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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Hippocampal Slice Wave Animations Resource Report Resource Website |
Hippocampal Slice Wave Animations (RRID:SCR_008372) | animation software, data or information resource, data processing software, data visualization software, portal, resource, simulation software, software application, software resource, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 29, 2013. Supplemental data for the paper Changes in mitochondrial function resulting from synaptic activity in the rat hippocampal slice, by Vytautas P. Bindokas, Chong C. Lee, William F. Colmers, and Richard J. Miller that appears in the Journal of Neuroscience June 15, 1998. You can view digital movies of changes in fluorescence intensity by clicking on the title of interest. | animation, hippocampal, hippocampus, mitochondrial, movie, neuroscience, rat, slice, wave | MRC of Canada MT10520; NIDA DA02575; NIDA DA02121; NIMH MH40165; NIDDK DK42086; NIDDK DK44840; NINDS NS-33502; NIGMS 5T32GM07151-22; NICHD HD07009 |
PMID:9614233 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25609 | SCR_008372 | GIF Animations | 2026-09-05 06:26:21 | 0 | |||||||
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Emergent Resource Report Resource Website 1+ mentions |
Emergent (RRID:SCR_008500) | Emergent | data or information resource, narrative resource, simulation software, software application, software resource, wiki | emergent is a comprehensive, full-featured neural network simulator that allows for the creation and analysis of complex, sophisticated models of the brain in the world. With an emphasis on qualitative analysis and teaching, it also supports the workflow of professional neural network researchers. Its high level drag-and-drop programming interface, built on top of a scripting language that has full introspective access to all aspects of networks and the software itself, allows one to write programs that seamlessly weave together the training of a network and evolution of its environment without ever typing out a line of code. Networks and all of their state variables are visually inspected in 3d, allowing for a quick visual regression of network dynamics and robot behavior. This same 3d world sports a highly accurate Newtonian physics simulation, allowing you to create rich robotics simulations (for example, a car). As a direct descendant of PDP (1986) and PDP (1999), emergent has been in development for decades. In the most recent versions available strive to distill it down to its essential elements. Those that take the time to learn the best practices will be rewarded with the ability to create and understand the most complicated neural models ever published. | neural, simulator, network, analysis, software, simulation, physics, newtonian |
is related to: PDP++ Software Home Page has parent organization: University of Colorado Boulder; Colorado; USA |
NIMH R01 MH069597-01; NIMH MH47566; DARPA/ONR N00014-05-1-0880; ONR N00014-03-1-0428 |
nif-0000-30515 | SCR_008500 | Emergent Neural Network Simulation System, PDP++ | 2026-09-05 06:26:23 | 4 | |||||||
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Brain's Inner Workings: Activities for Grades 9 through 12 Resource Report Resource Website 1+ mentions |
Brain's Inner Workings: Activities for Grades 9 through 12 (RRID:SCR_008842) | Brain's Inner Workings | data or information resource, narrative resource, training material, video resource | This comprehensive free collection of multimedia resources and inquiry-based activities tied to the National Science Education Standards help teachers and students learn about the structure, function and cognitive aspects of the human brain. The packet includes a teacher's manual, student manual, DVD of videos, and a CDROM of accompanying materials. | high school, brain, manual, student, teacher, brain structure, brain function, cognition, cerebral cortex, nerve cell, neurotransmitter, imaging, mri, mental disease, k-12 | has parent organization: NIMH Educational Resources | NIMH | nlx_146227 | SCR_008842 | The Brain's Inner Workings: Activities for Grades 9 through 12, Brains Inner Workings: Activities for Grades 9 through 12 | 2026-09-05 06:26:29 | 2 | |||||||
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gene Expression Analysis Resource Resource Report Resource Website 50+ mentions |
gene Expression Analysis Resource (RRID:SCR_017467) | gEAR | analysis service resource, data or information resource, portal, production service resource, service resource, software resource | Portal for visualization and analysis of multi omic data in public and private domains. Enables upload, visualization and analysis of scRNA-seq data. | Visualization, analysis, multi, omic, data, upload, scRNA-seq, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: University of Maryland School of Medicine; Maryland; USA |
Hearing Health Foundation (Hearing Restoration Project) ; NIDCD R01 DC013817; NIMH MH114788; NIMH R24 MH114815 |
Restricted | SCR_017467 | gene Expression Analysis Resource | 2026-09-05 06:28:24 | 91 | |||||||
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TReNA Resource Report Resource Website |
TReNA (RRID:SCR_017458) | data analysis software, data processing software, network analysis software, software application, software resource | Methods for reconstructing transcriptional regulatory networks. | Reconstructing, transcriptional, regulatory, network, BRAIN Initiative | is recommended by: BRAIN Initiative | NIMH MH114788 | Free, Available for download, Freely available | SCR_017458 | 2026-09-05 06:28:24 | 0 | |||||||||
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ChromHMM Resource Report Resource Website 50+ mentions |
ChromHMM (RRID:SCR_018141) | data analysis software, data processing software, software application, software resource | Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations. | Chromatin state discovery, chromatin characterization, genome annotation, non coding genome, epigenomic, cell, annotation, analysis, pattern |
is listed by: Debian is listed by: OMICtools |
Alfred P. Sloan Fellowship ; CAREER Award ; NHGRI RC1HG005334; NHGRI U01 HG007912; NHGRI U54 HG004570; NIEHS R01 ES024995; NIMH U01 MH105578; NSF 0905968 |
PMID:29120462 PMID:22373907 |
Free, Available for download, Freely available | OMICS_03490 | https://sources.debian.org/src/chromhmm/ | SCR_018141 | 2026-09-05 06:28:31 | 50 | ||||||
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Track-A-Worm Resource Report Resource Website 1+ mentions |
Track-A-Worm (RRID:SCR_018299) | data analysis software, data processing software, software application, software resource | Open source system for quantitative assessment of C. Elegans locomotory and bending behavior. Used for quantitative behavioral analyses to understand circuit and gene bases of behavior. Constantly records and analyzes position and body shape of freely moving worm at high magnification. | Quantitative assessment, C.Elegans locomotory, bending behavior, behavioral analysis, gene, moving worm position, body shape, automated recording | is related to: University of Connecticut; Connecticut; USA | NIGMS R01 GM083049; NIMH R01 MH085927 |
PMID:23922769 | Free, Available for download, Freely available | SCR_018299 | Tracker-A-Worm version 1.0, Tracker-A-Worm version 2.0 | 2026-09-05 06:28:34 | 4 | |||||||
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EpiModel Resource Report Resource Website 1+ mentions |
EpiModel (RRID:SCR_018539) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics. | Infectious disease, mathematical modeling, simulation, analysis, infectious disease dynamic, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIAID P30 AI027757; NIAID P30 AI050409; NICHD R01 HD068395; NICHD R21 HD075662; NICHD T32 HD007543; NIDA P30 DA027828; NIMH R21 MH112449 |
PMID:29731699 | Free, Available for download, Freely available | biotools:epimodel | https://bio.tools/epimodel | SCR_018539 | 2026-09-05 06:28:38 | 8 | ||||||
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piNET Resource Report Resource Website 1+ mentions |
piNET (RRID:SCR_018693) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. | Analysis, visualization, proteomics data, integrated annotation, quantitative proteomics data, PTM network, LINCS library integration, genetic perturbation signature, peptide, protein, post translational modification site, PTM site, data | is related to: LINCS Project | NCATS UL1 TR001425; NCI T32 CA236764; NHLBI U54 HL127624; NIEHS P30 ES006096; NIGMS U01 GM120953; NIMH R01 MH107487 |
DOI:10.1093/nar/gkaa436 | Free, Freely available | SCR_018693 | 2026-09-05 06:28:41 | 4 | ||||||||
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Scalable Analytics for Brain Exploration Research Resource Report Resource Website 1+ mentions |
Scalable Analytics for Brain Exploration Research (RRID:SCR_018812) | SABER, saber | data processing software, software application, software library, software resource, software toolkit, workflow software | Library of containerized tools and workflow deployment system for enabling processing of large neuroimaging datasets. Provides canonical neuroimaging workflows specified in standard workflow language (CWL), integration with workflow execution engine (Airflow), imaging database (bossDB), and parameter database (Datajoint) to deploy workflows at scale, and tools to automate deployment and optimization of neuroimaging pipelines. | Running containerized workflow, large neuroimaging datasets, canonical neuroimaging workflow, neuroimaging pipeline deployment, neuroimaging pipeline optimization | is related to: Brain Observatory Storage Service and Database (BossDB) | NIMH R24 MH114799 | DOI:10.1101/615161v1.full | Free, Available for download, Freely available | SCR_018812 | 2026-09-05 06:28:42 | 1 | |||||||
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RAVE Resource Report Resource Website 1+ mentions |
RAVE (RRID:SCR_019040) | data analysis software, data processing software, data visualization software, software application, software resource | Open source software tool for reproducible analysis and visualization of intracranial EEG data. Used for analysis of intracranial electroencephalogram data, including data collected using strips and grids (electrocorticography, ECoG) and depth electrodes (stereotactic EEG). | Intracranial EEG data, data analysis, intracranial electroencephalogram data, electrocorticography data, depth electrodes, stereotactic EEG, iEEG data | NIMH R24 MH117529 | DOI:10.1016/j.neuroimage.2020.117341 | Free, Available for download, Freely available | SCR_019040 | R Analysis and Visualization of intracranial EEG | 2026-09-05 06:28:45 | 3 | ||||||||
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Open Ephys: Pulse Pal Resource Report Resource Website 1+ mentions |
Open Ephys: Pulse Pal (RRID:SCR_017203) | instrument resource | Open source pulse train generator that allows users to create and trigger software defined trains of voltage pulses with high temporal precision. Generates precisely timed pulse sequences for use in research involving electrophysiology or psychophysics. | instrument, generator, stimulation, voltage, puls, sequence, electrophysiology, psychophysics | McKnight Foundation ; NIMH R01 MH097061; NINDS R01 NS07553 |
DOI:10.3389/fneng.2014.00043 | Available for purchase | https://sanworks.io/shop/viewproduct?productID=1102, https://github.com/sanworks/PulsePal, https://sites.google.com/site/pulsepalwiki/specifications?authuser=0 | SCR_017203 | Pulse Pal v2 | 2026-09-05 06:28:20 | 2 | |||||||
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PIVOT software Resource Report Resource Website 10+ mentions |
PIVOT software (RRID:SCR_017210) | PIVOT | data analysis software, data processing software, software application, software resource | Software R package for interactive analysis and visualization of transcriptomics data. Operating systems are macOS, Linux, Windows. | Interactive, analysis, visualization, transcriptomics, data | is related to: University of Pennsylvania; Philadelphia; USA | NIMH U01 MH098953 | PMID:29304726 | Free, Available for download, Freely available | SCR_017210 | Platform for Interactive analysis and Visualization Of Transcriptomics, PIVOT, KimLabIDV | 2026-09-05 06:28:20 | 19 | ||||||
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Brain Image Library Resource Report Resource Website 10+ mentions |
Brain Image Library (RRID:SCR_017272) | BIL | data or information resource, data repository, service resource, storage service resource | Public, NIH-funded repository and analysis ecosystem for brain microscopy data, designed to store, share, and process massive volumetric datasets. It enables researchers to access whole-brain images, neuron morphologies, and spatial data without needing to download, fostering collaborative discovery. Used to deposit, analyze, mine, share and interact with large brain image datasets. | archive, dataset, confocal, microscopy, brain, image, data, brain microscopy data, |
is used by: BICCN is used by: BRAIN Initiative Cell Atlas Network is recommended by: National Library of Medicine is recommended by: BRAIN Initiative is listed by: DataCite is listed by: re3data.org is related to: BRAIN Initiative is related to: Allen Institute for Brain Science works with: CBI BrAinPI is organization facet of: BRAIN Initiative Cell Atlas Network |
BRAIN Initiative ; NIMH R24 MH114793 |
PMID:38187527 | Free, Available for download, Freely available | DOI:10.17616/R31NJN9G, DOI:10.35077, r3d100013956 | https://doi.org/10.17616/R31NJN9G, https://doi.org/10.17616/r31NJN9G, https://doi.org/10.35077/, https://dx.doi.org/10.35077/, https://doi.org/10.17616/R31NJN9G | SCR_017272 | Brain Image Library | 2026-09-05 06:28:21 | 20 | ||||
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Brain Observatory Storage Service and Database (BossDB) Resource Report Resource Website 10+ mentions |
Brain Observatory Storage Service and Database (BossDB) (RRID:SCR_017273) | BossDB, bossDB, BOSS DB | 3d spatial image, data or information resource, data repository, database, image, service resource, storage service resource | BossDB (Brain Observatory Storage Service and Database) is a cloud-based ecosystem for the storage and management of public large-scale volumetric neuroimaging and connectomics datasets. This includes volumetric Electron Microscopy and X-Ray Micro/Nanotomography data with support for multi-channel image data, segmentations, annotations, meshes, and connectomes. BossDB integrates with community resources for data access, processing, visualization, and analysis, and includes an API that enables metadata management, rendering, datatype conversions, and ingest. | Johns Hopkins University Applied Physics Laboratory, JHU/APL, database, electron microscopy, xray, data, storage, archive, BRAIN Initiative, EM, XRM, XNH, ecosystem |
is used by: BICCN is recommended by: National Library of Medicine is recommended by: BRAIN Initiative is related to: Scalable Analytics for Brain Exploration Research is related to: Ecosystem for Multi-modal Brain-behavior Experimentation and Research has parent organization: BRAIN Initiative has parent organization: Johns Hopkins University; Maryland; USA |
BRAIN Initiative ; NIMH R24 MH114785 |
DOI:10.1101/217745 | Open | https://github.com/jhuapl-boss/boss/ | SCR_017273 | Brain Observatory Storage Service, bossDB, Block and Object Storage Service, BOSSDB, Block and Object Storage Service Database, Brain Observatory Storage Service and Database, BossDB | 2026-09-05 06:28:21 | 31 | |||||
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Neuron Phenotype Ontology Resource Report Resource Website 1+ mentions |
Neuron Phenotype Ontology (RRID:SCR_017403) | NPO | controlled vocabulary, data or information resource, ontology | An ontology for describing the complex phenotypes of neurons. | Cell, type, phenotype, neuron, ontology |
is used by: BICCN is provided by: NIFSTD |
BRAIN Initiative ; NIMH U24 MH114827 |
Free, Freely available | SCR_017403 | 2026-09-05 06:28:24 | 2 | ||||||||
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BICCN Resource Report Resource Website 100+ mentions |
BICCN (RRID:SCR_015820) | BICCN | consortium, data or information resource, organization portal, 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 has organization facet: MapMyCells |
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) | 2026-09-05 06:28:00 | 234 | |||||
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NeMOarchive Resource Report Resource Website 100+ mentions |
NeMOarchive (RRID:SCR_016152) | NeMO | data or information resource, data repository, database, service resource, storage service resource | Data repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification, histone modification profiles and chromatin accessibility. | omic, neuroscience, neurobiology, bcbc, biccn, nih, brain, genomic, region, abnormal, transcription, factor, binding, site, chromatin, regulatory, element, data |
is used by: BRAIN Initiative Cell Atlas Network is used by: BICCN is recommended by: BRAIN Initiative is related to: NeMO Analytics has parent organization: University of Maryland School of Medicine; Maryland; USA |
BRAIN Initiative ; NIMH MH114788 |
Free, Freely available | https://data.nemoarchive.org/ | SCR_016152 | NeMO Archive, Neuroscience Multi-omic Data Archive, The Neuroscience Multi-Omic Archive, Neuroscience Multi-Omic Archive | 2026-09-05 06:28:04 | 126 | ||||||
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Mapping Population-based Structural Connectomes Resource Report Resource Website |
Mapping Population-based Structural Connectomes (RRID:SCR_016232) | data analysis software, data processing software, software application, software resource | Data analysis software that can simultaneously characterize a large number of white matter bundles within and across different subjects for group analysis. It has three major components: construction of the structural connectome for the whole brain, low-dimensional representation of streamlines in each connection, and multi-level connectome analysis. | dwi, t1, tractography, algorithm, white matter, bundle, gray matter, shape, analysis, network, workflow | CPRIT RR150054; NIMH MH086633; NIMH MH092335; NSF DMS-1407655; NSF DMS1127914; NSF SES-1357666 |
Free for non-commercial use, Available for download | SCR_016232 | 2026-09-05 06:28:05 | 0 | ||||||||||
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SnapATAC Resource Report Resource Website 10+ mentions |
SnapATAC (RRID:SCR_020981) | data analysis software, data processing software, software application, software resource, software toolkit | Software package for analyzing scATAC-seq datasets.Used to dissects cellular heterogeneity in unbiased manner and map trajectories of cellular states. Can process data from up to million cells. Incorporates existing tools into comprehensive package for analyzing single cell ATAC-seq dataset. | scATAC-seq datasets analysis, dissects cellular heterogeneity, cellular states, map trajectories | NCI K99 CA252020; NIMH U19 MH114831; UCSD School of Medicine |
PMID:33637727 | Free, Available for download, Freely available | https://github.com/r3fang/SnapATAC | SCR_020981 | Single Nucleus Analysis Pipeline for ATAC-seq | 2026-09-05 06:29:32 | 23 |
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
