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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Lyngby Resource Report Resource Website 1+ mentions |
Lyngby (RRID:SCR_007143) | Lyngby | data analysis software, data processing software, software application, software resource | Matlab toolbox for the analysis of functional neuroimages (PET, fMRI). The toolbox contains a number of models: FIR-filter, Lange-Zeger, K-means clustering among others, visualizations and reading of neuroimaging files. | functional, statistical, fmri, pet, matlab, neuroimaging |
is listed by: Biositemaps has parent organization: THOR Center for Neuroinformatics |
Human Brain Project ; Danish Research Council ; European Union ; BIOMED2 ; MAPAWAMO ; NASA ; NSF ; DOE ; NIDA R01 DA09246; NIMH P20 MH57180 |
Free, Non-commercial | nif-0000-00324 | SCR_007143 | SciCrunch Registry | Lyngby Toolbox, Lyngby - A Toolbox for Functional Neuroimaging | 2026-10-24 12:45:58 | 2 | ||||||
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VoxBo Resource Report Resource Website 10+ mentions |
VoxBo (RRID:SCR_002166) | VoxBo | data processing software, image analysis software, image processing software, software application, software resource | Software package for brain image manipulation and analysis, focusing on fMRI and lesion analysis. VoxBo can be used independently or in conjunction with other packages. It provides GLM-based statistical tools, an architecture for interoperability with other tools (they encourage users to incorporate SPM and FSL into their processing pipelines), an automation system, a system for parallel distributed computing, numerous stand-alone tools, decent wiki-based documentation, and lots more. | fmri, neuroimaging, brain, functional, statistical, volume, preprocessing, analysis, display, format conversion, linear, three dimensional display, workflow, lesion, analyze, c++, console (text based), dicom, image display, linux, macos, microsoft, magnetic resonance, nifti, no input/output (daemon), overlap metrics, posix/unix-like, quantification, regression, resampling, sinc function interpolation, spatial transformation, statistical operation, visualization, windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: Debian has parent organization: neurodebian |
NIDA R01DA014418; NIMH R01MH073529 |
PMID:22348882 | Free, Available for download, Freely available | nif-0000-00353 | https://sources.debian.org/src/voxbo/, https://github.com/kimberg/voxbo | http://www.voxbo.org/ | SCR_002166 | SciCrunch Registry | 2026-10-24 12:44:40 | 13 | ||||
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Center for Inherited Disease Research Resource Report Resource Website 100+ mentions |
Center for Inherited Disease Research (RRID:SCR_007339) | CIDR | analysis service resource, biomaterial analysis service, data computation service, material analysis service, production service resource, resource, service resource, training service resource | Next generation sequencing and genotyping services provided to investigators working to discover genes that contribute to disease. On-site statistical geneticists provide insight into analysis issues as they relate to study design, data production and quality control. In addition, CIDR has a consulting agreement with the University of Washington Genetics Coordinating Center (GCC) to provide statistical and analytical support, most predominantly in the areas of GWAS data cleaning and methods development. Completed studies encompass over 175 phenotypes across 530 projects and 620,000 samples. The impact is evidenced by over 380 peer-reviewed papers published in 100 journals. Three pathways exist to access the CIDR genotyping facility: * NIH CIDR Program: The CIDR contract is funded by 14 NIH Institutes and provides genotyping and statistical genetic services to investigators approved for access through competitive peer review. An application is required for projects supported by the NIH CIDR Program. * The HTS Facility: The High Throughput Sequencing Facility, part of the Johns Hopkins Genetic Resources Core Facility, provides next generation sequencing services to internal JHU investigators and external scientists on a fee-for-service basis. * The JHU SNP Center: The SNP Center, part of the Johns Hopkins Genetic Resources Core Facility, provides genotyping to internal JHU investigators and external scientists on a fee-for-service basis. Data computation service is included to cover the statistical genetics services provided for investigators seeking to identify genes that contribute to human disease. Human Genotyping Services include SNP Genome Wide Association Studies, SNP Linkage Scans, Custom SNP Studies, Cancer Panel, MHC Panels, and Methylation Profiling. Mouse Genotyping Services include SNP Scans and Custom SNP Studies. | gene, genome, array, custom, dna, genome wide association study, genotyping, genotyping service, linkage scan, methylation profiling, hereditary disease, single gene disorder, snp, statistical genetics, whole genome, whole exome, exome sequencing, high throughput sequencing, single nucleotide polymorphism, sequencing, disease |
is listed by: NIDDK Information Network (dkNET) has parent organization: Johns Hopkins University; Maryland; USA |
Aging | NHGRI ; NCI ; NEI ; NIA ; NIAAA ; NIAMS ; NICHD ; NIDA ; NIDCD ; NIDCR ; NIDDK ; NIEHS ; NIMH ; NINDS ; NHGRI N01-HG-65403; US Department of Health and Human Services HHSN268200782096C; S Department of Health and Human Services HHSN268201100011I; S Department of Health and Human Services HHSN268201200008I; NHGRI U01HG004438; NHGRI U54HG006542 |
nif-0000-00223 | SCR_007339 | SciCrunch Registry | CIDR - Center for Inherited Disease Research | 2026-10-24 12:45:56 | 207 | ||||||
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JAX Neuroscience Mutagenesis Facility Resource Report Resource Website 1+ mentions |
JAX Neuroscience Mutagenesis Facility (RRID:SCR_007437) | NMU | biomaterial supply resource, material resource, organism supplier | Produce new neurological mouse models that could serve as experimental models for the exploration of basic neurobiological mechanisms and diseases. The impetus for the program resulted from the recognition that: * The value of genomic data would remain limited unless more information about the functionality of its individual components became available. * The task of linking genes to specific behavior would best be accomplished by employing a combination of different approaches. In an effort to complement already existing programs, the Neuroscience Mutagenesis Facility decided to use: a random, genome-wide approach to mutagenesis, i.e.N-ethyl-N-nitrosourea (ENU) as the mutagen; a three-generation back-cross breeding scheme to focus on the detection of recessive mutations; behavioral screens selective for the detection of phenotypes deemed useful for the program goals. The resulting mutant mouse lines have been available to the scientific community for the last five years and over 700 NMF mice have been sent to interested investigators for research; these mutant mouse lines will remain available as frozen embryos (which can be re-derived on request) and can be ordered through the JAX customer service at 1-800-422-6423 (or 207-288-5845). The results of the work of the Neuroscience Mutagenesis Facility and that of two other neurogenesis centers, i.e. The Neurogenomics Project at Northwestern University, and the Neuromutagenesis Project of the Tennessee Mouse Genome Consortium, can also be seen at Neuromice.org, a common web site of these three research centers; in addition, information about all mutants produced by these groups has been recorded in MGI. | mouse model, mutant mouse line, mutant mouse, phenodeviant, phenodeviant mouse, heritability, phenotyping, genetic mapping |
is listed by: One Mind Biospecimen Bank Listing is related to: neuromice is related to: Mouse Genome Informatics (MGI) has parent organization: Jackson Laboratory is parent organization of: JAX Neuroscience Mutagenesis Facility Protocols is parent organization of: neuromice |
Neurobiological disease, Neurological disorder, Sensory disorder, Behavioral disorder, Aging | NIDA ; NIMH ; NINDS ; NEI ; NIA ; NIAAA ; NIDCD |
Public, Available to the scientific community | nif-0000-00784 | http://nmf.jax.org/ | SCR_007437 | SciCrunch Registry | JAX Neuromutagenesis Facility, JAX - Neuroscience Mutagenesis Facilty, Neuromutagenesis Facility, Neuroscience Mutagenesis Facility of the Jackson Laboratory | 2026-10-24 12:45:57 | 1 | ||||
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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 | SciCrunch Registry | GIF Animations | 2026-10-24 12:46:05 | 0 | |||||||
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Zebrafish Neurophenome Project Database Resource Report Resource Website 1+ mentions |
Zebrafish Neurophenome Project Database (RRID:SCR_004482) | ZNP | data or information resource, data repository, data set, service resource, storage service resource | Database of neurobehavioral and physiological data of adult zebrafish models, complementing the available repositories for zebrafish genetic information, by providing a dynamic, open-access data repository of comprehensive, curated collection of results from zebrafish neurobehavioral experiments. As of May 2012, it contains over 4,500 experimental results, from over 75 unique physiological and behavioral tests and 330 different drug treatments. ZNP incorporates validated and curated data from work published in this field, to improve the accessibility of current knowledge to researchers interested in using adult zebrafish models. Overall, this program will allow investigators to rapidly review data, to direct their research using these models. Data and protocol submissions are now being accepted. | zebrafish, behavior, pharmacology, psychopharmacology, drug, adult zebrafish, phenotype, model, neurobehavior, physiology |
is listed by: 3DVC has parent organization: Tulane University School of Medicine; Louisiana; USA has parent organization: Zebrafish Neuroscience Research Consortium |
Tulane University; Louisiana; USA ; NIDA DA030900-02 |
PMID:22171801 | Open-access, Please cite | nlx_143762 | http://www.tulane.edu/%E2%88%BCznpindex/search | SCR_004482 | SciCrunch Registry | ZNPdb, Zebrafish Neurophenome Project, ZNP Database, Zebrafish Neurophenome Database | 2026-10-24 12:49:06 | 2 | ||||
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USC Multimodal Connectivity Database Resource Report Resource Website 10+ mentions |
USC Multimodal Connectivity Database (RRID:SCR_012809) | UMCD | data or information resource, data repository, database, service resource, storage service resource | Web-based repository and analysis site for connectivity matrices that have been derived from neuroimaging data including different imaging modalities, subject groups, and studies. Users can analyze connectivity matrices that have been shared publicly and upload their own matrices to share or analyze privately. | fmri, dti, dsi, mri, eeg, meg, data set, image, computational hosting, connectivity, neuroimaging, data sharing, brain, rendering, diffusion-weighted mri, functional connectivity, graph theory, resting-state fmri, structural connectivity, image display, magnetic resonance, python, rendering, visualization, connectivity matrix, network, brain network, matrix, de-identified, male, female, apoe, child, adult |
is used by: NIF Data Federation is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: MGH-USC Human Connectome Project |
Normal, Lesioned, Attention deficit-hyperactivity disorder, Autism Spectrum Disorder, Obsessive-Compulsive Disorder, BDD, APOE 4/4, APOE 3/4, APOE 3/3, Alzheimer's disease | NRSA ; NIH Blueprint for Neuroscience Research ; NIA F31AG035438-01; NIDA HHSN271200800035C |
PMID:23226127 PMID:20850551 |
The community can contribute to this resource, Some features require an account | nlx_83091 | http://www.nitrc.org/projects/umcd | http://jessebrown.webfactional.com/welcome/default/index | SCR_012809 | SciCrunch Registry | UCLA Connectivity Database, UCLA Multimodal Connectivity Database: Web-based brain network analysis and data sharing, UCLA Multimodal Connectivity Database | 2026-10-24 12:46:54 | 26 | ||
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National Institute on Drug Abuse Center for Genetic Studies Resource Report Resource Website 1+ mentions |
National Institute on Drug Abuse Center for Genetic Studies (RRID:SCR_013061) | NIDA Center for Genetic Studies | data or information resource, data repository, data set, service resource, storage service resource | Site for collection and distribution of clinical data related to genetic analysis of drug abuse phenotypes. Anonymous data on family structure, age, sex, clinical status, and diagnosis, DNA samples and cell line cultures, and data derived from genotyping and other genetic analyses of these clinical data and biomaterials, are distributed to qualified researchers studying genetics of mental disorders and other complex diseases at recognized biomedical research facilities. Phenotypic and Genetic data will be made available to general public on release dates through distribution mechanisms specified on website. | drug abuse, family, family structure, genetic analysis, genetics, addiction, age, biomaterial, cell line, citation, clinical, clinical status, data, diagnosis, dna, genotyping, human, mental disorder, mutation analysis, phenotype, publications, sex, clinical data, genotype, gene, GWAS |
is recommended by: National Library of Medicine is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: NIH Data Sharing Repositories has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA has parent organization: Rutgers University; New Jersey; USA |
NIDA ; NIH Blueprint for Neuroscience Research |
Free, Freely available | nif-0000-00181 | https://zork5.wustl.edu//nida/ | http://zork.wustl.edu/nida/ | SCR_013061 | SciCrunch Registry | National Institute of Drug Abuse (NIDA) Human Genetics Initiative, NIDA Center for Genetic Studies | 2026-10-24 12:49:10 | 7 | ||||
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numerical-fitting Resource Report Resource Website |
numerical-fitting (RRID:SCR_016025) | software library, software resource, software toolkit | Software for a numerical computation library that performs numerical calculations. Used in ABCD study. | numerical, computation, library, calculation, performing, client, side, javascript, js, abcd |
is related to: University of California at San Diego; California; USA works with: ABCD Study |
NIDA U24 DA041123 | Free, Available for download | SCR_016025 | SciCrunch Registry | 2026-10-24 12:49:12 | 0 | |||||||||
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pMAT Resource Report Resource Website 1+ mentions |
pMAT (RRID:SCR_022570) | pMAT | data analysis software, data processing software, software application, software resource | Open source software suite for analysis of fiber photometry data. | fiber photometry data analysis, fiber photometry | NIDA DA043572 | PMID:33385438 | SCR_022570 | SciCrunch Registry | Photometry Modular Analysis Tool | 2026-10-24 12:49:20 | 8 | ||||||||
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JAX Animal Behavior System Resource Report Resource Website 1+ mentions |
JAX Animal Behavior System (RRID:SCR_023721) | JABS | software resource | Video based phenotyping platform for laboratory mouse. Provides complete details of software and hardware, including 3D designs used for data collection. Data acquisition system consists of video collection hardware and software, behavior labeling and active learning app, and online database for sharing classifiers. Hardware and software solution collects high quality data for behavior analysis. | OpenBehavior, data acquisition system, integrated mouse phenotyping platform, behavior analysis, | is listed by: OpenBehavior | Jackson Laboratory Directors Innovation Fund ; NIDA DA041668; NIDA DA048634 |
DOI:10.1101/2022.01.13.476229 | Free, Available for download, Freely available | SCR_023721 | SciCrunch Registry | 2026-10-24 12:49:34 | 1 | |||||||
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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 | SciCrunch Registry | 2026-10-24 12:47:58 | 8 | ||||||
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RatsPub Resource Report Resource Website |
RatsPub (RRID:SCR_018905) | data access protocol, software application, software resource, text-mining software, web service | Web service that conducts comprehensive literature mining to identify roles of genes in addiction. Searches PubMed to find abstracts containing genes of interest and list of curated addiction related keywords. | Literature mining, addiction gene, PubMed abstract, gene, addiction, addiction relationship, neurogenetics | NIDA P30 DA044223; NIDA U01 DA047638 |
Free, Freely available | https://github.com/chen42/ratspub | SCR_018905 | SciCrunch Registry | rats.pub, Rats.pub, Relationship with Addiction Through Searches of PubMed | 2026-10-24 12:48:04 | 0 | ||||||||
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redcap-importer Resource Report Resource Website |
redcap-importer (RRID:SCR_016032) | data acquisition software, data processing software, software application, software resource | Software that automates the process of retrieving and converting data to the format of a RedCap table and allows selection of directories and files for import. | automate, process, retrvinig, converting, data, format, research, electronic, data, capture, table, selection, directory, import | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016032 | SciCrunch Registry | 2026-10-24 12:47:31 | 0 | |||||||||
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ABCDreport Resource Report Resource Website |
ABCDreport (RRID:SCR_016030) | data analysis software, data processing software, software application, 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 | SciCrunch Registry | 2026-10-24 12:47:34 | 0 | |||||||||
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FIONASITE Resource Report Resource Website 1+ mentions |
FIONASITE (RRID:SCR_016012) | data acquisition software, data management software, data processing software, data transfer software, software application, software resource | Software for uploading data to FIONA and capturing MR images and k-space data from medical image systems. It provides a web-interface to automate the data review (image viewer), integrate with the centralized electronic data record for assigning anonymized id's, and forward the data to the central archive. | automate, data, upload, collection, network, appliance, abcd, study | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016014, SCR_016013 | http://qi.ucsd.edu/news-article.php?id=2342&go=newer | SCR_016012 | SciCrunch Registry | 2026-10-24 12:47:31 | 1 | |||||||
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Minimally-Processed-Image-Sharing Resource Report Resource Website |
Minimally-Processed-Image-Sharing (RRID:SCR_016016) | data distribution software, data management software, data processing software, data transfer software, software application, software resource | Software to share ABCD minimally processed data. It uploads minimally-processed MRI data to the NDA ( Non-Disclosure Agreement) ABCD (Adolescent Brain Cognitive Development) repository. | share, data, minimally processed, image, files, fast-track, non-processed, link, store, upload |
is related to: University of California at San Diego; California; USA works with: ABCD Study |
NIDA U24 DA041123 | SCR_016016 | SciCrunch Registry | 2026-10-24 12:47:31 | 0 | ||||||||||
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enroll Resource Report Resource Website 10+ mentions |
enroll (RRID:SCR_016011) | data management software, data processing software, data storage software, software application, software resource | Software which provides a framework for the secure storage of Personal Identifyable Information (PII) for a multi-site longitudinal project centrally. Used in Adolescent Brain Cognitive Development (ABCD) Study. | database, secure, framework, multisite, personal, identifiable, information, adolescence, abcd |
has parent organization: University of California at San Diego; California; USA works with: ABCD Study |
NIDA U24 DA041123 | Free, Available for download | SCR_016011 | SciCrunch Registry | 2026-10-24 12:47:31 | 13 | |||||||||
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tick-tock Resource Report Resource Website |
tick-tock (RRID:SCR_016023) | data processing software, data visualization software, software application, software resource, web application | Software for research study observation that visualizes study related events per day. Any event generating function sends a 'tick' event to this application which will be visible on this applications web-interface. | application, research, study, visualization, event, web, interface, observation, abcd |
is related to: University of California at San Diego; California; USA works with: ABCD Study |
NIDA U24 DA041123 | Free, Available for download | SCR_016023 | SciCrunch Registry | 2026-10-24 12:47:31 | 0 | |||||||||
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FIONA-protocol-compliance Resource Report Resource Website |
FIONA-protocol-compliance (RRID:SCR_016027) | data analysis software, data processing software, software application, software resource | Software that contains multiple sequential lines of MATLAB commands and function calls for numerical computing for ABCD study protocol compliance. | application, multiple, sequential, lines, commands, function, numerical, computing, protocol, compliance | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016027 | SciCrunch Registry | 2026-10-24 12:47:31 | 0 |
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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.
