and distributes genetic stocks and information about stocks of the small free-living nematode Caenorhabditis elegans for use by investigators initiating or continuing research on this genetic model organism.",whole,others,"ontology & data mngmt.* database",biochemical,annotation,"clinical & dev. neurobiol.* neuroinformatics","user manual FAQs","freeware licensed*",University of Minnesota; Minnesota; USA,NIH 63,PMC3417225,http://www.nitrc.org/projects/candi_share,CANDI Neuroimaging Access Point,"The Child and Adolescent NeuroDevelopment Initiative (CANDI) at UMass Medical School is making available a series of structural brain images, as well as their anatomic segmentations, demographic and behavioral data and a set of related morphometric resources (static and dynamic atlases).",regions,primates,"software atlas*",anatomical,visualization,"neuroinformatics clinical & dev. neurobiol.* neuroanatomy cogn. & behav. neurosci.","user manual user forum",open source,University of Massachusetts Medical School,NIH-NIMH 64,PMC4038780,http://www.lcs.poli.usp.br/~baccala/pdc/canon/,Canonical Block/Canonical PDC/DC Module,"Partial directed coherence (PDC) and directed coherence (DC) which describe complementary aspects of the directed information flow between pairs of univariate components that belong to a vector of simultaneously observed time series have recently been generalized as bPDC/bDC, respectively",regions,all,software,functional,modeling & simulation,"cell., mol., & syst. neurosci.* comput. neurosci.",user manual,open source,Princeton University, 65,PMC4152885,https://capocaccia.ethz.ch/capo/wiki/2015,Capo Caccia Cognitive Neuromorphic Engineering Workshop,"This is a very unconventional and exciting workshop where we bring together experts in neuroscience, neuromorphic engineering, cognitive sciences and robotics to discuss about the open problems in these fields and attempt to find routes to their resolution.",whole,all,"topical portal ontology & data mngmt.*",functional,"annotation neurotechnology*","cell., mol., & syst. neurosci. neuroinformatics*","user manual citations",freeware,ETH Zurich,iniForum 66,"PMC3546310 nif-0000-00016",http://brainvis.wustl.edu/wiki/index.php/Caret:About,Caret,"Caret is a free, open-source, software package for structural and functional analyses of the cerebral and cerebellar cortex. Caret runs on Apple (Mac OSX), Linux, and Microsoft Windows operating systems.","whole* regions",primates,software,"functional* anatomical",visualization,cogn. & behav. neurosci.,"user forum blog/social networking citations",freeware,"Washington University School of Medicine, Saint Louis, Missouri","primates Brain Project, NSF, NIMH, NCI, NLM, NASA, National Partnership for Advanced Computational Infrastructure" 67,24497233,http://www.socsci.uci.edu/~jkrichma/CARLsim/,CARLsim,CARLsim is an efficient C/C++-based Spiking Neural Network (SNN) simulator that allows execution on both generic x86 CPUs and standard off-the-shelf GPUs.,"whole regions*",all,software,functional,modeling & simulation,"comput. neurosci.* cogn. & behav. neurosci.","user manual citations",open source,"University of California, Irvine",Defense Advanced Research Projects Agency (DARPA) 68,PMC4005939,http://www.carmen.org.uk/,CARMEN,CARMEN is an online collaborative Virtual Laboratory (VL) for neurophysiology that provides data and analysis resources.,"cellular* regions whole",all,"software* ontology & data mngmt. topical portal",physiological,"data analysis* annotation modeling & simulation","cell., mol., & syst. neurosci.* neuroinformatics comput. neurosci.","user manual citations",freeware,"Computer Science Department at the University of York, UK,",Biotechnology and Biological Sciences Research Council (UK) 69,PMC4224098,http://www.sci.utah.edu/software/chm.html,Cascaded Hierarchical Model (CHM),"Cascaded hierarchical model is an image segmentation framework, which learns contextual information in a hierarchical framework.","cellular macromol.*",all,software,anatomical,"annotation* visualization modeling & simulation","neuroinformatics comput. neurosci.*","user manual citations",open source,The University of Utah, 70,nif-0000-00007,http://ccdb.ucsd.edu,Cell centered database (CCDB),"Database for high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging that makes unique and valuable datasets available to the scientific community for visualization, reuse and reanalysis.",cellular,"rodents* primates insects others","database* ontology & data mngmt.",anatomical,"visualization* annotation","cell., mol., & syst. neurosci.* neuroanatomy neuroinformatics","user manual citations",freeware,University of California at San Diego; California; USA,"NCRR, The primates Brain Project., NSF, NIDA, NIMH, NIBIB" 71,"nif-0000-20828 10.4249/scholarpedia.3036",http://cellml.org/models,CellML,"Repository of biological models created using CellML, a free, open-source, extensible markup language based standard for defining mathematical models of cellular function.",cellular,all,"software* database ontology & data mngmt.","anatomical functional physiological*",modeling & simulation,"comput. neurosci.* cell., mol., & syst. neurosci. neuroinformatics","user manual citations",open source,CellML,"Wellcome Trust, Royal Society of New Zealand, (Maurice Wilkins Centre for Molecular Biodiscovery)" 72,20361275,http://nba.uth.tmc.edu/cds/,Cellular Dynamic Simulator (CDS),"CDS was designed to simulate diffusion and chemical reactions within crowded molecular environments. CDS employs an event driven algorithm that allows precise calculation of the timing of collisions, reactions and other events for each molecule in the environment.",macromol.,all,software,biochemical,"modeling & simulation* visualization","comput. neurosci.* cell., mol., & syst. neurosci.","user manual citations",open source,University of Texas,NIH 73,10.4249/scholarpedia.3036,http://cor.physiol.ox.ac.uk/,Cellular Open Resource (COR),"COR (Cellular Open Resource) is a Microsoft Windows environment for cellular modeling that is built CellML (except for reactions and metadata which are not supported). It offers, through CellML, an""out of the box""access to a large database of single cell models.",cellular,all,software,physiological,modeling & simulation,"comput. neurosci.* cell., mol., & syst. neurosci. neuroinformatics","user manual FAQs citations",open source,University of Oxford, 74,10.4249/scholarpedia.5749,http://www.cnns.org/,Center for network neuroscience,"The UNT Center for Network Neuroscience was established January 1, 1987 to facilitate transdisciplinary studies of the self-organization and electrophysiological dynamics of mammalian networks in cell culture.",cellular,all,instrumentation,physiological,modeling & simulation,"comput. neurosci.* cell., mol., & syst. neurosci.","user manual citations",licensed,University of north texas, 75,PMC3572679,http://www.centropiaggio.unipi.it/software,Centro E.piaggio software,"A collection of software including NeMO, an image processing and morphometrics extraction software that performs 3-way PCA on neuronal images.",cellular,all,software,anatomical,"visualization data analysis*","neuroanatomy* comput. neurosci. neuroinformatics","user manual citations",open source,"Interdepartmental Research Center E. Piaggio, University of Pisa", 76,nif-0000-10193,https://cerebellum.neuroinf.jp/,Cerebellar Platform,"Cerebellar Platform is a digital research archive for cerebellar research. Available resources include mini-reviews of contemporary cerebellar research, list of papers and mathematical models for cerebellar operation.",regions,mammals,"topical portal* database","anatomical* physiological","modeling & simulation* annotation","neuroinformatics neuroanatomy*","user manual user forum citations",freeware,RIKEN BSI,Japan Society for the Promotion of Science 77,nif-0000-02655,http://www.ebi.ac.uk/chebi/,ChEBI,"Freely available dictionary of molecular entities focused on 'small' chemical compounds. The term molecular entity refers to any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.",macromol.,all,"database ontology & data mngmt.* software",biochemical,"data analysis annotation*","cell., mol., & syst. neurosci.* neuroinformatics","user manual user forum FAQs citations",freeware,European Bioinformatics Institute,"European Commission, (SLING, FELICS, BioBabel), BBSRC" 78,2380278,http://childes.psy.cmu.edu/,CHILDES,CHILDES is the child language component of the TalkBank system. TalkBank is a system for sharing and studying conversational interactions,whole,primates,"database* software ontology & data mngmt. topical portal",functional,"data analysis* annotation","cogn. & behav. neurosci.* neuroinformatics","user manual citations",freeware,Carnegie Mellon University,NIH 79,PMC4053074,http://www.chronux.org/,Chronux,"Chronux is an open-source software package for the analysis of neural data. It was originally developed through a collaborative research effort based at the Mitra Lab in Cold Spring Harbor Laboratory. This software includes several specialized mini-packages for spike sorting, local regression, audio segmentation, and other data-analysis tasks typically encountered by a neuroscientist. This software is now maintained by medametrics, LLC.",whole,all,software,"functional* physiological",data analysis,"cell., mol., & syst. neurosci.","user manual citations",open source,"Cold Spring Harbor Laboratory, Cold Spring Harbor, NY","NIMH, medametrics LLC" 80,nif-0000-37639,http://cellimagelibrary.org,CIL-Cell Image Library,"Freely accessible, public repository of vetted and annotated microscopic images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. Explore by Cell Process, Cell Component, Cell Type or Organism. The Cell includes images acquired from historical and modern collections, publications, and by recruitment. Contributions are welcome.",cellular,all,"database* ontology & data mngmt.","anatomical* biochemical","visualization* annotation","cell., mol., & syst. neurosci.* neuroanatomy clinical & dev. neurobiol. neuroinformatics","user manual citations",freeware,American Society for Cell Biology,NIGMS 81,nlx_152559,http://clarityresourcecenter.org/,CLARITY resources,"Protocols and other training materials related to the CLARITY protocol, a technique for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (cross-linked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable.","whole macromol.*","rodents* primates",topical portal,"anatomical* biochemical",visualization,"neuroanatomy* cell., mol., & syst. neurosci.","user manual citations",freeware,Stanford University; California; USA,"NIMH, NSF, Simons Foundation, Stanford University; California; USA, NIDA, DARPA, (REPAIR program), Wiegers Foundation, Snyder Foundation, Christopher and Dana Reeve Foundation, Gatsby Charitable Foundation, Yu Foundation, Burroughs Wellcome Fund, Samsung, Helen Hay Whitney Foundation, NIH, (MSTP)" 82,25048627,https://www.nmr.mgh.harvard.edu/lab/mripredict,Clinical Predictions from Structural Brain MRI,"This website is dedicated to support and disseminate the empirical data employed in a large-scale experiment, where clinical variables are predicted from structural brain MRI scans.","whole* regions",primates,"ontology & data mngmt.* software",anatomical,data analysis,"clinical & dev. neurobiol.* cogn. & behav. neurosci. neuroinformatics",user manual,freeware,Massachusetts General Hospital,NIH 83,"nif-0000-21091 PMC3594762",http://clinicaltrials.gov,Clinicaltrials.gov,ClinicalTrials.gov offers up-to-date information for locating federally and privately supported clinical trials for a wide range of diseases and conditions. A clinical trial (also clinical research) is a research study in human volunteers to answer specific health questions. Interventional trials determine whether experimental treatments or new ways of using known therapies are safe and effective under controlled environments.,whole,primates,"database* ontology & data mngmt.",functional,"annotation* data analysis","clinical & dev. neurobiol.* neuroinformatics cogn. & behav. neurosci.","user manual citations",freeware,NLM,NLM 84,nlx_151671,http://ncbi.nlm.nih.gov/clinvar,ClinVar,"Freely accessible, public archive of aggregated information about sequence variation and its relationship to human health that provides reports of the relationships among human variations and phenotypes along with supporting evidence. ",macromol.,all,"database* ontology & data mngmt.",functional,"data analysis* annotation","neuroinformatics* clinical & dev. neurobiol. cell., mol., & syst. neurosci.","user manual FAQs citations",freeware,NCBI, 85,"nif-0000-00022 PMC3530798",http://cocomac.g-node.org/drupal/,CoCoMac 2nd edition,"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.","regions* whole",primates,database,"anatomical* physiological","visualization* data analysis modeling & simulation","cell., mol., & syst. neurosci. cogn. & behav. neurosci. comput. neurosci.* neuroinformatics","user manual citations",freeware,German Neuroinformatics Node,"German neuroinformatics node, Computational and Systems Neuroscience group at the Juelich research institute" 86,25240319,http://www.cognitiveatlas.org/,Cognitive Atlas,The Cognitive Atlas is a collaborative knowledge building project that aims to develop a knowledge base (or ontology) that characterizes the state of current thought in cognitive science.,"whole* regions",primates,ontology & data mngmt.,"functional anatomical*",annotation,"cogn. & behav. neurosci.* neuroinformatics",user manual,freeware,Stanford University,NIMH 87,21643732,http://www.wiki.cogpo.org,CogPO Wiki,"The goal of CogPO is to develop, evaluate, and distribute a domain ontology of cognitive paradigms for application and use in the functional neuroimaging community","whole regions*",primates,ontology & data mngmt.,functional,"annotation* visualization","neuroinformatics cogn. & behav. neurosci.*","user manual citations",freeware,UT Health Science Center,NIMH 88,PMC3727653,http://coins.mrn.org/,COINS,"As neuroimaging research continues to grow, dynamic neuroinformatics systems are necessary to store, retrieve, mine, and share the massive amounts of data. The Collaborative Informatics and Neuroimaging Suite (COINS) has been created to facilitate communication and cultivate a data community.","whole* regions",primates,database,"anatomical* functional",data analysis,"clinical & dev. neurobiol.* cogn. & behav. neurosci. neuroinformatics","user manual FAQs citations",freeware,Mind Research Network,NIH 89,10.3389/frobt.2014.00009,http://www.neuro.com/,Compumedics Neuroscan,"Compumedics Neuroscan is a world-leading developer of research software for neurophysiology, neuroimaging, and neurodiagnostic systems. Neuroscan provides tools to increase understanding and improve treatment of this most complex and least understood system of the human body; the brain.","whole* regions",primates,"software instrumentation*","functional* physiological","data analysis neurotechnology*","cogn. & behav. neurosci.* cell., mol., & syst. neurosci. clinical & dev. neurobiol. neuroinformatics","user manual citations",licensed,Australia Corporate HQ, 90,PMC4026698,http://www.nitrc.org/projects/conn,CONN : functional connectivity toolbox,"CONN is a Matlab-based cross-platform software for the computation, display, and analysis of functional connectivity in fMRI (fcMRI).","regions whole*",primates,software,functional,"visualization data analysis*","cogn. & behav. neurosci. clinical & dev. neurobiol.* neuroinformatics","user manual user forum FAQs citations",freeware,MIT, 91,22437992,http://software.incf.org/software/csa,Connection-Set Algebra,"The connection-set algebra (CSA) is a novel and general formalism for the description of connectivity in neuronal network models, from small-scale to large-scale structure.",whole,all,"software ontology & data mngmt.*",functional,modeling & simulation,"comput. neurosci. cogn. & behav. neurosci.*","user manual citations",freeware,"School of Computer Science and Communication, KTH, 10044 Stockholm, Sweden",European Union 92,PMC3381445,http://web.mit.edu/swg/software.htm,CONN-fMRI connectivity toolbox,"The toolbox performs seeded voxel correlations by estimating maps showing temporal correlations between the BOLD signal from given seed and that at every brain vox","whole regions*",primates,software,"anatomical functional*","visualization* data analysis","cogn. & behav. neurosci. neuroinformatics*","user manual citations",open source,Massachusetts Institute of Technology (MIT), 93,24968872,http://www.nitrc.org/projects/ccsegthickness,Corpus Callosum Thickness Profile Analysis Pipeline,"An end-to-end pipeline for corpus callosum processing that provides automated midsagittal alignment, CC segmentation with a quality control tool, and thickness profile generation.",regions,primates,software,anatomical,"visualization* data analysis","clinical & dev. neurobiol.* neuroinformatics","user manual user forum",open source,Murdoch Childrens Research Institute,Murdoch Childrens Research Institute 94,nif-0000-00255,http://crcns.org,CRCNS - Collaborative Research in Computational Neuroscience,Host and make available high quality experimental data sets valuable for testing computational models of the brain and new analysis methods.,"whole* regions cellular","primates rodents* insects others","ontology & data mngmt.* topical portal",physiological,"data analysis* modeling & simulation","cogn. & behav. neurosci. neuroinformatics* comput. neurosci.","user forum citations",freeware,University of California at Berkeley; California; USA,"NIH, NSF" 95,PMC3516126,http://david.abcc.ncifcrf.gov,"Database for Annotation, Visualization, and Integrated Discovery (DAVID)",DAVID now provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.,macromol.,primates,"database* software ontology & data mngmt.",functional,"data analysis* annotation",neuroinformatics,"user manual FAQs citations",freeware,"SAIC, NIAID",NIH 96,PMC4053686,http://incf.org/resources/data-space,Dataspace,"The purpose of the INCF Dataspace is to enable collaboration between researchers through the sharing of neuroscience data, text, images, sounds, movies, models and simulations.",all,all,"database* software ontology & data mngmt.",functional,"modeling & simulation* data analysis","neuroinformatics* comput. neurosci.","user manual citations",freeware,INCF, 97,24952892,http://inlab.ibfm.cnr.it/PET_template.php,Dementia-Specific [18F]FDG-PET template for SPM normalization,"The Dementia-Specific [18F]-FDG-PET template is intended for use as templates for SPM automated normalization. Created for SPM5 but compatible with previous SPM99, SPM2 and with following SPM8 and SPM12b.","regions* whole",primates,software,anatomical,"visualization* data analysis","clinical & dev. neurobiol.* comput. neurosci. neuroinformatics",user manual,freeware,University College London; London; United Kingdom,wellcome trust 98,20838938,http://www.nitrc.org/projects/dfbidb,DFBIdb,"DFBIdb is a suite of tools for efficient management of neuroimaging project data. Specifically, DFBIdb was designed to allow users to quickly perform routine management tasks of sorting, archiving, exploring, exporting and organising raw data.","regions* whole",primates,"ontology & data mngmt.* software",anatomical,"annotation data analysis*","cogn. & behav. neurosci.* neuroinformatics","user manual user forum citations",open source,Murdoch Childrens Research Institute, 99,PMC3385559,http://diademchallenge.org/,DIADEM,This site is a resource for those wishing to engage in the DIADEM challenge to create algorithmic methods for automated neuronal tracing.,cellular,all,"software* topical portal",anatomical,"visualization* modeling & simulation","neuroinformatics* cell., mol., & syst. neurosci. neuroanatomy","user manual FAQs citations",open source,Howard hughes medical institute,"Howard hughes medical institute, Allen brain institute, George mason university" 100,PMC3880907,http://medical.nema.org/standard.html,DICOM,Digital Imaging and Communication in Medicine (DICOM) is a data sharing standard that faciliates sharing of neuroimaging data.,"whole* regions",primates,ontology & data mngmt.,anatomical,annotation,"clinical & dev. neurobiol.* neuroinformatics cogn. & behav. neurosci.","user manual citations",freeware,Medical Imaging & Technology Alliance, 101,22932976,http://www.nitrc.org/projects/dots,Diffusion-Oriented Tract Segmentation (DOTS),"DOTS is a fast, scalable tool developed at the Johns Hopkins University to automatically segment the major anatomical fiber tracts within the human brain from clinical quality diffusion tensor MR imaging.","regions* whole",primates,software,anatomical,"visualization* annotation","cogn. & behav. neurosci. neuroanatomy* neuroinformatics","user manual user forum",open source,Johns Hopkins University,NIH 102,PMC3342677,http://www.empirisoft.com/DirectRT.aspx,DirectRT,"DirectRT--when milliseconds really matter, this extraordinary software provides you with the accuracy you need. DirectRT was designed specifically for experiments requiring high precision stimulus presentation and reaction times from a wide variety of input hardware.",whole,primates,"instrumentation* software","physiological* functional",data analysis,cogn. & behav. neurosci.,"user manual FAQs citations",licensed,Empirisoft corp., 103,nlx_143827,http://disco.neuinfo.org,"DISCO: Extensible Web resource DISCOvery, registration and interoperation framework",DISCO is an information integration approach designed to facilitate interoperation among Internet resources. It consists of a set of tools and services that allows resource providers who maintain information to share it with automated systems such as NIF. NIF is then able to harvest the information and keep those sets of information up-to-date.,all,all,"software ontology & data mngmt.*",all,"data analysis* annotation",neuroinformatics,"user manual citations",open source,Yale University School of Medicine,NIH 104,10.4249/scholarpedia.3036,http://doqcs.ncbs.res.in/,DOQCS - Database of Quantitative Cellular Signaling,"The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions.",macromol.,mammals,"database* ontology & data mngmt.",biochemical,modeling & simulation,"comput. neurosci.* cell., mol., & syst. neurosci. neuroinformatics","user manual FAQs citations",open source,"NCBS, Bangalore, India","NCBS, TIFR India" 105,PMC3885811,http://www.nitrc.org/projects/dtiatlasbuilder/,DTIAtlasBuilder,This tool creates an Atlas image as an average of several DTI images that will be registered,regions,primates,"software atlas*",anatomical,"visualization data analysis*","neuroinformatics* cogn. & behav. neurosci.","user manual user forum",open source,University of North Carolina at Chapel Hill (UNC-CH), 106,PMC3885811,http://www.nitrc.org/projects/dti_tract_stat,DTIAtlasFiberAnalyzer,This is a software which allows the user to study the behavior of water diffusion (using DTI data) along the length of the white matter fiber-tracts.,regions,primates,"software atlas*",anatomical,"visualization data analysis*","cogn. & behav. neurosci.* neuroinformatics","user manual user forum",open source,University of Utah - UNC Chapel Hill,"NIH, NSF" 107,PMC3885811,http://www.nitrc.org/projects/dtiprep/,DTIPrep,"DTIPrep performs a""Study-specific Protocol""based automatic pipeline for DWI/DTI quality control and preparation. This is both a GUI and command line tool.",whole,primates,software,anatomical,"visualization* data analysis","neuroinformatics* cogn. & behav. neurosci.","user manual user forum",open source,, 108,22467471,http://trueta.udg.edu/DTI/,DTIWeb Application,Automatically obtain bundles of fibers grouped into anatomical regions using information-theoretic approach for automated white matter fiber tracts reconstruction,"regions* whole",primates,"software* atlas ontology & data mngmt.",anatomical,"visualization* annotation","neuroanatomy neuroinformatics* comput. neurosci.",user manual,open source,"University of Girona, Girona, Spain", 109,PMC4162418,http://www.civm.duhs.duke.edu/,DUKE CENTER for IN VIVO MICROSCOPY (CIVM),"Small animal imaging includes MRI, CT, x-ray, ultrasound, confocal, optical, and SPECT, all at the highest possible spatial resolution.","whole regions*",all,atlas,anatomical,"visualization* annotation","neuroinformatics neuroanatomy*","user manual citations",freeware,Duke university,NIH/NBIB 110,PMC3437523,http://www.easycap.de/easycap/,Easycap,"Easy-to-order complete cap sets for EEG from 19/21, 32/40 and 64/80 channels. The electrode arrangments are based on the international 10%-system. The chosen electrode positions allow equidistant setups, suitable for all basic and advanced data analysis methods.",whole,primates,instrumentation,physiological,"data analysis neurotechnology*","cogn. & behav. neurosci.* cell., mol., & syst. neurosci.","user manual citations",licensed,, 111,20872095,http://eeg.pl/epi,EEG.PL,Open Database of Epileptic EEG with MRI and Post operational Assessment of Foci a Real World Verification for the EEG Inverse Solutions,whole,primates,database,"physiological* anatomical","data analysis* visualization","clinical & dev. neurobiol.* neuroinformatics cell., mol., & syst. neurosci.","user manual citations",freeware,"Memorial Child Hospital, Warsaw, Poland",Polish funds for science 112,nif-0000-08190,http://eegdatabase.kiv.zcu.cz,EEGbase,"EEG base is a system for storage and management of EEG/ERP resources - data, metadata, tools and materials related to EEG/ERP experiments.",whole,primates,"database* ontology & data mngmt.",physiological,data analysis,cogn. & behav. neurosci.,user manual,open source,University of West Bohemia; Pilsen; Czech Republic,"Ministry of Education, Czech Science Foundation" 113,PMC3578351,http://sccn.ucsd.edu/eeglab/,EEGLAB,"EEGLAB is an interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics, and several useful modes of visualization of the averaged and single-trial data.",whole,primates,software,physiological,"visualization* data analysis","neuroinformatics cell., mol., & syst. neurosci.* cogn. & behav. neurosci.","user manual user forum citations",open source,"The Swartz Center for Computational Neuroscience (SCCN), UCSD", 114,PMC4050739,http://www.uccs.edu/~lbecker/,Effect size calculator,Calculate Cohen's d and the effect-size correlation,whole,primates,software,functional,data analysis,comput. neurosci.,"user manual citations",freeware,University of colarado, 115,PMC4162418,http://www.emouseatlas.org/emap/home.html,EMAP,"EMA, the e-Mouse Atlas. A 3-D anatomical atlas of mouse embryo development including detailed histology. EMA includes the EMAP ontology of anatomical structure.",whole,rodents,"atlas* ontology & data mngmt.",anatomical,"visualization* annotation","neuroinformatics neuroanatomy clinical & dev. neurobiol.*","user manual FAQs citations",freeware,"Western General Hospital, Edinburg, UK", 116,"nif-0000-21145 PMC3620563",http://ensembl.org,ensembl,Freely available genome databases for vertebrates and other eukaryotic species. Users can browse or search genomes as well as DNA and protein sequences. The site also links to the Ensembl blog with updates on new species and sequences as they are added to the database.,macromol.,all,database,biochemical,data analysis,neuroinformatics,"user manual FAQs blog/social networking citations",freeware,"European Bioinformatics Institute, Wellcome Trust Sanger Institute; Hinxton; United Kingdom","Wellcome Trust, EMBL, EU, (FP7, FP6), MRC, NHGRI, BBSRC" 117,10.4249/scholarpedia.1463,http://www.e-swarm.org/,E-SWARM: Engineering Swarm Intelligence Systems,"The main goals of E-SWARM are: the development of scientific foundations for the engineering of artificial swarm intelligence systems the creation of an engineering methodology for the construction of swarm intelligence systems the development of concrete tools and techniques with which to construct swarm intelligence systems",whole,all,"software topical portal*",functional,"modeling & simulation neurotechnology*","cell., mol., & syst. neurosci. cogn. & behav. neurosci. comput. neurosci.* neuroinformatics","user manual citations",freeware,"IRIDIA, UniversiteLibre de Bruxelles, Brussels, Belgium",European Research Council 118,nlx_151313,http://clinicaltrialsregister.eu,EU Clinical Trials Register,"Database of European clinical trials containing information on interventional clinical trials on medicines. The information available dates from 1 May 2004 when national medicine regulatory authorities began populating the EudraCT database, the application that is used by national medicine regulatory authorities to enter clinical trial data.",whole,primates,database,functional,"annotation* data analysis",clinical & dev. neurobiol.,"user manual citations",freeware,European Medicines Agency, 119,nif-0000-04375,http://central.xnat.org,Extensible Neuroimaging Archive Toolkit CENTRAL,"Online repository of open access images including MR Sessions, MRI, Freesurfer APARC, Freesurfer ASEGs, Clinical Assessments, Atlas Scaling Factors, and Fast Segmentations data. CENTRAL currently contains 374 Projects, 3808 Subjects, and 5174 Imaging Sessions (June 2014). Central is powered by XNAT (The Extensible Neuroimaging Archive Toolkit), an open source software platform designed to facilitate management and exploration of neuroimaging and related data.",whole,primates,"database* software","anatomical* physiological functional","visualization data analysis* annotation","cogn. & behav. neurosci.* neuroinformatics clinical & dev. neurobiol.","user manual citations",freeware,Washington University School of Medicine in St. Louis; Missouri; USA, 120,PMC3885811,http://www.nitrc.org/projects/fadtts/,FADTTS,"A functional analysis of diffusion tensor tract statistics (FADTTS) pipeline was developed for delineating the association between multiple diffusion properties along major white matter fiber bundles with a set of covariates of interest, such as age, diagnostic status, genetic marker (e.g., SNP), and gender, and the structure of the variability of these white matter tract properties in various diffusion tensor imaging studies.",whole,primates,software,functional,visualization,"clinical & dev. neurobiol.* neuroinformatics","user manual user forum",open source,, 121,21487683,http://www.farsight-toolkit.org/wiki/Main_Page,FARSIGHT,The goal of the FARSIGHT project is to develop and disseminate a next-generation toolkit of image analysis methods to enable quantitative studies of complex & dynamic tissue microenvironments that are imaged by modern optical microscopes.,cellular,all,software,"anatomical biochemical*","visualization* data analysis","neuroinformatics* neuroanatomy","user manual citations",open source,"University of Houston, Houston, Texas","NIBIB, DARPA, NSF" 122,PMC3885811,http://www.nitrc.org/projects/fvlight/,FiberViewerLight,Fiber ViewerLight is an open-source C++ application to analyze fiber bundles.,whole,primates,software,anatomical,"data analysis* visualization","neuroanatomy* neuroinformatics","user manual user forum",open source,,NIH Roadmap for Medical Research 123,24323305,http://www.zib.de/software/neuron-reconstruction,Filament Editor,"The Filament Editor allows for simultaneous visualization of complex neuronal tracings and image data in a 3D viewer, proof-editing of neuronal tracings, alignment and interconnection across sections, and morphometric analysis in relation to 3D anatomical reference structures.",cellular,all,software,anatomical,"visualization* data analysis","neuroinformatics* neuroanatomy cell., mol., & syst. neurosci.","user manual citations",freeware,Max Planck Florida Institute, 124,22258828,https://code.google.com/p/findv1/,findv1,A model of cells in primary visual cortex fitted to electrophysiological data,cellular,primates,software,physiological,modeling & simulation,"comput. neurosci.* neuroinformatics cogn. & behav. neurosci.",user manual,open source,University of Nottingham,Welcome Trust grant 125,25129841,http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT,FLIRT,FLIRT (FMRIB's Linear Image Registration Tool) is a fully automated robust and accurate tool for linear (affine) intra- and inter-modal brain image registration.,"whole* regions",primates,software,anatomical,"visualization* data analysis","cogn. & behav. neurosci. neuroinformatics*","user manual FAQs citations",freeware,"FMRIB, Oxford, UK",UK EPSRC and the Wellcome Trust 126,nif-0000-00558,http://flybase.org,FlyBase,"Database of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions.",macromol.,insects,"database ontology & data mngmt.* software",biochemical,annotation,"cell., mol., & syst. neurosci.* neuroinformatics","user manual user forum citations",freeware,"Harvard University; Massachusetts; USA, University of Cambridge; Cambridge; United Kingdom, Indiana University; Indiana; USA, University of New Mexico; New Mexico; USA","NHGRI, NIH, British Medical Research Council, NSF" 127,24692020,http://flycircuit.tw,FlyCircuit,"FlyCircuit is a public database for online archiving, cell type inventory, browsing, searching, analysis and 3D visualization of individual neurons in the Drosophila brain.",cellular,insects,"database* ontology & data mngmt. software","anatomical* biochemical","visualization* data analysis","cell., mol., & syst. neurosci.* neuroinformatics neuroanatomy","user manual citations",freeware,"NCHC (National Center for High-performance Computing)?and NTHU (National Tsing Hua University), Hsinchu, Taiwan", 128,PMC3411070,http://flyfly.se,FlyFly,"FlyFly is a free, high level interface, written in MatLab and Psychophysics toolbox, for use in motion vision research.",whole,insects,software,physiological,visualization,"cell., mol., & syst. neurosci.","user manual FAQs",freeware,Uppsala University, 129,PMC4224204,http://flytrap.med.yale.edu,FlyTrap Protein Trapping Project,Drosophila proteins tagged with Green Flourescent Protein (GFP) were created by insertion into genes of an artificial exon encoding GFP flanked by splice acceptor (SA) and splice donor (SD) sequences so that expression of GFP relies on splicing into mature mRNAs and in-frame fusion,macromol.,insects,ontology & data mngmt.,functional,"visualization* annotation","neuroinformatics neuroanatomy*","user manual citations",freeware,Yale school of Medicine, 130,24664409,https://www.force11.org/node/4463,FORCE11,"Force11 is a community of scholars, librarians, archivists, publishers and research funders that has arisen organically to help facilitate the change toward improved knowledge creation and sharing. Individually and collectively, we aim to bring about a change in modern scholarly communications through the effective use of information technology.",all,all,"ontology & data mngmt.* topical portal",functional,annotation,"neuroinformatics* comput. neurosci.","user manual blog/social networking citations",open source,,Gordon and Betty Moore Foundation 131,PMC3303090,http://www.fnih.org,Foundation for the National Institute of Health (FNIH),"The Foundation for NIH, as part of its portfolio, manages several large biomedical research partnerships or Key Initiatives. These partnerships leverage the resources of the National Institutes of Health with the public and private sectors, including government agencies, industry, academia, foundations, associations, and the philanthropic community.",all,all,topical portal,all,"data analysis* modeling & simulation","clinical & dev. neurobiol.* cogn. & behav. neurosci. comput. neurosci.","user manual citations",freeware,NIH,NIH 132,23504659,http://www.med.unc.edu/bric/ideagroup/free-softwares,Free softwares from IDEAgroup,"The IDEA lab is devoted to the development of novel image analysis methods and tools, and their applications to various clinical research and trials. The developed methods include deformable registration (HAMMER), deformable segmentation (AFDM), and multivariate pattern classification algorithms. These methods have been applied to various studies on brain diseases and development (including MCI, AD, Schizophrenia, and Neonate Development Study), heart, breast cancer, and prostate cancer.","whole* regions",primates,software,"anatomical* functional","visualization* data analysis","cogn. & behav. neurosci.* clinical & dev. neurobiol. neuroanatomy","user manual citations",freeware,"UNC chapel hill, NC",NIH 133,23712897,http://sites.google.com/site/fr2eborn,FreeBorN (FBN) consortium,The FreeBorN (FBN) consortium is a free association of scientists working on the French territory. The consortium aims at promoting the interaction and visibility of the research teams studying brain connectivity and network theory. ,"whole regions*",primates,software,"functional physiological* anatomical","visualization modeling & simulation*","neuroinformatics comput. neurosci.*",user manual,open source,"CNRS UMR-7225, Hopital de la Salpetriere, Paris, France",Cochlear Inc. 134,"PMC3880907 20502987",http://surfer.nmr.mgh.harvard.edu/,FreeSurfer Software Suite,An open source software suite for processing and analyzing (human) brain MRI images.,"regions* whole",primates,"software atlas*",anatomical,"visualization data analysis* annotation","neuroinformatics cogn. & behav. neurosci.*","user manual user forum FAQs citations",freeware,,"NCRR, BIRN, NINDS, NIBIB, MIND, NIH" 135,nlx_64373,http://physionet.org/physiobank/database/gaitndd/,Gait Dynamics in Neuro-Degenerative Disease Data Base,"Database of records from patients with Parkinson's disease (n = 15), Huntington's disease (n = 20), or amyotrophic lateral sclerosis (n = 13). Records from 16 healthy control subjects are also included here.",whole,primates,database,"functional physiological*",data analysis,"neuroinformatics clinical & dev. neurobiol.*","user manual citations",,Physiobank, 136,PMC3644699,https://github.com/rossant/galry,Galry,"High-performance interactive visualization in Python based on OpenGL. It allows to interactively visualize very large plots (tens of millions of points) in real time, by using the graphics card as much as possible.",whole,all,software,"anatomical physiological*",visualization,"neuroinformatics comput. neurosci.*","user manual user forum FAQs citations",open source,by Cyrille Rossant, 137,21882083,http://www.nitrc.org/projects/gamma_suite,GAMMA,GAMMA suite is an open-source cross-platform data mining software package designed to analyze neuroimaging data. A neuroimaging study often focuses on biomarker detection and classification.,"regions* whole",primates,software,"anatomical* functional","data analysis* visualization","clinical & dev. neurobiol.* neuroanatomy neuroinformatics","user manual user forum",open source,,NIH 138,nif-0000-08127,http://chibi.ubc.ca/Gemma,Gemma,"Database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Gemma contains data from thousands of public studies, referencing thousands of published papers. Users can search, access and visualize coexpression and differential expression results.",macromol.,"primates* rodents insects others","database* ontology & data mngmt.","biochemical* functional","visualization* data analysis annotation",neuroinformatics,"user manual citations",freeware,University of British Columbia; British Columbia; Canada,NIH 139,nif-0000-02915,http://geneontology.org/,Gene Ontology Consortium,"A community-based bioinformatics resource consisting of three structured controlled vocabularies (ontologies) for the annotation of gene products with respect to their molecular function, cellular component, and biological role in a species-independent manner.","macromol.* cellular",all,"ontology & data mngmt.* database","functional* biochemical","visualization* data analysis","cell., mol., & syst. neurosci.* neuroinformatics","user manual FAQs citations",freeware,Gene Ontology Consortium,"NHGRI, European Union, (RTD Programme Quality of Life and Management of Living Resources), AstraZeneca" 140,nif-0000-00517,http://geneweaver.org/,Gene Weaver,"A freely accessible phenotype-centered database with integrated analysis and visualization tools. It combines diverse data sets from multiple species and experiment types, and allows data sharing across collaborative groups or to public users.",macromol.,all,"database* ontology & data mngmt.",functional,"annotation data analysis*","cell., mol., & syst. neurosci.* clinical & dev. neurobiol. neuroinformatics","user manual citations",freeware,Jackson Laboratory,"NIAAA, Integrative Neuroscience Initiative on Alcoholism" 141,nif-0000-00380,http://genenetwork.org,GeneNetwork,"A group of linked data sets and tools used to study complex networks of genes, molecules, and higher order gene function and phenotypes. It combines more than 25 years of legacy data generated by hundreds of scientists together with sequence data (SNPs) and massive transcriptome data sets (expression genetic or eQTL data sets).",macromol.,"rodents* primates insects",database,"functional* biochemical","visualization data analysis*","cell., mol., & syst. neurosci.* neuroinformatics","user manual citations",freeware,University of Tennessee Health Science Center; Tennessee; USA,"UT Center for Integrative and Translational Genomics, NIAAA, NIDA, NIMH, NCI, NCRR" 142,PMC4162418,http://genepaint.org,Genepaint,GenePaint.org is a digital atlas of gene expression patterns in the mouse.,"whole regions* macromol.",rodents,"atlas* database",anatomical,"visualization* annotation","neuroinformatics clinical & dev. neurobiol.* neuroanatomy","user manual citations",freeware,"Max-Planck-Institute of Biophysical Chemistry, Germany", 143,"10.4249/scholarpedia.1378 10.4249/scholarpedia.1383 ",http://genesis-sim.org/GENESIS/,Genesis 2,"GENESIS (short for GEneral NEural SImulation System) is a general purpose simulation platform that was developed to support the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, simulations of large networks, and systems-level models.","macromol. cellular*",all,software,all,modeling & simulation,"cell., mol., & syst. neurosci.* comput. neurosci. neuroinformatics","user manual citations",open source,James Bower lab at caltech,"NIH, Health Affairs of the University of Texas System, NCRR" 144,nif-0000-33506,http://www.jurgott.org/linkage/ListSoftware.html,Genetic Analysis Software (GAS),"Listing of computer software for the gene mapping community on the following topics: genetic linkage analysis for human pedigree data, QTL analysis for animal/plant breeding data, genetic marker ordering, genetic association analysis, haplotype construction, pedigree drawing, and population genetics.",macromol.,all,software,functional,data analysis,"cell., mol., & syst. neurosci.* neuroinformatics","user manual citations",open source,North Shore LIJ Research Institute, 145,"nif-0000-00130 PMC4091307",http://gensat.org/index.html,GENSAT,"Publicly available gene expression atlas of the developing and adult central nervous system in the mouse, using both in situ hybridization and transgenic mouse techniques. It is a collection of pictorial gene expression maps of the brain and spinal cord of the mouse. ","macromol. cellular*",rodents,"database* atlas ontology & data mngmt.","anatomical functional*","visualization* annotation","cell., mol., & syst. neurosci. neuroinformatics*","user manual citations","freeware licensed*",Rockefeller University; New York; USA,"NINDS, NIMH, NIH Blueprint for Neuroscience Research" 146,PMC3001749,http://geomalgorithms.com/,Geometry algorithms home,The purpose of this site is to provide practical geometric algorithms for the software developer.,cellular,all,software,anatomical,"visualization* modeling & simulation","neuroanatomy* comput. neurosci. neuroinformatics","user manual citations",open source,by Dan Sunday, 147,PMC4053686,http://projects.g-node.org/ginjang/,GinJang project,Neural basis of auditory processing in the honeybee: Neurocomputational modeling and simulation for the deciphering neuron morphology and development,"cellular* regions",insects,topical portal,"anatomical physiological*",modeling & simulation,"comput. neurosci. neuroinformatics*",user manual,freeware,Japan Science and Technology Agency (JST),"Japan Science and Technology Agency (JST), German Federal Ministry of Education and Research" 148,10.1007/s12021-013-9198-x,http://bitbucket.org/palday/ginnungagap-code,Ginnungagap-Code,A computational model for analyzing and constructing sentence-level meaning from the experimentally derived EEG input data,whole,primates,software,physiological,"modeling & simulation* data analysis","comput. neurosci.* cogn. & behav. neurosci.","user manual user forum citations",open source,"Department of Germanic Linguistics, University of Marburg, Deutschhausstr, Germany",German Research Foundation 149,nif-0000-00339,http://gara.bio.uci.edu/,Glomerular Activity Response Archive,"This database of images depicts the spatial distribution of 2-deoxyglucose uptake evoked in the glomerular layer of the rat olfactory bulb in response to a wide range of defined odorant stimuli, an archive that is being provided as a service to the olfactory research community.",regions,rodents,database,"anatomical biochemical*","visualization* data analysis","cell., mol., & syst. neurosci.* neuroinformatics","user manual FAQs citations",freeware,University of California at Irvine; California; USA,"primates Brain Project, NIMH, NIDCD" 150,PMC3246589,http://glovepie.org,GlovePie,"GlovePIE stands for Glove Programmable Input Emulator. It doesn't have to be used with VR Gloves, but it was originally started as a system for emulating Joystick and Keyboard Input using the Essential Reality P5 Glove. Now it supports emulating all kinds of input, using all kinds of devices, including Polhemus, Intersense, Ascension, WorldViz, 5DT, and eMagin products. It can also control MIDI or OSC output.",whole,primates,"instrumentation* software",functional,neurotechnology,cogn. & behav. neurosci.,"user manual user forum blog/social networking citations",freeware,by Carl Kenner, 151,24085487,http://www3.imperial.ac.uk/personalrobotics,HAMMER,"Advancing intelligent robotics for the physical, cognitive and social well-being of humans, through intelligent perception, machine learning, user modelling, cognitive control architectures, and personalised assistance generation.",whole,primates,"instrumentation* software","anatomical functional*","visualization modeling & simulation data analysis neurotechnology*","cogn. & behav. neurosci.* neuroinformatics comput. neurosci.","user manual citations",open source,"Imperial college, London", 152,nlx_40070,http://www.hhmi.org/biointeractive/explore-neuroscience,HHMI's Biointeractive,"A rich variety of videos, interactive modules, and animations to teach about the nervous system.",all,all,topical portal,functional,"visualization* annotation",neuroinformatics,user manual,freeware,HHMI,HHMI 153,PMC4162418,http://www.hms.harvard.edu/research/brain/atlas.html,High Resolutions Mouse Brain Atlas,"Construct atlases of 3D reconstructon of the brain of the mouse from integration of multidisciplinary data, serial slices, and of data dissemination.","whole regions*",rodents,"atlas* ontology & data mngmt.",anatomical,"visualization annotation*","neuroanatomy* neuroinformatics","user manual citations",freeware,,NIH 154,PMC3539731,https://www.humanbrainproject.eu/,Human Brain Project (HBP),"HBP researchers will simulate the human brain, develop brain-inspired computing technologies, map brain diseases, perform targeted mapping of the mouse and human brain, develop six Information and and Communications Technology (ICT) platforms, drive translation of research into products and services, and implement programmes of education and knowledge management. All these efforts will be made in the context of a responsible research and innovation (RRI) strategy.",whole,"primates* rodents",topical portal,functional,"visualization modeling & simulation* data analysis",neuroinformatics,"user manual citations",freeware,"Brain Mind Institute, EPFL",European commission 155,24777386,http://humanconnectome.org/,Human Connectome Project (HCP),"Comprehensively mapping human brain circuitry in a target number of 1200 healthy adults using cutting-edge methods of noninvasive neuroimaging. It will yield invaluable information about brain connectivity, its relationship to behavior, and the contributions of genetic and environmental factors to individual differences in brain circuitry and behavior.",whole,primates,"database* software topical portal","anatomical functional*","visualization data analysis*","neuroinformatics cogn. & behav. neurosci. cell., mol., & syst. neurosci.*","user manual FAQs citations",freeware,"Washington University in Saint Louis, University of Minnesota, Oxford University",NIH Blueprint 156,20567938,http://www.nitrc.org/projects/hid/,Human Imaging Database (HID),HID is an extensible database management system developed to handle the increasingly large and diverse datasets collected as part of the MBIRN and FBIRN collaboratories and throughout clinical imaging communities at large.,whole,primates,"database* software",anatomical,data analysis,"clinical & dev. neurobiol.* neuroinformatics","user manual user forum",open source,BIRN,NIH 157,23055044,http://www.nitrc.org/projects/ibeat,iBEAT,"iBEAT (Infant Brain Extraction and Analysis Toolbox, previously called LIBRA) is a toolbox with graphical user interfaces for processing infant brain MR images.",whole,primates,software,anatomical,"visualization* data analysis","clinical & dev. neurobiol.* neuroinformatics","user manual user forum citations",freeware,University of North Carolina - Chapel Hill,NIH 158,23836390,http://www.nitrc.org/projects/ibsr,IBSR,The Internet Brain Segmentation Repository (IBSR) provides manually-guided expert segmentation results along with magnetic resonance brain image data.,whole,primates,"database* software",anatomical,"visualization* data analysis","neuroanatomy* neuroinformatics","user manual user forum citations",freeware,,primates brain project 159,PMC3459005,http://wavemetrics.com/,IGOR Pro,"IGOR Pro 6 is an extraordinarily powerful and extensible scientific graphing, data analysis, image processing and programming software tool for scientists and engineers.","cellular* regions",all,software,physiological,"visualization data analysis*","comput. neurosci.* cell., mol., & syst. neurosci. neuroinformatics","user manual user forum citations",licensed,"Wavemetrics, inc", 160,PMC3276361,http://developer.imagej.net,ImageJ,"ImageJ can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and""raw"". It supports""stacks"", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.","whole* cellular",all,software,"anatomical* functional","visualization* data analysis","cogn. & behav. neurosci. neuroinformatics* comput. neurosci.","user forum FAQs blog/social networking citations",open source,NIH image,NIH 161,nlx_151660,http://www.mousephenotype.org,International mouse Phenotype Consortium (IMPC),Produce knockout mouse and carry out high-throughput phenotyping of each line in order to determine the function of every gene in the mouse genome.,whole,rodents,"ontology & data mngmt.* database",functional,annotation,"neuroinformatics* clinical & dev. neurobiol.","user manual user forum citations",freeware,International rodents Phenotyping Consortium, 162,nif-0000-09876,http://findmice.org,International Mouse Strain Resource,"Database of mouse strains and stocks available worldwide, that will assist the international research community in finding the mouse resources they need, including inbred, mutant, and genetically engineered mice.","whole* macromol. cellular",rodents,"ontology & data mngmt.* topical portal","biochemical* functional",annotation,neuroinformatics,"user manual citations",freeware,"MGI, MRC Mammalian Genetics Unit",NLM 163,21931990,http://www.nitrc.org/projects/ibvd,Internet Brain Volume Database (IBVD),The IBVD provides a web-based searchable database of brain neuroanatomic volumetric observations. This is designed to access both group volumetric results as well as volume observations in individual cases.,whole,primates,"database* ontology & data mngmt.",anatomical,"data analysis* annotation","neuroanatomy* neuroinformatics","user manual user forum citations",freeware,University of Massachusetts Medical School,primates Brain Project 164,21409556,http://software.incf.org/software/icsd-2d,inverse Current Source Density (iCSD 2D),The MATLAB toolbox allows to apply different variants of CSD to voltage data recorded on 2D regular grids.,cellular,rodents,software,physiological,data analysis,"cell., mol., & syst. neurosci. neuroinformatics*","user manual citations",open source,Nencki Institute of Experimental Biology of the Polish Academy of Sciences,Polish Ministry of Science and Higher Education research grants 165,20502987,http://sourceforge.net/projects/iqr/,iqr,"iqr is a simulation software to graphically design and control large-scale neuronal models. Simulations in iqr can control real-world devices in real-time. iqr can be extended by new neuron, and synapse types, and custom interfaces to hardware.",cellular,all,software,"functional* physiological","modeling & simulation neurotechnology*","cell., mol., & syst. neurosci. neuroinformatics* comput. neurosci.","user manual citations",open source,"Universitat Pompeu Fabra, Roc Boronat, Barcelona, Spain",Synthetic Forager project 166,"PMC4053686 21373993",http://www.itksnap.org/,itk-SNAP,"ITK-SNAP provides semi-automatic segmentation using active contour methods, as well as manual delineation and image navigation.",regions,all,software,anatomical,visualization,"neuroanatomy* neuroinformatics comput. neurosci.","user manual citations",open source,"University of Pennsylvania, University of Utah",NIH 167,PMC3924322,https://code.google.com/p/information-dynamics-toolkit,JIDT: an information-theoretic toolkit,"JIDT provides a stand-alone, open-source code Java implementation (also usable in Matlab, Octave, Python, R, Julia and Clojure) of information-theoretic measures of distributed computation in complex systems: i.e. information storage, transfer and modification.",all,primates,software,all,"data analysis* modeling & simulation","comput. neurosci.* cell., mol., & syst. neurosci. clinical & dev. neurobiol.","user manual citations",open source,"Computational Informatics, Marsfield, NSW, Australia", 168,22932976,http://www.nitrc.org/projects/jist,JIST: Java Image Science Toolkit,(JIST provides a native Java-based imaging processing environment similar to the ITK/VTK paradigm.,"whole regions*",primates,software,anatomical,data analysis,"neuroanatomy neuroinformatics*","user manual user forum citations",open source,Neurodebian, 169,PMC4058593,http://www.jwatcher.ucla.edu/,Jwatcher,JWatcher is a powerful tool for the quantitative analysis of behavior. It can be used to address any theoretical problem that requires a complex sequence of actions to be scored by a human observer.,whole,primates,"software* instrumentation",functional,"visualization* data analysis",cogn. & behav. neurosci.,"user manual citations",freeware,"University of California Los Angeles, Macquarie University","National Institute of Mental Health, The Australian Research Council, Macquarie University" 170,PMC4162418,http://kesm.cs.tamu.edu/home/,KESM Brain atlas,Knife-Edge Scanning Microscopy Brain Atlas,regions,rodents,"atlas software*",anatomical,visualization,"neuroinformatics neuroanatomy*","user manual citations",freeware,Texas A&M University,"NIH, NSF" 171,nlx_31015,http://www.kegg.jp/,Kyoto Encyclopedia of Genes and Genomes (KEGG),"KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information.",macromol.,all,"database ontology & data mngmt.* software",functional,data analysis,"clinical & dev. neurobiol.* neuroinformatics","user manual citations",freeware,"Institute for Chemical Research, Kyoto University, Institute of Medical Science, University of Tokyo","Japanese Ministry of Education Culture Sports Science and Technology (MEXT), JST - Japan Science and Technology Agency" 172,nlx_143941,http://vision.ucsf.edu/hortonlab/ResearchProgram.html,Laboratory for Visual Neuroscience,"Devise better ways to prevent and treat vision loss due to amblyopia and strabismus, and to advance medical science by understanding the human visual system.","whole regions*",primates,topical portal,functional,visualization,"clinical & dev. neurobiol.* cogn. & behav. neurosci. neuroinformatics",user manual,,University of California at San Francisco; California; USA, 173,PMC3653101,http://lamhdi.org/,LAMHDI,"LAMHDI, the initiative to Link Animal Models to human DIsease, is designed to accelerate the research process by providing biomedical researchers with a simple, comprehensive Web-based resource to find the best animal models for their research",whole,all,"database ontology & data mngmt.*",functional,annotation,"neuroinformatics* clinical & dev. neurobiol.",user manual,freeware,"University of Washington, University of Wisconsin-Madison, niversity of California, San Diego, ",NIH/NCRR 174,PMC4174883,https://github.com/LEMS/jLEMS,LEMS,"A compact, hierarchical, XML-based language called LEMS (Low Entropy Model Specification), that can define the structure and dynamics of a wide range of biological models in a fully machine readable format.",cellular,all,ontology & data mngmt.,"anatomical* functional","modeling & simulation* annotation","neuroinformatics* cell., mol., & syst. neurosci.","user manual citations",freeware,"University College London, London, UK",Wellcome Trust 175,PMC4001034,http://software.incf.org/software/libneurosim,Libneurosim,Libneurosim is intended as a place to put standard API:s and common smaller utility code for the computational neuroscience community.,cellular,all,software,functional,modeling & simulation,"cell., mol., & syst. neurosci. neuroinformatics*",user manual,open source,INCF, 176,"10.4249/scholarpedia.1313 25086878",http://cng.gmu.edu:8080/Lm/,L-Measure,Neuroinformatics tool that allows researchers to extract quantitative morphological measurements from neuronal reconstructions.,cellular,all,software,anatomical,data analysis,"neuroanatomy* neuroinformatics","user manual user forum FAQs citations",freeware,"Krasnow institute for Advanced study, George mason university",N IH 177,24692020,http://mirlab.org/jang/matlab/toolbox/machineLearning/,Machine Learning Toolbox (MLT),"Provides a number of essential functions for machine learning, especially for data clustering and pattern recognition. The full version of MLT is published by the Terasoft.",cellular,insects,software,anatomical,"modeling & simulation* data analysis","neuroanatomy* comput. neurosci. neuroinformatics","user manual citations","freeware licensed*",by Roger Jang, 178,"PMC3547329 22426994",http://ric.uthscsa.edu/mango/,Mango,Mango short for Multi-image Analysis GUI is a viewer for medical research images. It provides analysis tools and a user interface to navigate image volumes.,whole,primates,"software* ontology & data mngmt.","anatomical functional*","visualization* annotation data analysis","neuroinformatics cogn. & behav. neurosci.*","user manual user forum citations",freeware,University of Texas Health Science Center,"NIH/NIMH, NIH/NIBIB" 179,10.1007/s12021-014-9223-8,http://bitbucket.org/grotegerd/mania/downloads,MANIA: Machine learning Application for Neuroimaging Analyses,A Pattern Classification Toolbox for Neuroimaging Data,"whole* regions",primates,software,"functional* anatomical",data analysis,"neuroinformatics* cogn. & behav. neurosci.",citations,open source,"Department of Psychiatry, University of Mnster, Albert-Schweitzer- Campus Mnster, Germany", 180,22068921,http://cobre.mrn.org/megsim/,MEG-SIM,"Aims to construct realistic simulated data sets in formats used by each of the 3 major MEG manufacturers. These can then be directly tested using various algorithms which include multidipole, spatiotemporal modeling, current reconstruction, minimum norm, and beamforming methods.",whole,primates,"database* software",physiological,modeling & simulation,"cell., mol., & syst. neurosci.","user manual citations",freeware,"The Mind Research Network, Albuquerque, NM",NIH 181,PMC3629334,http://wws.weizmann.ac.il/mcb/UriAlon/download/network-motif-software,mfinder: Network motifs detection tool,mfinder is a software tool for network motifs detection.,cellular,all,software,anatomical,"visualization data analysis* modeling & simulation","comput. neurosci. neuroinformatics*","user manual citations",open source,"Weizmann Institute of Science,Rehovot Israel", 182,PMC3468957,http://mialab.mrn.org/software/,MIALAB - Medical image analysis lab,"Fusion ICA toolbox is a MATLAB toolbox which implements the jointICA, parallel ICA and CCA with joint ICA methods. It is used to examine the shared information between the features (SPM contrast image, EEG signal or SNPdata).",regions,primates,software,"anatomical physiological*","visualization data analysis*","cogn. & behav. neurosci.* neuroinformatics","user manual citations",freeware,"The Mind Research Network, University of new mexico",National Institutes of Health Blueprint 183,PMC4115634,https://wiki.mouseimaging.ca/display/MICePub/MICe-build-model,Mice-build-model,Its goal is to use image registration to bring all scans from a particular study into correspondence in order to derive measures about anatomical variation or changes in tissue intensities.,"whole regions*",rodents,ontology & data mngmt.,anatomical,"data analysis visualization*","clinical & dev. neurobiol.* neuroanatomy neuroinformatics","user manual citations",freeware,"The Hospital for Sick Children, Toronto, Ontario", 184,PMC4115634,http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC,MINC,MINC is a comprehensive medical imaging data format and an associated set of tools and libraries,"whole regions*",primates,ontology & data mngmt.,anatomical,"data analysis* annotation","cogn. & behav. neurosci.* neuroinformatics","user manual citations",open source,McGill University, 185,22932976,http://mipav.cit.nih.gov/,"MIPAV (Medical Image Processing, Analysis, and Visualization)","MIPAV enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy.",whole,primates,"software ontology & data mngmt.*","anatomical* functional","visualization* data analysis","clinical & dev. neurobiol.* neuroinformatics","user manual citations",open source,NIH,National Institutes of Health Center for Information Technology 186,nif-0000-00004,http://senselab.med.yale.edu/modeldb,ModelDB,ModelDB provides an accessible location for storing and efficiently retrieving computational neuroscience models.,cellular,all,"database* software ontology & data mngmt.","physiological* functional",modeling & simulation,comput. neurosci.,"user manual blog/social networking citations","freeware* open source",Yale University; Connecticut; USA,"NIMH, NINDS, NCI" 187,21305364,http://www.dia.fi.upm.es/~concha/dendriticsimulation/,Models and Simulation of 3D Neuronal Dendritic Trees Using Bayesian Networks,A class of probabilistic graphical models called Bayesian networks to generate virtual dendrites from layer III pyramidal neurons from three different regions of the neocortex of the mouse.,cellular,rodents,software,anatomical,"modeling & simulation* visualization","comput. neurosci.* neuroanatomy neuroinformatics","user manual citations",open source,Universidad Politecnica de Madrid,Cajal Blue Brain Project 188,nlx_152525,http://monarchinitiative.org,Monarch Initiative,"Repository of information about model organisms, in vitro models, genes, pathways, gene expression, protein and genetic interactions, orthology, disease, phenotypes, publications, and authors, and the the ability to navigate multi-scale spatial and temporal phenotypes across in vivo and in vitro model systems in the context of genetic and genomic data, using semantics and statistics.",whole,all,"ontology & data mngmt.* database",functional,annotation,neuroinformatics,"user manual user forum",open source,"Oregon Health and Science University; Oregon; USA, Lawrence Berkeley National Laboratory, University of California at San Diego; California; USA, University of Pittsburgh; Pennsylvania; USA",NIH Office of the Director 189,PMC4162418,http://map.loni.usc.edu/,Mouse Atlas Project 2.0,"MAP2.0 seeks to gather multimodal image datatypes from a large collection of C57BL/6J mouse brains, including: MRI, DTI, blockface, histochemical, and tract-tracing. Each set of brain data will be co-registered into a common atlas framework with detailed labeling of anatomical structures.","whole regions*",rodents,"atlas* ontology & data mngmt.",anatomical,"visualization* annotation","neuroinformatics neuroanatomy*","user manual citations",freeware,"Laboratory of Neuroimaging (LONI), UCLA", 190,PMC4162418,http://www.mbl.org/mbl_main/atlas.html,Mouse Brain Atlases,Coronal and horizontal atlases of different Mouse species,whole,rodents,"atlas* database ontology & data mngmt. software",anatomical,"visualization* annotation","neuroanatomy* clinical & dev. neurobiol. neuroinformatics","user manual citations",freeware,,"NIMH, NIDA, NSF" 191,"PMC3632786 nif-0000-00096",http://informatics.jax.org,Mouse Genome Informatics (MGI),"International database for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. Its primary mission is to facilitate the use of the mouse as a model system for understanding human biology and disease.",whole,rodents,"database ontology & data mngmt.* software","anatomical functional*",annotation,"neuroinformatics* clinical & dev. neurobiol.","user manual citations",freeware,Jackson Laboratory,"NHGRI, NICHD, NCI" 192,nlx_152633,http://mmpc.org/,Mouse Metabolic Phenotyping Centers,"Biomaterial analysis service for the scientific community with standardized, high quality metabolic and physiologic phenotyping services for mouse models of diabetes, diabetic complications, obesity and related disorders. ",whole,rodents,"database* topical portal",biochemical,annotation,"neuroinformatics* clinical & dev. neurobiol.","user manual citations","freeware licensed*",Georgia Regents University; Georgia,"The National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Heart, Lung, and Blood Institute (NHLBI)" 193,nif-0000-03160,http://phenome.jax.org/,Mouse Phenome Database,Characterizes strains of laboratory mouse to assist in selection of mouse strains for experimental studies and to facilitate translational discoveries.,whole,rodents,ontology & data mngmt.,functional,"annotation* data analysis","neuroinformatics cell., mol., & syst. neurosci.*","user manual citations",freeware,Jackson Laboratory,"NIDA, NIH" 194,PMC3462416,http://mouse-phenotype.org/,Mouse Phenotype Database,The mouse Phenotype Database consists of the raw data of behavioral tests from the mouse strain that are published in articles.,whole,rodents,"database* ontology & data mngmt. software",functional,annotation,cogn. & behav. neurosci.,"user forum citations",freeware,, 195,22194186,http://www.mccauslandcenter.sc.edu/mricro/index.html,MRIcro,"A simple image viewer with basic drawing tools. While we suggest people consider using the more advanced MRIcron, this older software remains popular","whole regions*",primates,"software ontology & data mngmt.*",anatomical,"visualization data analysis* annotation","cogn. & behav. neurosci. clinical & dev. neurobiol.*","user manual user forum FAQs citations",freeware,"University of South Carolina, Columbia SC, USA", 196,PMC3885811,http://www.nitrc.org/projects/mriwatcher/,MriWatcher,This simple visualization tool allows to load several images at the same time. The cursor across all windows are coupled and you can move/zoom on all the images at the same time.,"whole* regions",primates,software,anatomical,"visualization annotation data analysis*","neuroanatomy* neuroinformatics","user manual user forum citations",open source,, 197,PMC4162418,http://brainatlas.mbi.ufl.edu/,MRM NeAT (Neurological atlas),3D Digital MRM (magnetic resonance microscopy) imaging Atlas of Adult C57BL/6J mouse Brains,"whole regions*",rodents,atlas,anatomical,"visualization* data analysis","neuroinformatics neuroanatomy*","user manual citations",freeware,University of Florida,NIH 198,PMC4019854,http://www.nitrc.org/projects/multimodal,Multi-Modal MRI Reproducibility Resource,"This is intended to be a resource for statisticians and imaging scientists to be able to quantify the reproducibility of their imaging methods using data available from a generic""1 hour""session at 3T.",whole,primates,ontology & data mngmt.,anatomical,"visualization* annotation","cogn. & behav. neurosci. neuroinformatics neuroanatomy*","user manual user forum citations",open source,,"NIH/NCRR, NIH/NINDS" 199,24395057,http://cajalbbp.cesvima.upm.es/audispine/,Musical Representation of Dendritic Spine Distribution,A new method with musical feedback for exploring dendritic spine morphology and distribution patterns in pyramidal neurons.,cellular,primates,software,anatomical,data analysis,"cell., mol., & syst. neurosci.* neuroanatomy",user manual,freeware,"Universidad Rey Juan Carlos (URJC), Madrid, Spain",Cajal Blue Brain Project 200,PMC3901007,https://code.google.com/p/n2a/,N2A,"""Neurons to Algorithms""(N2A) is a language for modeling neural systems, along with a software tool for editing models and simulating them.",cellular,all,software,"functional anatomical* physiological",modeling & simulation,"neuroinformatics* comput. neurosci.",user manual,open source,"Sandia National Laboratories, Albuquerque, NM, USA",Sandia National Laboratories 201,22622767,http://ndar.nih.gov/,National Database for Autism Research (NDAR),"The National Database for Autism Research (NDAR) is an NIH-funded research data repository that aims to accelerate progress in autism spectrum disorders (ASD) research through data sharing, data harmonization, and the reporting of research results.",whole,primates,"database* software",functional,data analysis,"neuroinformatics* clinical & dev. neurobiol.","user manual FAQs citations",freeware,NIH,"NIMH, NINDS, NIEHS, NICHD, CIT" 202,nlx_86401,http://www.ninds.nih.gov/disorders/disorder_index.htm,National Institute of Neurological Disorders and Stroke (NINDS),The mission of the National Institute of Neurological Disorders and Stroke is to seek fundamental knowledge about the brain and nervous system and to use that knowledge to reduce the burden of neurological disease,all,primates,"topical portal* ontology & data mngmt.",all,annotation,"clinical & dev. neurobiol. neuroinformatics*","user manual FAQs citations",freeware,NIH,NIH 203,nif-0000-02801,http://ncbi.nlm.nih.gov/gene,NCBI Gene,"Database of genes, from RefSeq genomes, and defined by sequence and/or located in the NCBI Map Viewer.",macromol.,all,"database* software ontology & data mngmt.",functional,"data analysis* annotation","neuroinformatics* cell., mol., & syst. neurosci.","user manual FAQs citations",freeware,NCBI, 204,23274962,http://nemosim.sourceforge.net/index.html,NeMo,"NeMo is a high-performance spiking neural network simulator which simulates networks of Izhikevich neurons on CUDA-enabled GPUs, aiming for real-time simulation of 100 000s of realistically connected spiking neurons.","cellular* whole",all,"software instrumentation*","functional* anatomical",modeling & simulation,"comput. neurosci.* neuroinformatics neuroanatomy","user manual user forum",open source,Imperial College London,EPSRC 205,PMC3880998,https://github.com/ctn-waterloo/nengo,Nengo: Large-scale brain modelling in Python,"Nengo is a software tool that can be used to build and simulate large-scale models based on the Neural Engineering Framework (NEF); currently, it is the primary resource for both teaching how the NEF is used, and for doing research that generates specific NEF models to explain experimental data.",whole,all,software,functional,modeling & simulation,"comput. neurosci. cell., mol., & syst. neurosci.* neuroinformatics","user manual user forum",open source,"University of Waterloo, Waterloo, ON, Canada","NSERC Discovery, NSERC Graduate Fellowships, NSERC Banting Fellowship, ONR" 206,22644867,http://sci.utah.edu/~liz/nerv.html,Neron Reconstruction Viewer (NeRV),"NeRV is the research code developed by Jurrus et. a. that enables users to view large EM datasets, evaluate the segmentations, and make corrections to both the 2D membrane detection and the joining of regions through the sections to segment a neuron in 3D.",cellular,all,software,anatomical,visualization,"neuroanatomy neuroinformatics*","user manual citations",open source,"Scientific Computing and Imaging Institute, University of Utah",NIH 207,10.4249/scholarpedia.1430,http://nest-simulator.org,NEST (NEural Simulation Tool),The Neural Simulation Tool NEST is a computer program for simulating large heterogeneous networks of point neurons or neurons with a small number of compartments.,cellular,all,software,"anatomical physiological*",modeling & simulation,"comput. neurosci.* neuroinformatics","user manual user forum",open source,Cole Polytechnique Federale de Lausanne,"DAAD, DIP, EU, BMBF" 208,23111491,http://atlas.gcsc.uni-frankfurt.de/~neugen/,NeuGen,NeuGen is made for generation of dendritic and axonal morphology of realistic neurons and networks in 3D,"cellular* regions",all,software,anatomical,modeling & simulation,"comput. neurosci.* neuroinformatics","user manual citations",open source,Goethe-Universitat Frankfurt, 209,21562803,http://www.neurogeometry.net/,Neural Circuit Tracer,Neural Circuit Tracer (NCTracer) is open source software for automated and manual tracing of neurites from light microscopy stacks of images.,cellular,all,software,anatomical,visualization,"cell., mol., & syst. neurosci. comput. neurosci. neuroinformatics*","user manual citations",open source,"Northeastern university, Boston, MA",NIH 210,23893006,http://nemo.nic.uoregon.edu/wiki/NEMO,Neural ElectroMagnetic Ontologies (NEMO),EEG and MEG ontology for ERP and ERF databasing.,whole,primates,"ontology & data mngmt.* software database",physiological,"data analysis annotation*","neuroinformatics* cell., mol., & syst. neurosci. cogn. & behav. neurosci.","user manual user forum citations",freeware,Univeristy of oregon,NIH 211,PMC3930095,http://neuralensemble.org,NeuralEnsemble,"NeuralEnsemble is a multilateral effort to coordinate and organize Neuroscience software development efforts into a larger meta-simulator software system, a natural and alternate approach to incrementally address what is known as the complexity bottleneck, presently a major roadblock for neural modelling.",cellular,all,"software ontology & data mngmt.*",physiological,"data analysis modeling & simulation*","comput. neurosci.* neuroinformatics","user manual user forum FAQs citations",open source,"Centre de Recherche en Neuroscience de Lyon, CNRS, France",BrainScaleS project 212,PMC3322488,http://www.neurobs.com/,neurobehavioralsystems,"Presentation is a stimulus delivery and experimental control program for neuroscience. It runs on any Windows PC, and delivers auditory, visual and multimodal stimuli with sub-millisecond temporal precision.",whole,primates,"software instrumentation*","physiological* functional",data analysis,"cogn. & behav. neurosci.* neuroinformatics","user manual FAQs citations",licensed,"Neurobehavioral Systems, Inc", 213,nlx_151885,http://neuroelectro.org/,NeuroElectro,The goal of the NeuroElectro Project is to extract information about the electrophysiological properties (e.g. resting membrane potentials and membrane time constants) of diverse neuron types from the existing literature and place it into a centralized database.,cellular,all,"database* ontology & data mngmt.",physiological,"annotation data analysis*","cell., mol., & syst. neurosci.* neuroinformatics","user manual FAQs citations",freeware,University of British Columbia and Carnegie Mellon University, 214,10.4249/scholarpedia.1903,http://neurofitter.sourceforge.net,Neurofitter,Neurofitter is a parameter tuning package for electrophysiological neuron models.,cellular,all,software,"functional physiological*","modeling & simulation* data analysis","comput. neurosci.* cell., mol., & syst. neurosci. neuroinformatics","user manual citations",open source,"Okinawa Institute of Science and Technology, University of Antwerp", 215,10.4249/scholarpedia.1313,http://www.mbfbioscience.com/neurolucida/,Neurolucida,"Neurolucida is a powerful tool for creating and analyzing realistic, meaningful, and quantifiable neuron reconstructions from microscope images.",cellular,all,"software instrumentation*",anatomical,"visualization data analysis*","cell., mol., & syst. neurosci.* neuroinformatics neuroanatomy","user manual blog/social networking citations","freeware licensed*",MBF Bioscience, 216,nif-0000-00175,http://neuromab.ucdavis.edu,NeuroMab,A national mouse monoclonal antibody generating resource for biochemical and immunohistochemical applications in mammalian brain.,macromol.,"mammals* others","database* ontology & data mngmt.",biochemical,"visualization* annotation","cell., mol., & syst. neurosci.* clinical & dev. neurobiol.","user manual citations",freeware,University of California at Davis; California; USA,"NINDS, NIMH, NIH Blueprint for Neuroscience Research, NIH Roadmap for Medical Research, Office of Rare Diseases Research, Antibodies Inc., NIH" 217,"PMC3305991 10.4249/scholarpedia.1313",http://sourceforge.net/projects/neuromantic/,Neuromantic,Neuromantic is a free application for the semi-manual or semi-automatic reconstruction of neurons for single images or image stacks.,cellular,all,"software* ontology & data mngmt.",anatomical,"annotation visualization*","neuroinformatics* neuroanatomy","user manual blog/social networking citations",open source,"University of Reading, Reading, UK","EPSRC grant, statistics/graphing aspects by Nuffield Foundation grant" 218,PMC3459005,http://neuromatic.thinkrandom.com/,NeuroMatic,NeuroMatic is a collection of Igor Pro functions for analyzing and acquiring electrophysiological data.,cellular,all,software,physiological,"visualization* data analysis","cell., mol., & syst. neurosci.* comput. neurosci.",,open source,University College London,"MRC, wellcome trust" 219,10.1002/cnm.2486,http://www.neuromechanic.com/,Neuromechanic,"NEUROMECHANIC is a simulated physical environment for developing and testing neural control models. Rigid body dynamic equations of motion, phenomenological muscle models, and simplified neuron models are incorporated.",whole,all,"software instrumentation*","anatomical functional*","neurotechnology* modeling & simulation","cell., mol., & syst. neurosci.* comput. neurosci.","user manual user forum",freeware,Emory University and Georgia Institute of Technology, 220,"10.4249/scholarpedia.3036 PMC4174883",http://www.morphml.org/,NeuroML,The NeuroML project focuses on the development of an XML (eXtensible Markup Language) based description language that provides a common data format for defining and exchanging descriptions of neuronal cell and network models.,"cellular* regions whole",all,software,"anatomical physiological*","modeling & simulation* visualization","cell., mol., & syst. neurosci. comput. neurosci. neuroinformatics*","user manual user forum citations",open source,"University College London, United Kingdom"," UK Medical Research Council, NIH, NSF, Wellcome Trust, INCF" 221,"nif-0000-00006 10.4249/scholarpedia.1313 PMC4053686 21181305",http://neuromorpho.org,NeuroMorpho.Org,A centrally curated inventory of digitally reconstructed neurons that contains some of the most complete axonal arborizations digitally available in the community.,cellular,all,"database* ontology & data mngmt.",anatomical,"visualization* annotation data analysis","neuroinformatics* neuroanatomy cell., mol., & syst. neurosci.","user manual FAQs citations",freeware,"George mason university, fairfax, VA",NIH 222,10.4249/scholarpedia.1378,http://www.neuron.yale.edu/,NEURON,"The NEURON Simulation Environment is designed for modeling individual neurons and networks of neurons, and is widely used by experimental and theoretical neuroscientists.",cellular,all,"software ontology & data mngmt.*","anatomical physiological*","visualization modeling & simulation* data analysis","neuroinformatics* comput. neurosci. cell., mol., & syst. neurosci.","user manual user forum FAQs blog/social networking citations",freeware,Yale university, 223,PMC4053686,http://www.neuronland.org/NL.html,Neuronland,Neuronland provides free software tools for the experimental neuroscience and neuron mathematical modeling communities.,cellular,all,"software* ontology & data mngmt.",anatomical,"visualization* annotation","neuroinformatics neuroanatomy*","user manual citations",freeware,, 224,23765606,http://research.mssm.edu/cnic/tools-ns.html,NeuronStudio,"NeuronStudio provides tools for manual, semi-manual, and automatic tracing of the dendritic arbor as well as manual and automatic detection and classification of dendritic spines.",cellular,all,software,anatomical,visualization,"neuroinformatics neuroanatomy*","user manual citations",freeware,"CNIC, Mount Sinai School of Medicine", 225,PMC3368231,http://neuronvisio.org/,Neuronvisio,Neuronvisio is a Graphical User Interface for NEURON simulator environment with 3D capabilities. Neuronvisio makes easy to select and investigate sections properties and it offers easy integration with matplotlib for plotting the results.,cellular,all,"software* ontology & data mngmt.","anatomical* physiological","visualization* modeling & simulation","neuroinformatics comput. neurosci.*","user manual user forum",open source,Wellcome Trust Genome Campus, 226,PMC3351760,https://sites.google.com/site/neurorighter/,NeuroRighter,"NeuroRighter is an open-source electrophysiology platform for conducting closed-loop, multichannel neural recording and stimulation experiments.","whole* regions","primates rodents*","instrumentation* software","physiological* functional",data analysis,"cell., mol., & syst. neurosci.","user manual citations",open source,Georgia Tech,NSF 227,PMC3930095,http://neuroshare.org,neuroshare.org,Neuroshare.org is a site created to support the collaborative development of open library and data file format specifications for neurophysiology and distribute open-source data handling software tools for neuroscientists.,cellular,all,"ontology & data mngmt.* software",physiological,annotation,"neuroinformatics comput. neurosci.*","user manual citations",open source,, 228,23828255,http://cran.r-project.org/web/packages/neuRosim/,neuRosim,The package allows users to generate fMRI time series or 4D data. Some high-level functions are created for fast data generation with only a few arguments and a diversity of functions to define activation and noise. For more advanced users it is possible to use the low-level functions and manipulate the arguments.,whole,primates,software,functional,"modeling & simulation* data analysis","comput. neurosci.* neuroinformatics","user manual citations",open source,Ghent University, 229,nlx_55906,http://neurosynth.org,NeuroSynth.org,"Platform for large-scale, automated synthesis of functional magnetic resonance imaging (fMRI) data extracted from published articles. It's a website wrapped around a set of open-source Python and JavaScript packages. Neurosynth lets you run crude but useful analyses of fMRI data on a very large scale. ","regions* whole",primates,"database* software ontology & data mngmt.","anatomical* functional","visualization data analysis*","neuroinformatics cogn. & behav. neurosci.*","user manual FAQs user forum citations",open source,University of Colorado Boulder; Colorado; USA,NIH 230,22350719,http://neuroviisas.med.uni-rostock.de/index.htm,neuroVIISAS,"neuroVIISAS (neuro Visualization, Imagemapping, Information System for Analysis and Simulation) is an open framework for integrative data analysis, visualization and population simulations.","regions* whole","rodents* primates","atlas ontology & data mngmt. software*",anatomical,"visualization modeling & simulation* annotation data analysis","neuroinformatics cogn. & behav. neurosci. cell., mol., & syst. neurosci.*","user manual citations",freeware,"University of Rostock, Germany",University of Rostock 231,PMC4132371,http://sim.igi.tugraz.at/nevesim/,NEVESIM,"NEVESIM is a software package for event-driven simulation of networks of spiking neurons with a fast simulation core in C++, and a scripting user interface in the Python programming language.","regions cellular*",all,software,functional,modeling & simulation,"cell., mol., & syst. neurosci.* comput. neurosci. neuroinformatics","user manual FAQs",open source,Graz University of Technology, 232,PMC4010752,http://www.newbehavior.com/,NewBehavior AG,Company develops state-of-the art technology for automated measuring and shaping of animal behavior,whole,rodents,instrumentation,functional,"visualization* data analysis",cogn. & behav. neurosci.,"user manual citations",licensed,"Zurich Switzerland", 233,nif-0000-21981,https://datashare.nida.nih.gov/,NIDA Data Share,"The NIDA Data Share web site is an electronic environment that allows data from completed clinical trials to be distributed to investigators and the public in order to promote new research, encourage further analyses, and disseminate information to the community. Secondary analyses produced from data sharing multiply the scientific contribution of the original research.",macromol.,primates,"database* ontology & data mngmt.","functional biochemical*",data analysis,"clinical & dev. neurobiol.* neuroinformatics","user manual FAQs citations",freeware,NIDA,NIH 234,23912507,http://nidb.sourceforge.net/,NIDB ( NeuroInformatics DataBase),"Its a database designed to store your neuroimaging data, make it easily accessible to you, and allow you to easily share your data with collaborators.","whole* regions",primates,"database ontology & data mngmt.*","functional anatomical*","visualization* annotation","cogn. & behav. neurosci. neuroinformatics*",user manual,open source,"Hartford Hospital, Hartford, CT, USA","NIH, NIMH, NHLBI" 235,PMC3402830,http://messagelab.monash.edu.au/Nimrod,Nimrod,"Nimrod uses a simple declarative parametric modeling language to express a parametric experiment and provides machinery that automates the task of formulating, running, monitoring, and collating the results from the multiple individual experiments.",regions,rodents,software,"anatomical physiological*","modeling & simulation* data analysis","cell., mol., & syst. neurosci.* neuroinformatics comput. neurosci.","user manual citations",freeware,,Australian Research Council 236,nlx_18447,http://www.nitrc.org/ir/app/template/Index.vm,NITRC-IR,"XNAT-based Image Registry that supports both NIfTI and DICOM images to promote re-use and integration of valuable NIH-funded data. NITRC-IR currently contains 7 Projects, 4764 Subjects, and 4779 Imaging Sessions.",whole,primates,ontology & data mngmt.,"functional* anatomical","data analysis* visualization","clinical & dev. neurobiol.* cogn. & behav. neurosci. neuroinformatics","user manual FAQs citations",freeware,NITRC,NIH 237,PMC3427544,http://www.nordicneurolab.com/,NordicNeuroLab,NordicNeuroLab provides products and solutions that define the field of functional MR imaging.,"whole regions*",primates,instrumentation,"anatomical* functional","neurotechnology* data analysis visualization","cogn. & behav. neurosci.* neuroinformatics clinical & dev. neurobiol.","user manual citations",licensed,NordicNeuroLab, 238,nlx_143665,http://www.novusbio.com/,Novus Biologicals,Novus Biologicals was organized to provide the biological research community with a mechanism for commercializing unique biological materials.,macromol.,"rodents primates*","ontology & data mngmt.* database",biochemical,annotation,"cell., mol., & syst. neurosci.* neuroinformatics","user manual FAQs Blog/social networking citations",licensed,Novus, 239,nif-0000-00387,http://oasis-brains.org/,OASIS - Open Access Series of Imaging Studies,"Freely available MRI data sets of the brain including: Cross-sectional MRI Data in Young, Middle Aged, Nondemented and Demented Older Adults, Longitudinal MRI Data in Nondemented and Demented Older Adults, and Resting State Functional MRI Data in Young Adults.","whole* regions",primates,ontology & data mngmt.,anatomical,"annotation visualization*","cogn. & behav. neurosci.* neuroinformatics","user manual citations",freeware,"Washington University Alzheimer's Disease Research Center, Washington University School of Medicine, Biomedical Informatics Research Network (BIRN)", 240,19787067,http://obart.brainarchitecture.org/obart/,OBART,The Online Brain Atlas Reconciliation Tool (OBART) aims to provide a quantitative solution to the so-called neuroanatomical nomenclature problem by comparing overlap relations between regions defined as spatial entities in different digital human brain atlases.,"whole regions*",primates,"atlas* ontology & data mngmt.",anatomical,"annotation visualization*","neuroinformatics* neuroanatomy","user manual citations",,Brain architecture project,WM Keck Foundation 241,PMC3385559,http://www.olympusmicro.com/primer/digitalimaging/deconvolution/deconintro.html,Olympus microscopy resource center,Confocal and wide field microscopy imaging,cellular,all,"instrumentation* topical portal",anatomical,neurotechnology,"cell., mol., & syst. neurosci.* clinical & dev. neurobiol.","user manual FAQs citations",licensed,"Columbia University, New York, NY, USA", 242,25240319,https://bioportal.bioontology.org/ontologies/ONL-MSA,ONL-MSA,"This ontology is a module of the OntoNeuroLOG ontology, developed in the context of the NeuroLOG project, a french project supported by ANR (ANR-06-TLOG-024 grant) aiming at integrating distributed heterogeous resources in neuroimaging.","whole* regions",primates,"software ontology & data mngmt.*",anatomical,"annotation* data analysis","cogn. & behav. neurosci. clinical & dev. neurobiol. neuroinformatics*",user manual,freeware,"Sorbonne Universites, UPMC Univ Paris",french ANR 243,PMC3338117,http://obofoundry.org/,Open Biological and Biomedical Ontologies,The OBO Foundry is a collaborative experiment involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain.,all,all,ontology & data mngmt.,all,"annotation visualization*","neuroinformatics* cell., mol., & syst. neurosci.","user manual FAQs citations",,Berkeley Bioinformatics Open Source Project (BBOP),OBO Foundry Operations Committee 244,PMC3945519,http://www.g-node.org/projects/odml,Open Metadata Markup Language (odML),"odML is an initiative to define and establish an open, flexible and easy-to-use format to transport metadata.",cellular,all,"ontology & data mngmt.* software",physiological,annotation,neuroinformatics,"user manual citations",freeware,German Neuroinformatics Node,German Federal Ministry of Education and Research and hosted by Ludwig-Maximilians-Universitat Mnchen 245,nlx_152590,http://opensourcebrain.org,Open Source Brain,"A resource for sharing and collaboratively developing computational models of neural systems. While models can be submitted and developed in any format, the use of open standards such as NeuroML and PyNN is encouraged, to ensure transparency, modularity, accessibility and cross simulator portability. OSB will provide advanced facilities to analyze, visualize and transform models in these formats, and to connect researchers interested in models of specific neurons, brain regions and disease states.","regions* whole cellular","mammals* others","ontology & data mngmt.* software","physiological* functional","modeling & simulation* Annotation","comput. neurosci.* neuroinformatics","user manual blog/social networking citations",open source,University College London; London; United Kingdom,Wellcome Trust 246,25129841,http://www.dcm4che.org/,Open Source Clinical Image and Object Management,"dcm4che is a collection of open source applications and utilities for the healthcare enterprise. These applications have been developed in the Java programming language for performance and portability, supporting deployment on JDK 1.4 and up.","whole* regions",primates,"database* software",anatomical,data analysis,"cogn. & behav. neurosci. neuroinformatics*","user manual user forum citations",open source,, 247,PMC3945519,http://www.khronos.org/opencl/,OpenCL,"OpenCL is the first open, royalty-free standard for cross-platform, parallel programming of modern processors found in personal computers, servers and handheld/embedded devices. OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications",cellular,all,"software instrumentation*","physiological* functional",modeling & simulation,"neuroinformatics comput. neurosci.*","user manual user forum citations",open source,by Kyle Lutz, 248,PMC3703526,https://openfmri.org/,OpenFMRI project,Aims to provide the neuroimaging community with a resource to support open sharing of task-based fMRI studies.,whole,primates,"database* ontology & data mngmt.","functional* anatomical","annotation visualization*","neuroinformatics* cogn. & behav. neurosci.","user manual FAQs citations",open source,University of Texas at Austin,NSF 249,PMC4017157,http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases/striatumconn,Oxford-GSK-Imanova Striatal Connectivity Atlas,"Probabilistic maps of the cortical striatal connectivity profiles, calculated from 26 subjects. The probabilities stored in these maps are calculated for each cortical zone and each striatal voxel, with one map/image of the striatum provided for each zone.","whole* regions",primates,"atlas* software topical portal","anatomical* functional","visualization* data analysis annotation",cogn. & behav. neurosci.,"user manual user forum FAQs citations",freeware,"FMRIB, Oxford, UK",UK EPSRC and the Wellcome Trust 250,23828255,http://cran.r-project.org/web/packages/fmri/,"Package""fmri""for R","The R-package""fmri""provides functions for analyzing single run fmri data with structure adaptive smoothing procedure. This includes I/O function for ANALYZE, AFNI, or DICOM files, linear modeling with hemodynamic response functions, signal detection using Random Field Theory. Additionally, the structural adaptive segmentation method from Polzehl et al. 2010 is implemented.","regions* whole",primates,software,"functional* anatomical",data analysis,"cogn. & behav. neurosci.* comput. neurosci. neuroinformatics","user manual citations",open source,"Weierstrass Institute for Applied Analysis and Stochastics, Berlin, Germany.",DFG Research Center Matheon and support from the Cervical Spine Research Society 251,PMC3949323,http://painresearchforum.org/,PainResearchForum,"PRF is a community of chronic pain researchers, established with the goal of fostering collaboration and communication among pain researchers.",whole,primates,"ontology & data mngmt.* topical portal",functional,annotation,"neuroinformatics clinical & dev. neurobiol.* cell., mol., & syst. neurosci.","user manual user forum FAQs citations",freeware,Harvard NeuroDiscovery Center,"Curvey Family Foundation, the Mayday Fund, the Guthart Family Foundation, Purdue Pharma L.P. and Genentech." 252,PMC3578208,http://www.nitrc.org/projects/panda,PANDA - Pipeline for Analyzing braiN Diffusion imAges,"A matlab toolbox for pipeline processing of diffusion MRI images. For each subject, PANDA can provide outputs in 2 types: i) diffusion parameter data that is ready for statistical analysis; ii) brain anatomical networks constructed by using diffusion tractography.",whole,primates,software,anatomical,"visualization data analysis*","cogn. & behav. neurosci. neuroinformatics*",user manual,open source,Beijing Normal University, 253,nlx_84521,http://pantherdb.org,PANTHER,"Classification system that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.",macromol.,all,"database* ontology & data mngmt.","biochemical* functional","annotation data analysis*","neuroinformatics* cell., mol., & syst. neurosci.","user manual citations",freeware,University of Southern California; California; USA,NIGMS 254,PMC3437523,http://polhemus.com/scanning-digitizing/patriot-digitizer,Patriot Digitizer,"The PATRIOT Digitizer is a high-end, full 6DOF digitizer, and is the most cost effective digitizer on the market. This easy-to-use system allows you to move freely--around, under and behind objects--and has the capability to digitize both big and small items.",whole,primates,instrumentation,physiological,"data analysis neurotechnology*","neuroinformatics* cogn. & behav. neurosci.","user manual citations",licensed,Polhemus, 255,nif-0000-00135,http://rcsb.org/pdb,PDB,An Information Portal to 105839 Biological Macromolecular Structures,macromol.,all,"database* ontology & data mngmt. software","anatomical biochemical*","visualization data analysis* annotation","neuroinformatics* cell., mol., & syst. neurosci.",user manual,freeware,"University of California at San Diego; California; USA, Rutgers University; New Jersey; USA","NSF, NIGMS, DOE, NLM, NCI, NINDS, NIDDK" 256,nif-0000-01866,http://pdsp.med.unc.edu/pdsp.php,"PDSP Ki Database, Ki Database",Database of information on the abilities of drugs to interact with an expanding number of molecular targets. ,macromol.,all,database,"biochemical* anatomical functional","annotation data analysis*","neuroinformatics cell., mol., & syst. neurosci.*","user manual citations",freeware,University of North Carolina at Chapel Hill; North Carolina; USA,"NIMH, Heffter Research Institute" 257,nif-0000-03266,http://www.peptideatlas.org/,PeptideAtlas,"Multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. ",macromol.,all,"database* atlas ontology & data mngmt.","biochemical* functional","annotation data analysis*",neuroinformatics,"user manual FAQs",freeware,Institute for Systems Biology; Washington; USA,"EU, NCI, NHGRI, NIGMS" 258,PMC4019854,https://github.com/jeffduda/Petiole,Petiole,"This module incorporates and extends an existing implementation of a graph class (Tustison et al., 2008) and provides ITK functions for a variety of graph metrics while using the Matlab-based Brain Connectivity Toolkit (Rubinov and Sporns, 2010) for algorithmic guidance.","regions* whole",primates,software,anatomical,"visualization* data analysis modeling & simulation","neuroanatomy* neuroinformatics",user manual,open source,"Penn Image Computing and Science Laboratory, Department of Radiology, University of Pennsylvania", 259,PMC3284145,http://pngu.mgh.harvard.edu/~purcell/plink/,PLINK,"PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.",macromol.,primates,software,functional,"data analysis annotation*","neuroinformatics cogn. & behav. neurosci.*","user manual user forum FAQs citations",freeware,"Primates Genetic Research (CHGR), Massachusetts General Hospital (MGH)", 260,22644868,http://sourceforge.net/projects/powermap/,PowerMap,A power calculator for medical imaging studies. Implements theoretical power calculation algorithms based on non-central random field theory. It can also calculate power for statistical analyses with FDR (false discovery rate) corrections.,"whole regions*",all,software,functional,data analysis,"cogn. & behav. neurosci.* neuroinformatics","user manual citations",,"Wake Forest School of Medicine, Winston-Salem, NC,",National Institute of Neurological Disorders and Stroke (NINDS) 261,23417655,http://www.mlnl.cs.ucl.ac.uk/pronto/,PRoNTo: pattern recognition for neuroimaging toolbox,Is a software toolbox based on pattern recognition techniques for the analysis of neuroimaging data. Statistical pattern recognition is a field within the area of machine learning which is concerned with automatic discovery of regularities in data through the use of computer algorithms.,whole,primates,software,anatomical,"visualization* data analysis","cogn. & behav. neurosci. clinical & dev. neurobiol.* neuroinformatics","user manual user forum citations",freeware,University College London,"PASCAL Harvest framework, The Wellcome Trust" 262,24163114,http://protege.stanford.edu/,Protege ontology editor,"A free, open-source ontology editor and framework for building intelligent systems",all,all,"software ontology & data mngmt.*",functional,"visualization annotation*","neuroinformatics clinical & dev. neurobiol.* comput. neurosci.","user manual user forum blog/social networking citations",freeware,Stanford Center for Biomedical Informatics Research at the Stanford University School of Medicine,National Institute of General Medical Science 263,PMC3411070,http://psychtoolbox.org/,Psychtoolbox,Psychophysics Toolbox Version 3 (PTB-3) is a free set of Matlab and GNU Octave functions for vision and neuroscience research.,whole,insects,software,"functional physiological*",visualization,"cell., mol., & syst. neurosci.* neuroinformatics","user manual user forum FAQs citations",open source,by Mario Kleiner, 264,nlx_86401,http://www.ncbi.nlm.nih.gov/pubmedhealth/,PubMed Health,Clinical effectiveness research finds answers to the question What works in medical and health care.,whole,all,"database* ontology & data mngmt.",functional,annotation,"neuroinformatics* clinical & dev. neurobiol.","user manual citations",freeware,NCBI, 265,23893006,http://www2.ece.ohio-state.edu/~aleix/ASLdatabase.htm,Purdue ASL Database,Database of American Sign Language (ASL) videos and transcriptions,"whole* regions",primates,database,functional,visualization,"cogn. & behav. neurosci.* neuroinformatics","user manual citations",freeware,Purdue University,NSF 266,10.1007/s12021-013-9188-z,http://sourceforge.net/projects/py3dn,Py3DN,"Py3DN, is an open-source solution providing novel tools to analyze and visualize 3D data collected with the widely used Neurolucida (MBF) system.",cellular,all,software,anatomical,"visualization* data analysis",neuroinformatics,"user manual citations",open source,Centro de Matem˜tica da Universidade do Porto,European Regional Development Fund 267,PMC4115634,https://github.com/Mouse-Imaging-Centre/pydpiper,pydpiper,pydpiper is a set of python modules that offers programmatic control over pipelines.,all,all,software,functional,"data analysis* visualization","neuroinformatics* cogn. & behav. neurosci.",user manual,open source,"Rodents Imaging Centre, Hospital for Sick Children, Toronto, ON, Canada",Canadian Institutes of Health Research 268,PMC3989728,http://www.pyhrf.org/,PyHRF,"PyHRF is a set of tools for within-subject fMRI data analysis, which focuses on the characterization of the hemodynamics.","whole regions*",primates,software,"functional* anatomical","data analysis* visualization",cogn. & behav. neurosci.,user manual,freeware,"LNAO, Gif-Sur-Yvette, France", 269,PMC3426793,http://www.pymvpa.org/,PyMVPA - Multivariate Pattern Analysis in Python,"PyMVPA is 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. It is designed to integrate well with related software packages, such as scikit-learn, and MDP","whole regions*",primates,software,"functional anatomical*",data analysis,"cogn. & behav. neurosci. neuroinformatics*","user manual user forum citations",open source,"University of Magdeburg, Germany","CIMeC, the Autonomous Province of Trento, the Fondazione Cassa Risparmio Trento e Rovereto" 270,24777387,http://r2agui.sourceforge.net/,r2aGUI,"The R2AGUI converts raw data from PHILIPS MRI scanners (PAR/REC format) to the popular ANALYZE 7.5 format, which is used in SPM and many other imaging software packages.","whole regions*",primates,"software ontology & data mngmt.*",anatomical,"visualization annotation*","cogn. & behav. neurosci.* neuroinformatics","user manual citations",open source,, 271,nif-0000-10407,http://columbia.edu/cu/biology/faculty/yuste/databases.html,Rafael Yustes Laboratory,Laboratory that aims to understand the function of the cortical microcircuit by reverse-engineering of the cortical microcircuit using the mouse neocortex in vitro and in vivo as their experimental preparations.,"regions* whole cellular",rodents,"database* topical portal","physiological* anatomical functional","visualization* modeling & simulation"," cell., mol., & syst. neurosci.* comput. neurosci.","user manual citations",freeware,Columbia University; New York; USA, 272,nif-0000-00134,http://rgd.mcw.edu/,Rat Genome Database (RGD),"Centralized database that collects, manages, and distributes data generated from ongoing rat genetic and genomic research efforts and makes these data widely available to the scientific community.",macromol.,rodents,"database ontology & data mngmt.*",functional,"annotation* visualization data analysis","neuroinformatics* cell., mol., & syst. neurosci.","user manual user forum citations",freeware,"Bioinformatics Research Center, Medical College of Wisconsin",NIH 273,nif-0000-03390,http://www.reactome.org/,Reactome,"Open-source, open access, manually curated and peer-reviewed pathway database with pathway annotations authored by expert biologists.",macromol.,all,"database* ontology & data mngmt.","biochemical* anatomical functional","annotation modeling & simulation* visualization","neuroinformatics* cell., mol., & syst. neurosci.","user manual user forum blog/social networking citations",freeware,"Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, European Bioinformatics Institute, New York University School of Medicine; New York; USA","NHGRI, European Union, (FP6, ENFIN), Ontario Research Fund, European Molecular Biology Laboratory" 274,PMC4228977,http://www.mrc-cbu.cam.ac.uk/methods-and-resources/toolboxes/,Representational Similarity Analysis (RSA),A matlab toolbox for RSA. RSA characterizes the representation in each brain region by a representational dissimilarity matrix,"whole* regions",primates,software,"anatomical physiological*","data analysis visualization*","neuroanatomy* neuroinformatics","user manual user forum citations",freeware,MRC Cognition and Brain Sciences Unit,European Research Council 275,PMC4137278,http://www.nimh.nih.gov/research-priorities/rdoc/nimh-research-domain-criteria-rdoc.shtml#toc_matrix,Research Domain Criteria (RDoC) of the National Institute of Mental Health,"The structure of the RDoC is described as a matrix in which the rows represent various constructs grouped hierarchically into broad domains of function. The columns of the matrix denote different levels of analysis, from genetic, molecular, and cellular levels, proceeding to the circuit-level to the level of the individual, family environment, and social context",all,primates,topical portal,functional,"data analysis annotation*","cogn. & behav. neurosci. clinical & dev. neurobiol.* neuroinformatics",user manual,freeware,NIMH, 276,PMC4046318,http://restfmri.net/forum/index.php,Resting-State fMRI,"Resting-State fMRI Data Analysis Toolkit (REST) is a convenient toolkit to calculate Functional Connectivity (FC), Regional Homogeneity (ReHo), Amplitude of Low-Frequency Fluctuation (ALFF), Fractional ALFF (fALFF), Gragner causality, degree centrality, voxel-mirrored homotopic connectivity (VMHC) and perform statistical analysis.",whole,primates,software,"functional* anatomical","visualization modeling & simulation*","cogn. & behav. neurosci. neuroinformatics*","user manual user forum blog/social networking citations",open source,"State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China", 277,22281931,http://cobweb.cs.uga.edu/~tliu/neuroinformatics/neuroinformatics_jointmodeling.htm,ROI Optimization,"A novel methodology to computationally optimize ROIs locations derived from task-based fMRI data for individuals so that the optimized ROIs are more consistent, reproducible and predictable across brains.",whole,primates,software,"functional anatomical*","visualization data analysis*",cogn. & behav. neurosci.,user manual,open source,"Northwestern Polytechnical University, Xian, China",NIH 278,24777387,http://www.nitrc.org/projects/rosetta/,Rosetta Bit,"The Rosetta Bit project will house public datasets that have been transcoded into multiple formats. This library of valid file format conversions (DICOM->NIFTI, DICOM->PAR/REC, etc.) will provide a reference for tool developers seeking to support multiple sources of data.","whole regions*",primates,"software ontology & data mngmt.*",anatomical,"visualization annotation* data analysis","cogn. & behav. neurosci. neuroinformatics*","user manual user forum",open source,"Vanderbilt University, Nashville, TN, USA",NIH 279,PMC3284145,http://schizophreniaforum.org/,Schizophrenia Research Forum (SRF),"The mission of the SRF is to help in the search for causes, treatments, and understanding of the devastating disease of schizophrenia.",macromol.,primates,topical portal,all,"annotation data analysis*","cogn. & behav. neurosci. clinical & dev. neurobiol.* cell., mol., & syst. neurosci. neuroinformatics","user manual user forum citations",freeware,,"NIMH, Brain & Behavior Research Foundation (BBRF)" 280,10.4249/scholarpedia.2929,http://www.scilab.org,Scilab,Scilab is free and open source software for numerical computation providing a powerful computing environment for engineering and scientific applications.,whole,all,software,"anatomical functional*","visualization modeling & simulation* data analysis","neuroinformatics comput. neurosci.*","user manual blog/social networking citations",open source,Scilab Enterprises, 281,PMC3439738,http://scimedia.com/,SciMedia,High speed membrane potential imaging of rat in vivo preparation stained with voltage-sensitive dye.,"cellular macromol.*",rodents,"software instrumentation* ontology & data mngmt.",anatomical,"visualization* data analysis","neuroinformatics* comput. neurosci.","user manual user forum FAQs citations",licensed,SciMedia Ltd., 282,nif-0000-10427,https://gene.sfari.org/autdb/Welcome.do,SFARI Gene: AutDB,"Curated public database for autism research built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The genetic information includes data from linkage and association studies, cytogenetic abnormalities, and specific mutations associated with ASD.",macromol.,"rodents primates*","database* ontology & data mngmt.","functional biochemical*","annotation* data analysis","clinical & dev. neurobiol.* neuroinformatics","user manual citations",freeware,SFARI - Simons Foundation Autism Research Initiative,MindSpec: Informatics for Neurodevelopmental Conditions 283,PMC4172099,http://www.losonczylab.org/sima/0.3/,SIMA,SIMA (Sequential IMage Analysis) is an Open Source package for analysis of time-series imaging data arising from fluorescence microscopy.,cellular,all,software,anatomical,"visualization* data analysis","neuroinformatics cell., mol., & syst. neurosci.*",user manual,freeware,"Columbia University in the City of New York, New York, NY, USA",Howard Hughes Medical Institute International Student Research fellowship 284,10.4249/scholarpedia.1738,https://www.mrt.uni-jena.de/simbio/index.php/Main_Page,SimBio,"The SimBio software consists of two subpackages: IPM (Inverse Problem Method) toolbox containing algorithms for inverse EEG and MEG source analysis. NeuroFEM, which allows Finite Element Method (FEM) based EEG and MEG forward solutions.",whole,primates,software,physiological,"modeling & simulation* visualization","comput. neurosci.* cell., mol., & syst. neurosci. neuroinformatics","user manual user forum citations",open source,, 285,nif-0000-23302,http://simtk.org,Simtk.org,"A National NIH Center for Biomedical Computing that focuses on physics-based simulation of biological structures and provides open access to high quality simulation tools, accurate models and the people behind them.","macromol.* whole",all,software,"functional biochemical*","visualization modeling & simulation*","neuroinformatics* comput. neurosci.","user manual user forum citations",open source,Simbios,NIH 286,23949335,http://neurospeech.org/sldb,SLDB - Speech/Language Disorders Database,Genes implicated in speech and language phenotypes,macromol.,rodents,"database* software",functional,"visualization* data analysis annotation","neuroinformatics* cell., mol., & syst. neurosci. cogn. & behav. neurosci.","user manual citations",freeware,Boston University,National Science Foundation 287,22194186,http://www.slicer.org/,Slicer,"Slicer, or 3D Slicer, is a free, open source software package for visualization and image analysis. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X.","whole regions*",primates,"software ontology & data mngmt.*",anatomical,"visualization* data analysis annotation","clinical & dev. neurobiol.* neuroinformatics","user manual user forum FAQs citations",open source,"Brigham and Women's Hospital, Harvard Medical School, Boston, MA","NIH, Neuroimage Analysis Center (NAC)" 288,10.4249/scholarpedia.1568,http://www.cis.hut.fi/research/som_lvq_pak.shtml,SOM_PAK and LVQ_PAK,"Two public-domain software packages, SOM_PAK for the Self-Organizing Map algorithm and LVQ_PAK for the Learning Vector Quantization algorithms are developed to demonstrate the implementation of these algorithms and to ease first experiments.",all,all,software,"anatomical functional*",modeling & simulation,"comput. neurosci.* cell., mol., & syst. neurosci.","user manual citations",open source,Academy of Finland and Helsinki University of Technology, 289,23504659,http://www.miketipping.com/sparsebayes.htm,Sparse Bayesian Models (and the RVM),Sparse Bayesian Models (and the RVM),regions,primates,software,"anatomical functional*",modeling & simulation,"cogn. & behav. neurosci. clinical & dev. neurobiol.* comput. neurosci.","user manual citations",open source,By Mike Tipping, 290,24338729,http://www.public.asu.edu/~jye02/Software/SLEP,Sparse Learning and Efficient Projections (SLEP),"A toolkit for finding sparse representation. The main functions were written in Matlab The main functions are written in MATLAB, while the codes for key subroutines the related Euclidean projections were written in C.",whole,primates,software,anatomical,data analysis,"neuroinformatics* clinical & dev. neurobiol.","user manual citations",open source,Arizona State University, 291,PMC3620507,http://spatstat.org,spatstat:Open source software for spatial statistics,"spatstat is a package for analyzing spatial point pattern data. Its functionality includes exploratory data analysis, model-fitting, and simulation.","regions* cellular",all,software,anatomical,"data analysis* modeling & simulation visualization","neuroanatomy comput. neurosci.* neuroinformatics","user manual FAQs citations",open source,"University of Western Australia, University of New Brunswick", 292,23274962,http://spikestream.sourceforge.net/,SpikeStream,"SpikeStream is a tool for the creation, visualization, storage and analysis of spiking neural networks, with a plugin architecture that enables it to wrap neural simulators, such as NeMo, and interface with external devices.","regions* cellular",all,"software* database","anatomical* physiological","visualization* modeling & simulation neurotechnology","comput. neurosci.* neuroinformatics","user manual citations",,Imperial College London,"EPSRC grant, NVIDIA University Program" 293," 24692020",http://life.nthu.edu.tw/~lablcc/SPIN/,SPIN: a method of Skeleton-based Polarity Identification for Neurons,"SPIN was designed to work with large-scale neuronal databases in which tracing-line data are available. In SPIN, a classifier is first trained by neurons with known polarity in two steps: 1) identifying morphological features that most correlate with the polarity and 2) constructing a linear classifier by determining a discriminant axis (a specific combination of the features) and decision boundaries.",cellular,insects,software,anatomical,"annotation* data analysis","neuroanatomy* neuroinformatics",user manual,open source,"NCHC (National Center for High-performance Computing) and NTHU (National Tsing Hua University), Hsinchu, Taiwan", 294,24253973,http://bimpa.group.shef.ac.uk/SpineML,SpineML: Spiking Neural Mark-up Language,The Spiking Neural Mark-up Language (SpineML) is a declarative XML based model description language for large scale neural network models. It is partially based upon on the INCF NineML syntax utilizing the LEMS (Low Entropy Model Specification) common model specification syntax which is proposed to unite a range of INCF supported simulators including NeuroML v2.0 and PyNN.,"whole* regions cellular",all,ontology & data mngmt.,"physiological* anatomical biochemical",modeling & simulation,"neuroinformatics* comput. neurosci.","user manual user forum citations",freeware,"Department of Automatic Control and Systems Engineering, University of Sheffield, Sheffield, UK","ESPRC via the Biologically-Inspire Massively Parallel Architectures (BIMPA) EPSRC Delivery Plan Kickstart funding" 295,PMC3350955,http://plato.stanford.edu/entries/mental-imagery/,Stanford Encyclopedia of Philosophy,"Welcome to the Stanford Encyclopedia of Philosophy (SEP). From its inception, the SEP was designed so that each entry is maintained and kept up-to-date by an expert or group of experts in the field. All entries and substantive updates are refereed by the members of a distinguished Editorial Board before they are made public.",whole,primates,topical portal,functional,"visualization* annotation",cogn. & behav. neurosci.,"user manual citations",freeware,Stanford, 296,24446234,http://sourceforge.net/projects/structurebasedneuronretrieval/,Structure-based neuron retrieval,Code for Structure-based neuron retrieval across Drosophila brains,"regions* cellular",insects,software,anatomical,"data analysis* visualization","neuroanatomy* comput. neurosci. neuroinformatics",user manual,open source,"Medical University of Vienna, Vienna, Austria","European Union, Austrian Sciences Fund" 297,"PMC3508475 nif-0000-00016",http://sumsdb.wustl.edu/sums/index.jsp,SumsDB (Surface Management System Database),SumsDB is a repository of brain-mapping data (surfaces & volumes; structural & functional data) from many laboratories.,"regions* whole","primates rodents*","atlas* software database",anatomical,"visualization* annotation","neuroinformatics comput. neurosci.* cogn. & behav. neurosci.","user manual citations",freeware,Washington University in St. Louis??School Of Medicine,HBP 298,10.4249/scholarpedia.1463 ,http://www.swarmanoid.org/,Swarmanoid,"The main scientific objective of this research project is the design, implementation and control of a novel distributed robotic system. The system will be made up of heterogeneous, dynamically connected, small autonomous robots.",whole,all,"instrumentation* software topical portal",functional,neurotechnology,cogn. & behav. neurosci.,"user manual citations",freeware,,European Commission 299,21181305,http://synapses.clm.utexas.edu/,SynapseWeb,SynapseWeb is a portal into the 3D ultrastructure of the brain,macromol.,all,"topical portal ontology & data mngmt.*",anatomical,"visualization* annotation","cell., mol., & syst. neurosci.",user manual,freeware,The University of Texas at Austin,NIH/NIBIB/NIMH 300,PMC3701254,http://cajalbbp.cesvima.upm.es/sas/,Synaptic Apposition Surface (SAS),Software for visualizing geometrical features of chemical synapses from morphological studies of active zone (AZ) and the postsynaptic density (PSD) components of the synaptic junction,cellular,all,software,anatomical,visualization,"cell., mol., & syst. neurosci.* neuroanatomy",user manual,freeware,"Universidad Politecnica de Madrid, Madrid, Spain",Cajal Blue Brain Project 301,10.4249/scholarpedia.3036 ,http://sbml.org,Systems Biology Markup Language (SBML),"A free and open interchange format for computer models of biological processes. SBML is useful for models of metabolism, cell signaling, and more.",macromol.,all,"ontology & data mngmt.* software",physiological,"annotation modeling & simulation* visualization","neuroinformatics cell., mol., & syst. neurosci.*","user manual user forum citations",freeware,Caltech,"NIH/NIGMS, Caltech, EBML-EBI" 302,23161265,http://cal-r.org/index.php?id=software,TD model simulator,"Temporal Difference (TD) (Sutton and Barto, 19871) is a real-time error correction model in which learning is computed according to the difference between successive predictions and a discount factor that decays exponentially, reflecting the fact that predictors closer to a reinforce (the unconditioned stimulus, US) are based on more recent information and thus more accurate.",all,all,software,functional,modeling & simulation,"cogn. & behav. neurosci.* clinical & dev. neurobiol.","user manual citations",open source,"Centre for Computational and Animal Learning Research, St Albans, UK", 303,nif-0000-24805,http://temporal-lobe.com/,Temporal-lobe.com,"In the connectome featured on this website, the three-dimensional organization of the projection patterns between and within the hippocampal formation, the parahippocampal region and the retrosplenial cortex are visualized in an interactive connectome. All reported projections concerning this system for the rat were collected and stored in a database and visualized in an interactive pdf document.","regions* cellular","rodents* primates","atlas* ontology & data mngmt.",anatomical,"visualization* annotation","neuroanatomy* neuroinformatics","user manual citations",freeware,Norwegian University of Science and Technology; Trondheim; Norway,Norwegian Research Council 304,10.1007/s12021-010-9075-9,http://biopsynltoolbox.sourceforge.net,The Biopsychology Nonlinear Analysis Toolbox,The major goal of this project was to provide a toolbox for non-linear time series analysis that is easily accessible to a wide range of neuroscientists.,whole,primates,software,"physiological* functional",data analysis,"cogn. & behav. neurosci.* cell., mol., & syst. neurosci. neuroinformatics","user manual user forum citations",open source,"Institute for Cognitive Neuroscience, Department of Biopsychology, Ruhr-Universitat Bochum, Germany",Research Department Neuroscience of Ruhr-University Bochum 305,PMC3942659,http://www.braininitiative.nih.gov/index.htm,The Brain Initiative,Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative is part of a new Presidential focus aimed at revolutionizing our understanding of the human brain.,"cellular* whole",all,topical portal,functional,neurotechnology,"neuroinformatics clinical & dev. neurobiol. cell., mol., & syst. neurosci.*","user manual citations",open source,NIH,NIH 306,PMC3112315,http://connectome.ch,The connectome mapping toolkit,"A python-based open source toolkit for magnetic resonance connectome mapping, data management, visualization and analysis.","whole* regions",primates,"ontology & data mngmt.* software","anatomical* functional","data analysis* visualization","neuroinformatics* neuroanatomy cogn. & behav. neurosci.","user manual citations",open source,EPFL & UNIL-CHUV, 307,PMC3585434,http://foodcast.sissa.it/neuroscience,The FoodCast research image database (FRIDa),"The Foodcast Research Image Database (FRIDa) is a comprehensive collection of both food and nonfood items that can be used for non-commercial purposes. FRIDa has been validated and the results have been published in Frontiers in human Neuroscience (Foroni, Pergola, Argiris, Rumiati, 2013).",whole,primates,database,functional,"visualization* annotation","cogn. & behav. neurosci.* neuroinformatics",user manual,open source,"Cognitive Neuroscience Sector, SISSA - Trieste, Trieste, Italy",SISSA 308,nif-0000-00088,https://msu.edu/~brains/brains/human,The Human Brain Atlas,A labeled three-dimensional atlas of the human brain created from MRI images.,"whole* cellular",primates,"atlas* ontology & data mngmt.",anatomical,visualization,"neuroanatomy* neuroinformatics","user manual citations",freeware,Michigan State University; Michigan; USA,NSF 309,10.4249/scholarpedia.1463,http://www.eecs.harvard.edu/ssr/projects/progSA/kilobot.html,The Kilobot Project,"A low-cost robot designed to make testing collective algorithms on hundreds or thousands (""kilos"") of robots accessible to robotics researchers. Each robot has the basic capabilities required for a swarm robot, but is made with low-cost parts, and is mostly assembled by an automated process.",whole,all,"software instrumentation*",functional,"neurotechnology* visualization","cell., mol., & syst. neurosci.* comput. neurosci.","user manual citations",licensed,Wyss Institute for Biologically Inspired Engineering,"WYSS Institute for Biologically Inspired Engineering, NSF" 310,23250668,http://mmspg.epfl.ch,The Multimedia Signal Processing Group (MMSPG),"The group is active in research and teaching in the field of multimedia signal processing. Research topics span over three highly interconnected disciplines of multimedia signal processing, namely multimedia coding, multimodal processing, analysis and interpretation, and media security.","whole regions*",primates,"instrumentation* software",physiological,"data analysis neurotechnology*","cell., mol., & syst. neurosci.* comput. neurosci. neuroinformatics","user manual citations",freeware,Swiss Federal Institute of Technology (EPFL),Swiss National Foundation for Scientic Research 311,23893006,http://www.cis.upenn.edu/~treebank/,The Penn Treebank Project,The Penn Treebank Project annotates naturally-occuring text for linguistic structure.,"whole* regions",primates,"database ontology & data mngmt.*",functional,data analysis,"cogn. & behav. neurosci.* neuroinformatics","user manual citations",freeware,University of Pennsylvania, 312,PMC4162418,http://www.rbwb.org,The Rodent Brain Workbench,The Rodent Brain WorkBench presents a collection of brain mapping and atlasing oriented resources,"whole regions*",rodents,"atlas* database software ontology & data mngmt.",anatomical,"visualization* annotation","neuroinformatics* neuroanatomy clinical & dev. neurobiol.","user manual citations","freeware licensed*","University of Oslo, Oslo, Norway",primates Brain Project 313,PMC3678125,http://www.thevirtualbrain.org,The Virtual Brain (TVB),"This simulation environment enables the model-based inference of neurophysiological mechanisms across different brain scales that underlie the generation of macroscopic neuroimaging signals including functional MRI (fMRI), EEG and MEG.","whole regions*",all,software,"physiological* anatomical functional","modeling & simulation* data analysis","comput. neurosci. cell., mol., & syst. neurosci.* neuroinformatics","user manual blog/social networking citations",open source,"Aix Marseille Universitat, Marseille, France",James S. McDonnell Foundation 314,PMC3159951,http://www.cs.princeton.edu/~blei/topicmodeling.html,Topic modeling,"Topic models are a suite of algorithms that uncover the hidden thematic structure in document collections. These algorithms help us develop new ways to search, browse and summarize large archives of texts.","whole regions*",primates,"software* topical portal ontology & data mngmt.",functional,"data analysis visualization annotation modeling & simulation*","neuroinformatics cogn. & behav. neurosci.* comput. neurosci.","user manual user forum citations",open source,Princeton University, 315,PMC3578208,http://trackvis.org/dtk/,TrackVis,"Diffusion Toolkit is a set of command-line tools with a GUI frontend that performs data reconstruction and fiber tracking on diffusion MR images. Basically, it does the preparation work for TrackVis.",whole,primates,"software* ontology & data mngmt.",anatomical,"visualization* data analysis","cogn. & behav. neurosci. neuroinformatics*","user manual user forum FAQs citations",freeware,"Department of Radiology, Massachusetts General Hospital",MGH GCRC and NIMH 316,21222051,http://www.treestoolbox.org,Trees Toolbox,"A freely distributed open-source software package, the TREES toolbox, written in Matlab (Mathworks, Natick, MA), in order to help to pool together the resources offered by a wide variety of novel approaches to studying dendritic and axonal branching that have recently become available.",cellular,all,software,anatomical,"visualization data analysis*","neuroanatomy* neuroinformatics","user manual citations",open source,"University College London, London, UK", 317,22426994,http://tulip.labri.fr/TulipDrupal/,Tulip,"Tulip aims to provide the developer with a complete library, supporting the design of interactive information visualization applications for relational data that can be tailored to the problems he or she is addressing.",all,all,"software* database",functional,"visualization* annotation",neuroinformatics,"user manual user forum",open source,, 318,PMC4026698,www.turtleseg.org,Turtleseg,TurtleSeg is an interactive segmentation tool designed for 3D medical images.,"whole* regions",primates,software,anatomical,"visualization* data analysis","neuroinformatics clinical & dev. neurobiol.*","user manual FAQs blog/social networking citations",licensed,Turtleseg, 319,PMC3620563,http://genome.ucsc.edu,UCSC Genome Bioinformatics,This site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides portals to ENCODE data at UCSC (2003 to 2012) and to the Neandertal project.,macromol.,all,"database* software",functional,"visualization data analysis*","cell., mol., & syst. neurosci. clinical & dev. neurobiol.* neuroinformatics","user manual blog/social networking FAQs citations","freeware licensed*",Genome Bioinformatics Group of UC Santa Cruz,"NHGRI, HHMI, California institute of science & innovation" 320,nlx_53981,http://www.uniprot.org,UniProt,"The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation.",macromol.,all,"database* software ontology & data mngmt.",functional,"visualization data analysis* annotation","neuroinformatics cell., mol., & syst. neurosci.* clinical & dev. neurobiol.","user manual FAQs citations",freeware,UniProt, 321,"PMC3508475 nlx_83091",http://umcd.humanconnectomeproject.org/,USC Multimodal Connectivity Database (UMCD),A web-based repository and analysis site for connectivity matrices that have been derived from de-identified neuroimaging data. Users can analyze connectivity matrices that have been shared publicly and upload their own matrices to share or analyze privately.,whole,primates,"database* software","anatomical functional*","data analysis visualization* annotation","neuroinformatics* cogn. & behav. neurosci.",user manual,freeware,University of California Los Angeles, 322,25310965,http://vaa3d.org,Vaa3D,A Swiss army knife for bioimage visualization & analysis,cellular,all,software,anatomical,"visualization* data analysis","neuroinformatics comput. neurosci.*","user manual citations",freeware,HHMI, 323,PMC3607831,http://dbm.neuro.uni-jena.de/vbm,VBM toolboxes,"The VBM toolboxes are a collection of extensions to the segmentation algorithm of SPM2, SPM5, and SPM8 (Wellcome Department of Cognitive Neurology) to provide voxel-based morphometry (VBM). The toolboxes are named according to the SPM version.",regions,primates,software,"anatomical* functional","visualization data analysis* modeling & simulation","comput. neurosci.* clinical & dev. neurobiol. neuroinformatics","user manual citations","freeware* licensed","University of Jena, Department of Psychiatry", 324,PMC3381445,http://social.cs.uiuc.edu/projects/vcode.html,VCode & Vdata,"VCode and VData are a suite of""open source""applications which create a set of effective interfaces supporting the video annotation workflow .",whole,primates,software,functional,visualization,"neuroinformatics cogn. & behav. neurosci.*","user manual citations",open source,University of Illinois at Urbana Champaign,NSF 325,PMC4222236,http://bioinformatics.psb.ugent.be/software/details/Venn-Diagrams,Venn diagram tool,With this tool you can calculate the intersection(s) of list of elements. It will generate a textual output indicating which elements are in each intersection or are unique to a certain list. If the number of lists is lower than 6 it will also produce a graphical output in the form of a venn diagram. You have the choice between symmetric (default) or non symmetric venn diagrams. Currently you are able to calculate the intersections of at maximum 30 lists.,all,all,software,functional,"visualization* annotation",neuroinformatics,"user manual citations",freeware,, 326,24234916,http://verbs.colorado.edu/~mpalmer/projects/verbnet.html,VerbNet,"VerbNet (VN) (Kipper-Schuler 2006) is the largest on-line verb lexicon currently available for English. It is a hierarchical domain-independent, broad-coverage verb lexicon with mappings to other lexical resources such as WordNet (Miller, 1990; Fellbaum, 1998), Xtag (XTAG Research Group, 2001), and FrameNet (Baker et al., 1998).",whole,primates,"database ontology & data mngmt.*",functional,"data analysis* annotation","neuroinformatics comput. neurosci.* cogn. & behav. neurosci.","user manual citations",freeware,"Department of Linguistics University of Colorado Boulder", 327,PMC3176413,http://vidriotechnologies.com/,Vidrio technologies,"Vidrio Technologies launched January 2014 to further the development, maintenance, and support of software for neuroscience imaging. Our core product is ScanImage, software for the control of experiments using two-photon laser scanning microscopy.",cellular,all,"software* instrumentation",physiological,"visualization* data analysis","cell., mol., & syst. neurosci.* neuroinformatics",user manual,open source,"vidrio technologies, LLC",Atlassian 328,PMC4053686,http://www.neurobiologie.fu-berlin.de/BeeBrain/Project.html,Virtual Atlas of the Honeybee Brain,"The Honeybee Standard Brain Atlas is calculated from 20 individual bee brain images that were immuno-stained, imaged as whole-mounts with the confocal microscope, and segmented along the borderlines of 22 neuropils.","whole* regions",insects,"atlas* ontology & data mngmt.","anatomical* physiological","annotation visualization*","neuroanatomy* neuroinformatics","user manual citations",freeware,Freie Universitat Berlin,Berlin School of Mind & Brain 329,nif-0000-00048,https://visiome.neuroinf.jp/,Visiome Platform,"Data sharing platform with a variety of digital research resources in vision science such as Experimental data, Mathematical model, Illusion stimulus, and Analytical tools.",regions,all,"database* software topical portal","anatomical physiological*","modeling & simulation* visualization","neuroinformatics comput. neurosci.*","user manual citations",freeware,"INCF Japan Node, RIKEN Brain Science Institute", 330,PMC4033674,http://cvcweb.ices.utexas.edu/cvcwp/?page_id=2089,VolRoverN,"VolRoverN is a software package that offers comprehensive functionality for geometric and electrophysiological neuronal simulation at multiple scales. It produces spatially realistic surface models of neuronal processes, glia, and intracellular organelles from cross-sectional traces.",cellular,rodents,software,anatomical,"visualization* data analysis","neuroanatomy comput. neurosci.* neuroinformatics","user manual citations",open source,"University of Texas, Austin, TX, USA","NIH, NSF" 331,nif-0000-20925,http://wikipathways.org,WikiPathways,"Open, collaborative platform dedicated to the curation of biological pathways. Each pathway has a dedicated wiki page, displaying the current diagram, description, references, download options, version history, and component gene and protein lists.",macromol.,all,ontology & data mngmt.,"biochemical functional*","visualization* annotation modeling & simulation","neuroinformatics cell., mol., & syst. neurosci.*","user manual citations",freeware,"University of California at San Francisco; California; USA, Maastricht University; Maastricht; Netherlands","NIH, Netherlands Bioinformatics Centre, Google Summer of Code program, NWO - Netherlands Organization for Scientific Research, NIGMS" 332,24234916,http://wordnet.princeton.edu/,WordNet,"WordNet is a large lexical database of English. Nouns, verbs, adjectives and adverbs are grouped into sets of cognitive synonyms (synsets), each expressing a distinct concept.",whole,primates,ontology & data mngmt.,functional,"visualization data analysis*","comput. neurosci. neuroinformatics*","user manual FAQs citations",freeware,Princeton University, 333,PMC3602642,http://www.wutech.com,WUtech,"Wu Technologies is a company specialized in Surveying and Engineering industries. We are dealers from the most recognized brands in the market such as Nikon, Spectra, Astech & Geosurv.","cellular regions*",rodents,instrumentation,physiological,visualization,"cell., mol., & syst. neurosci.* neuroinformatics","user manual blog/social networking citations",licensed,Wu-technologies store, 334,21479735,http://www.xcede.org,XCEDE,"XML-based Clinical and Experimental Data Exchange (XCEDE) provides an extensive metadata hierarchy for storing, describing and documenting the data generated by scientific studies",whole,primates,ontology & data mngmt.,anatomical,annotation,"cogn. & behav. neurosci.* neuroinformatics","user manual citations",freeware,BIRN,NIH/NCRR 335,PMC3483622,http://alivelearn.net/xjview8,Xjview:A viewing program for spm,Software for viewing and analyzing fMRI images,"whole* regions",primates,software,"functional* anatomical","visualization* data analysis annotation","neuroinformatics* cogn. & behav. neurosci.","user manual FAQs citations","freeware* licensed",Baylor College of Medicine, 336,nif-0000-00242,http://zebrafish.org,Zebrafish International Resource Center,"Supplies access to wild-type, mutant, and transgenic zebrafish lines, EST's/cDNAs, antibodies and fish health services.",whole,others,ontology & data mngmt.,functional,annotation,neuroinformatics,"user manual FAQs citations",licensed,University of Oregon; Oregon; USA,"NCRR, NIH Blueprint for Neuroscience Research" 337,nif-0000-21427,http://zfin.org/,ZFIN,The Zebrafish Model Organism Database,whole,others,"database* ontology & data mngmt. atlas",functional,"visualization data analysis*","neuroinformatics* neuroanatomy cell., mol., & syst. neurosci.","user manual user forum citations",freeware,University of Oregon; Oregon; USA,NHGRI