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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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User Friendly Functional Connectivity - UF²C Resource Report Resource Website 1+ mentions |
User Friendly Functional Connectivity - UF²C (RRID:SCR_016550) | UF²C | software application, data processing software, software resource, image analysis software, software toolkit, data analysis software | Software tool to standardize and facilitate connectivity studies through a graphical user interface and validated preset parameters. | standardize, functional, connectivity, brain, magnetic, resonance, imaging, graphical, user, interface, parameter |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: MATLAB |
FAPESP | Free, Available for download, Freely available | SCR_016550 | User Friendly Functional Connectivity | 2026-02-15 09:21:53 | 1 | |||||||
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nonparametricGGC_toolbox Resource Report Resource Website 1+ mentions |
nonparametricGGC_toolbox (RRID:SCR_016539) | nonparametricGGC | software application, data processing software, data analysis software, software resource | Software package for simulation framework and codes for estimating nonparametric Granger causality. Used to study brain functions. | nonparametric, Granger, causality, simulation, framework, code, estimate, brain, function | is related to: MATLAB | the Swiss National Science Foundation | Free, Available for download, Freely available | SCR_016539 | nonparametric Granger Geweke Causality | 2026-02-15 09:21:53 | 2 | |||||||
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NeuroAnatomy Toolbox Resource Report Resource Website 1+ mentions |
NeuroAnatomy Toolbox (RRID:SCR_016716) | nat, NAT | software application, data visualization software, data processing software, software resource, image analysis software, data analysis software | Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures. | biological, image, data, visualization, analysis, tracing, single, neuron, 3D, structure, brain |
is listed by: OMICtools is listed by: CRAN is related to: R Project for Statistical Computing is related to: elmr has parent organization: University of Cambridge; Cambridge; United Kingdom |
DOI:10.5281/zenodo.10171 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/nat/index.html |
SCR_016716 | NeuroAnatomy Toolbox, neuroanatomy toolbox, Neuro Anatomy Toolbox, neuro anatomy toolbox | 2026-02-15 09:21:48 | 5 | ||||||
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OpenBMI Resource Report Resource Website 1+ mentions |
OpenBMI (RRID:SCR_016876) | software application, data visualization software, data processing software, software resource, software toolkit, data analysis software | Software package for the development of Brain-Computer Interfaces with advanced pattern recognition algorithms. Used for analyzing brain signals which can be used to acquire, filter, process, classify and visualize brain signals in real time. | brain, computer, interface, analysis, signal, acquire, filter, process, visualize, data | has parent organization: Korea University; Seoul; South Korea | Free, Available for download, Freely available | http://openbmi.org/ | SCR_016876 | 2026-02-15 09:21:55 | 5 | |||||||||
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SpectraVis Resource Report Resource Website |
SpectraVis (RRID:SCR_016691) | software application, data visualization software, data processing software, software resource, web application, network graph visualization software, network analysis software, data analysis software | Web based neuroscience application for analyzing task-related functional networks over time and frequency. Interactive visualization tool for exploring functional brain connectivity. | functional, brain, conectivity, analyzing, network, time, frequency | Free, Available for download, Freely available | http://ericdeno.com/research/SpectraVis/ | SCR_016691 | 2026-02-15 09:21:54 | 0 | ||||||||||
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INCF-Neurobot Resource Report Resource Website 10+ mentions |
INCF-Neurobot (RRID:SCR_017004) | INCF Neurobot | data management software, software application, data processing software, software resource | Software tool for data management in clinical studies to improve care for patients with Traumatic Brain Injury (TBI). Used to search and find study variables with the associated information and export study data for further analysis. | data, management, clinical, study, brain, traumatic, injury |
has parent organization: Karolinska Institute; Stockholm; Sweden has parent organization: International Neuroinformatics Coordinating Facility |
Registration required | SCR_017004 | , International Neuroinformatics Coordinating Facility Neurobot, INCF Neurobot | 2026-02-15 09:21:53 | 16 | ||||||||
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COsleep Resource Report Resource Website 1+ mentions |
COsleep (RRID:SCR_017053) | cosleep | software application, data processing software, data analysis software, software resource | Software Python tool for sleep EEG analysis. Used for Closed and Open loop in Slow Ocillations, Sleep Stimulation in Auditory or Recording in full PSG using OpenBCI Cyton. | SpiSOP, OpenBCI, sleep, EEG, analysis, electroencephalogram, electrical, activity, brain, wave, pattern, disorder |
is related to: SpiSOP is related to: Python Programming Language |
Free, Available for download, Freely available | http://www.spisop.org/cosleep | SCR_017053 | Closed- and Open-loop Sleep Stimulations with Auditory Stimuli, Closed and Open loop sleep | 2026-02-15 09:21:54 | 1 | |||||||
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Prism Clinical Imaging Resource Report Resource Website 1+ mentions |
Prism Clinical Imaging (RRID:SCR_016977) | Prism Clinical Imaging, Inc. | software resource, service resource, data or information resource, training service resource, commercial organization | Provides Prism softwares and services that integrate advanced imaging into the clinical workflow for brain mapping from acquisition through processing, visualization, and export to PACS. Prism integrates functional MRI, diffusion MRI, perfusion, MR spectroscopy, and PET/CT into a unified workflow for diagnosis and treatment planning in brain disorders. Processing is also available as a cloud deployed service, Prism Serve. Research support includes import/export for imaging and derived quantitative data in both DICOM and research formats such as AFNI and Trackviz. | Commercial, organization, advance, imaging, diagnosis, treatment, brain, disorder, processing, clinical, support | SCR_016977 | 2026-02-15 09:21:56 | 4 | |||||||||||
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Computational Anatomy Toolbox for SPM Resource Report Resource Website 100+ mentions |
Computational Anatomy Toolbox for SPM (RRID:SCR_019184) | CAT | software application, data processing software, software resource, software toolkit, data analysis software | Software toolbox as extension to SPM12 to provide computational anatomy. This covers diverse morphometric methods such as voxel based morphometry, surface based morphometry, deformation based morphometry, and region or label based morphometry. | MRI, neuroimaging, brain, voxel based morphometry, surface based morphometry, deformation based morphometry, label based morphometry, region based morphometry | works with: SPM | Free, Available for download, Freely available | SCR_019184 | CAT12 | 2026-02-15 09:22:21 | 443 | ||||||||
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BECA Resource Report Resource Website 1+ mentions |
BECA (RRID:SCR_015846) | BECA | software application, data visualization software, data processing software, software resource, image analysis software | Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version. | visual exploration, brain, neuroscience, network, genetic determinant, fmri, neuroimaging, genome | has parent organization: Indiana University School of Medicine; Indiana; USA | NLM R01 LM011360; NIA U01 AG024904; NIA RC2 AG036535; NIA R01 AG19771; NIA P30 AG10133; NSF IIS-1117335; NIBIB R01 EB022574 |
PMID:27171688 | Free, Available for download | SCR_015846 | Brain Explorer for Connectome Analysis (BECA), BECA - Brain Explorer for Connectome Analysis | 2026-02-15 09:21:25 | 5 | ||||||
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BICCN Resource Report Resource Website 100+ mentions |
BICCN (RRID:SCR_015820) | BICCN | organization portal, data or information resource, consortium, portal | Consortium for the cell census in the brain. Integrated network of data generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate brains. | cell census, neuroscience, brain, brain initiative cell census network, whole mouse brain, |
uses: QuickNII uses: HistoloZee uses: CellLocator uses: Semi-Manual Alignment to Reference Templates uses: LoomPy uses: Cytosplore Viewer uses: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) uses: Blue Brain Cell Atlas uses: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas uses: Hippocampome.org uses: Neuron Phenotype Ontology uses: Brain Image Library uses: Distributed Archives for Neurophysiology Data Integration uses: NeuroMorpho.Org uses: Azimuth uses: Brain Observatory Storage Service and Database (BossDB) uses: Optimus Pipeline uses: scATAC Pipeline uses: Smart-seq2 Single Nucleus Multi Sample Pipeline uses: CEMBA MethylC Seq Pipeline uses: Brain Architecture Project uses: Single Cell Portal uses: MorphoHub uses: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas uses: Mouse Connectome Project uses: Allen Mouse Brain Reference Atlas uses: Allen Mouse Brain Common Coordinate Framework uses: Allen Human Reference Atlas, 3D, 2020 uses: NeMO Analytics uses: ANTS - Advanced Normalization ToolS uses: CloudReg uses: Brainome portal uses: CATlas uses: MetaNeighbor uses: Cell Annotation Platform uses: cellxgene uses: Neuroglancer uses: Vaa3D uses: QuickNII and VisuAlign uses: Hi5App uses: CloudVolume uses: neuroXiv uses: Brain Data Standards Ontology uses: Pittsburgh Supercomputing Center uses: Molecular Biosensor and Imaging Center uses: Generative Diffeomorphic Mapping uses: NIH NeuroBioBank uses: NeMOarchive lists: ccf_streamlines is related to: Mouse Connectome Project is related to: BarensLab Mini-Atlas is related to: Cumulus is related to: Pegasus is related to: Cirrocumulus is related to: Gene functional conservation across cell types and species is related to: BRAIN Initiative Cell Atlas Network is related to: ATAC Pipeline is related to: Slide-seq Pipeline is related to: Brain Knowledge Platform has parent organization: Allen Institute has parent organization: Allen Institute for Brain Science provides: mBrainAligner provides: BICCN Cell Registry provides: Cell Type Knowledge Explorer provides: Epiviz has organization facet: BICCN Anatomy and Morphology Project has organization facet: Cell Type Knowledge Explorer has organization facet: mBrainAligner has organization facet: Terra has organization facet: Allen Brain Cell Atlas has organization facet: Multiome Pipeline has organization facet: Allen Software Development Kit has organization facet: BICCN Imaging and analysis Techniques to Construct Cell Census Atlas of Human Brain has organization facet: Allen Brain Map BICCN Data Catalog has organization facet: snm3C Pipeline has organization facet: Paired-Tag Pipeline has organization facet: BuildIndices |
NIMH U19 MH114821; NIMH U19 MH114830; NIMH U19 MH114831 |
PMID:37390046 | Restricted | SCR_017266 | SCR_015820 | BICCN 2.0, BRAIN Initiative Cell Census Network, BRAIN Initiative Cell Census Network (BICCN) | 2026-02-15 09:21:26 | 227 | |||||
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ABCDreport Resource Report Resource Website |
ABCDreport (RRID:SCR_016030) | software application, data processing software, data analysis software, software resource | Software application as a simple system to review study progress. Used in ABCD study. | system, simple, review, study, progress, development, adolescence, brain, cognitive, report | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016030 | 2026-02-15 09:21:29 | 0 | |||||||||
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IMAGEN Resource Report Resource Website 100+ mentions |
IMAGEN (RRID:SCR_016045) | organization portal, portal, consortium, project portal, data or information resource | Research project examining how biological, psychological, and environmental factors during adolescence may influence brain development and mental health. Using brain imaging and genetics, the project will help develop prevention strategies and improved therapies for mental health disorders in the future., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | adolescence, teen, mental, health, study, brain, development, neurological, prevention, therapy, disorder, psychology | European Commission ; Medical Research Council ; National Institute for Health Research UK ; Swedish Research Council (Vetenskapsrådet) ; German Federal Ministry of Research & Education (BMBF) ; National Institute for Health Research US ; National Institute on Drug Abuse |
PMID:21102431 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016045 | IMAGEN Consortium, IMAGEN Project, IMAGEN Study | 2026-02-15 09:21:30 | 158 | ||||||||
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NeuroImage Field-of-View Normalization Tool Resource Report Resource Website 1+ mentions |
NeuroImage Field-of-View Normalization Tool (RRID:SCR_015957) | data or information resource, topical portal, portal | FSoftware for field-of-view normalization to minimize mismatch in different subjects' images. It aids that streamline analysis of large-scale brain MRI datasets. | normalization, fov, field, view, filed of view, brain, mri, magnetic, resonance, neuroimaging, imaging, atlas | DOI:10.1007/s12021-018-9359-z | Free, Available for download | SCR_015957 | Normalize FOV, normalizefov | 2026-02-15 09:21:29 | 4 | |||||||||
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UK Brain Expression Consortium Resource Report Resource Website 1+ mentions |
UK Brain Expression Consortium (RRID:SCR_015889) | UKBEC | organization portal, data or information resource, consortium, portal | Consortium studying the regulation and alternative splicing of gene expression in multiple tissues from human brains. The UKBEC dataset comprises of brains from individuals free of neurodegenerative disorders. | neurodegenerative, brain, disorder, mrna, dna, eqtl, snp, gene, visualization, expression | is parent organization of: Braineac | SCR_015889 | 2026-02-15 09:21:41 | 3 | ||||||||||
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Empenn Resource Report Resource Website |
Empenn (RRID:SCR_017074) | portal, community building portal, project portal, data or information resource, topical portal, disease-related portal | Project between Inria, Inserm, CNRS, and University of Rennes for biomedical image analysis for understanding neurological disease. Used to diagnose, monitor and deliver treatment for mental, neurological and substance use disorders by establishing multidisciplinary team between information sciences and medicine in medical imaging, neuroinformatics and population cohorts. | biomedical, image, analysis, disease, medical, imaging, neuroinformatics, population, cohort, brain, neurological, disorder |
is related to: Anima scripts is related to: VISAGES Research is related to: University of Rennes 1; Rennes; France is related to: Anima |
SCR_017074 | Brain | 2026-02-15 09:21:58 | 0 | ||||||||||
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NeuroInfo Resource Report Resource Website 10+ mentions |
NeuroInfo (RRID:SCR_017346) | software application, data visualization software, data processing software, software resource, 3d visualization software, image analysis software, image reconstruction software | Software for automatic identification and delineation of brain regions within experimental mouse brain sections. NeuroInfo registers serial section images of any orientation to Allen Mouse Brain Atlas, corrects for distortion due to histological processing, delineates anatomies in experimental section, and detects and reports on cell number within selected anatomies. | Allen Brain Atlas, Brain, mouse, histology, delineation, mbfbioscience | is related to: Allen Institute for Brain Science | DOI:10.1002/cne.24635 | Restricted | SCR_017346 | 2026-02-15 09:21:19 | 34 | |||||||||
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Connectome Computation System Resource Report Resource Website 10+ mentions |
Connectome Computation System (RRID:SCR_017342) | CCS | software application, data processing software, data analysis software, software resource | Software tool for multimodal human brain imaging data analysis. Computational pipeline for discovery science of human brain connectomes at macroscale with multimodal magnetic resonance imaging technologies. | Multimodal, human, brain, imaging, data, analysis, connectome, magnetic, resonance | DOI:10.1007/s11434-014-0698-3 | Free, Available for download, Freely available | SCR_017342 | 2026-02-15 09:21:19 | 15 | |||||||||
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Seizure-Waves Resource Report Resource Website |
Seizure-Waves (RRID:SCR_017455) | software application, data processing software, data analysis software, software resource | Analysis and modeling code for waves of seizure activity. | Analysis, modeling, wave, seizure, brain, activity, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF 1451384 | Free, Freely available | SCR_017455 | SeizureWaves, Seizure Waves, Seizure-Waves | 2026-02-15 09:22:04 | 0 | ||||||||
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brainGraph Resource Report Resource Website 10+ mentions |
brainGraph (RRID:SCR_017260) | software application, data processing software, data analysis software, software resource | Software R package for performing graph theory analyses of brain MRI data. | graph, theory, analysis, brain, MRI, data |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: CRAN |
Free, Available for download, Freely available | https://www.nitrc.org/projects/braingraph/ https://rdrr.io/cran/brainGraph/ https://www.r-pkg.org/pkg/brainGraph |
SCR_017260 | brainGraph - Graph Theory Analysis of Brain MRI Data in R, brainGraph | 2026-02-15 09:22:01 | 11 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
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