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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
map3d
 
Resource Report
Resource Website
1+ mentions
map3d (RRID:SCR_009628) map3d data processing software, data visualization software, software application, software resource A scientific visualization application written to display and edit complex, three-dimensional geometric models and scalar, time-based data associated with those models such as high resolution EEG, MEG, and ECG. c++, eeg, meg, electrocorticography, forward - inverse, linux, macos, microsoft, modeling, posix/unix-like, visualization, win32 (ms windows), windows, windows 95/98/2000 is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: University of Utah; Utah; USA
NCRR 5P41RR012553-15;
NIGMS 8 P41 GM103545-15
Map3d License nlx_155857 http://www.nitrc.org/projects/map3d SCR_009628 2026-09-12 12:57:14 3
MAPPFinder
 
Resource Report
Resource Website
10+ mentions
MAPPFinder (RRID:SCR_005791) MAPPFinder data analysis software, data processing software, software application, software resource MAPPFinder is an accessory program for GenMAPP. This program allows users to query any existing GenMAPP Expression Dataset Criterion against GO gene associations and GenMAPP MAPPs (microarray pathway profiles). The resulting analysis provides the user with results that can be viewed directly upon the Gene Ontology hierarchy and within GenMAPP, by selecting terms or MAPPs of interest. Platform: Windows compatible gene, gene ontology, gene association, gene expression, profile, microarray, pathway, statistical analysis is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: University of California at San Francisco; California; USA
has parent organization: Gene Map Annotator and Pathway Profiler
University of California at San Francisco; California; USA ;
San Francisco General Hospital; California; USA ;
NHLBI ;
NCRR MO1RR00083
PMID:12540299 Free for academic use nlx_149270 SCR_005791 2026-09-12 12:56:31 26
MNE software
 
Resource Report
Resource Website
100+ mentions
MNE software (RRID:SCR_005972) MNE data analysis software, data processing software, data visualization software, software application, software resource, software toolkit Software suite for processing magnetoencephalography and electroencephalography data. Open source Python software for exploring, visualizing, and analyzing human neurophysiological data including MEG, EEG, sEEG, ECoG . Implements all functionality of MNE Matlab tools in Python and extends capabilities of MNE Matlab tools to, e.g., frequency-domain and time-frequency analyses and non-parametric statistics. Magnetoencephalography data processing, electroencephaography data processing, data analysis, eeg, meg, linux, mac osx, human neurophysiological data, statistics is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Debian
is related to: MNE-BIDS
is related to: MATLAB
is related to: NumPy
is related to: SciPy
is related to: Matplotlib
is related to: Mayavi: 3D Scientific Data Visualization and Plotting Software Project
is related to: NiBabel
European Research Council (ERC) StG-263584;
NCRR P41 RR014075;
NIBIB P41 EB015896;
NIBIB R01 EB009048;
NIDCD F32DC012456;
NSF 0958669;
NSF 1042134
PMID:24161808
PMID:24431986
Free, Available for download, Freely available nlx_151346 https://sources.debian.org/src/python3-mne/, http://www.nitrc.org/projects/mne, http://www.nmr.mgh.harvard.edu/martinos/ncrr/sofMNE.html, https://github.com/mne-tools/, https://mne.tools/ SCR_005972 Minimum Norm Current Estimates Software, Minimum Norm Current Estimates, MNE tools for MEG and EEG data analysis, MNE-Python 2026-09-12 12:56:33 114
Manual Align RTS2000
 
Resource Report
Resource Website
Manual Align RTS2000 (RRID:SCR_007107) data processing software, image processing software, software application, software resource Software program to adjust the alignment of two adjacent images. Allows to correct for any misalignment that may occur during auto-alignment step. Serves as a bootstrap to get the images in approximately the right place. alignment, process, image, adjust, correct, misalignment is affiliated with: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: National Center for Microscopy and Imaging Research
NCRR P41 RR04050 Free, no longer available nif-0000-10514 SCR_007107 2026-09-12 12:56:50 0
Function BIRN
 
Resource Report
Resource Website
1+ mentions
Function BIRN (RRID:SCR_007291) FBIRN data or information resource, portal, topical portal The FBIRN Federated Informatics Research Environment (FIRE) includes tools and methods for multi-site functional neuroimaging. This includes resources for data collection, storage, sharing and management, tracking, and analysis of large fMRI datasets. fBIRN is a national initiative to advance biomedical research through data sharing and online collaboration. BIRN provides data-sharing infrastructure, software tools, strategies and advisory services - all from a single source. fmri, 3d model, data storage, imaging, map, morphology, mri, neuroinformatics, segmentation, software, talairach, volume, warping, analyze, application, c++, csh/tcsh, data, database, database application, data resource, dicom, javascript, linux, magnetic resonance, nifti, ontology, pl/sql, posix/unix-like, python, quality metrics, spatial transformation, statistical operation, tcl/tk, unix shell, visualization, web resource, web service, workflow is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Biomedical Informatics Research Network
is parent organization of: BXH/XCEDE Tools
is parent organization of: FBIRN Image Processing Scripts
NIGMS ;
NCRR 1U24-RR025736;
NCRR U24-RR021992;
NCRR U24-RR021760;
NCRR 1U24-RR026057-01
nif-0000-00070 http://www.nitrc.org/projects/fbirn http://nbirn.net/tools/browse_tools.shtm SCR_007291 Functional Imaging BIRN 2026-09-12 12:56:52 2
BIRN Coordinating Center
 
Resource Report
Resource Website
BIRN Coordinating Center (RRID:SCR_007290) BIRN-CC data or information resource, organization portal, portal, software application, software resource, systems interoperability software THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 06, 2013. It was established to develop, implement and support the information infrastructure necessary to achieve large-scale data sharing among the test bed participants (function, morphometry and mouse birn). The BIRN-CC consists of a unique and well-established partnership between computer scientists, neuroscientists and engineers. This partnership addresses a large array of technical, policy, and architectural issues to fundamentally enable a new suite of information technology supported database and analysis tools that allow scientists to analyze and interpret significantly larger sets of data than is possible in the traditional single-institution study paradigm. fmri, 3d models, anatomy, atlas, data management, data storage, dohhs architecture, imaging, map, model, mri, neuroinformatics, ontology, portal, software, talairach, warping has parent organization: University of Southern California; Los Angeles; USA
has parent organization: University of Chicago; Illinois; USA
has parent organization: University of California at Irvine; California; USA
has parent organization: University of California at Los Angeles; California; USA
NCRR THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-00068 SCR_007290 2026-09-12 12:56:52 0
Stimulate
 
Resource Report
Resource Website
10+ mentions
Stimulate (RRID:SCR_007375) data analysis software, data processing software, data visualization software, software application, software resource An fMRI analysis software package with a GUI (Graphical User Interface) front end. Stimulate offers a comprehensive set of fMRI analysis tools integrated into a single package for convenient and flexible data processing. Users can point and click with the mouse to modify analysis or display variables. Activation maps can be calculated from the fMRI data and overlaid onto structural MRI image displays. fmri, workflow, data visualization software, data analysis software has parent organization: University of Minnesota Twin Cities; Minnesota; USA NCRR RR08079 Free for use by non-profit research institutions, Not to be sold or used for profit. nif-0000-00344 SCR_007375 2026-09-12 12:56:54 10
Madison Metabolomics Consortium Database
 
Resource Report
Resource Website
50+ mentions
Madison Metabolomics Consortium Database (RRID:SCR_007803) MMCD data or information resource, database, resource A database which supports high-throughput NMR and MS approaches to the identification and quantification of metabolites present in biological samples. MMCD serves as a hub for information on small molecules of biological interest gathered from electronic databases and the scientific literature. Each metabolite entry in the MMCD is supported by information in separate data fields, which provide the chemical formula, names and synonyms, structure, physical and chemical properties, NMR and MS data on pure compounds under defined conditions where available, NMR chemical shifts determined by empirical and/or theoretical approaches, calculated isotopomer masses, information on the presence of the metabolite in different biological species, and links to images, references, and other public databases. The MMCD search engine supports versatile data mining and allows users to make individual or bulk queries on the basis of experimental NMR and/or MS data plus other criteria. database, metabolomics, metabolite, consortium, nmr, mas spectroscopy, FASEB list is listed by: 3DVC
has parent organization: University of Wisconsin-Madison; Wisconsin; USA
NIDDK R21 DK070297;
NCRR P41 RR02301
PMID:18259166 Public nif-0000-03148 SCR_007803 Madison Metabolomics Consortium Database (MMCD) 2026-09-12 12:56:57 63
Mouse Mutant Resource
 
Resource Report
Resource Website
1+ mentions
Mouse Mutant Resource (RRID:SCR_008367) MMR biomaterial supply resource, cell repository, material resource, organism supplier Producer and supplier of a collection of mice bearing spontaneous mutations. These mice contribute to a better understanding of the genetic bases of neurological, neuromuscular, sensory, metabolic, skeletal/craniofacial and developmental disorders and conditions such as diabetes, obesity and heart disease. live, cryopreserved, frozen, spontaneous mutation, dna, mutant, gene, disease model, mouse model, embryo, germplasm, mutation, phenotype is listed by: One Mind Biospecimen Bank Listing
has parent organization: Jackson Laboratory
Spontaneous mutation Jackson Laboratory ;
NCRR ;
NIH Blueprint for Neuroscience Research ;
NIH Office of the Director P40OD010972;
NIH Office of the Director OD01116302;
NCRR RR001183;
NCRR RR032339
Public nif-0000-25583 SCR_008367 JAX Mouse Mutant Resource, Mouse Mutant Gene Resource, The Mouse Mutant Resource 2026-09-12 12:57:03 2
Alamogordo Primate Facility
 
Resource Report
Resource Website
Alamogordo Primate Facility (RRID:SCR_008376) APF biomaterial supply resource, material resource, organism supplier THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. It houses chimpanzees that have been used in biomedical research, but no active, invasive research is conducted on the site. The APF provides for the long-term care and husbandry of chimpanzees that have been used in biomedical research. Charles River Laboratories Inc. operates the facility under contract with the National Institutes of Health. To be used in continuing virological research, the animals must be transferred to active chimpanzee research settings. All chimpanzees at the APF have been exposed to various microorganisms, such as hepatitis C virus and HIV. For this reason, they may be candidates for studies related to these diseases. The National Center for Research Resources (NCRR) may remove infected animals from the APF to other accredited chimpanzee facilities for research purposes. Investigators interested in the chimpanzees at the APF should contact Dr. Harold Watson in NCRR''s Division of Comparative Medicine to discuss research requirements. animal, biomedical, chimpanzee, comparative medicine, disease, hepatitis c, hiv, husbandry, infection, microorganism, primate, research, virological, virus NCRR THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-25894 SCR_008376 Alamogordo Primate Facility 2026-09-12 12:57:03 0
Charged Fluid Model for Brain Image Segmentation
 
Resource Report
Resource Website
Charged Fluid Model for Brain Image Segmentation (RRID:SCR_008281) CFMBIS data processing software, image analysis software, segmentation software, software application, software resource A computer-aided tool for 2-D brain image segmentation using an electrostatic charged fluid model. It allows researchers to perform 2-D image segmentation in brain MR image data. Each interactive visualization element corresponding to the embedded function enables the end user to easily manipulate the image data. The visual environment of this tool provides an easy-to-use means of inspection and interpretation of image data using the LONI jViewbox library. CFMBIS uses the Java Image I/O plug-in architecture to read a wide variety of common medical image file formats. plugin, software, 2D image, brain image segmentation, brain MR image, image analysis, segementation is related to: Laboratory of Neuro Imaging
has parent organization: University of Southern California; Los Angeles; USA
NIBIB 9P41EB015922-15;
NCRR 2-P41-RR-013642-15;
NCRR U54 RR021813
Available for educational and research purposes only nif-0000-23325 SCR_008281 2026-09-12 12:57:02 0
New Iberia Research Center
 
Resource Report
Resource Website
10+ mentions
New Iberia Research Center (RRID:SCR_008279) biomaterial supply resource, material resource, organism supplier NIRC maintains and provides available research facilities accredited by the Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) International; a ready source of chimpanzees of mixed ages and sex for use in biomedical and behavioral sciences, and also provides professional staff necessary to support investigators with their research needs. Current Research: Vaccine development and testing; pharmacokinetic, pharmacodynamic, preclinical safety, and efficacy studies. Services Provided: The University of Louisiana at Lafayette-New Iberia Research Center (UL Lafayette-NIRC) is an AAALAC-International-accredited nonhuman primate research facility dedicated to the support of basic and applied biomedical and behavioral research. All proposed programs must be approved by the presenting institution and the UL Lafayette-NIRC animal care and use committees. State-of-the-art biomedical support facilities are available that include access to ultrasound, radiography with automatic processor and computer imagery for diagnostic enhancement, and endoscopy and laparoscopy with video monitors, camera and color photo imagery. Diagnostic Laboratory: A 12,000-square-foot laboratory is available for investigators'' research support requirements. Capabilities within the laboratory include but are not limited to hematology, chemistry, microbiology, urinalysis, parasitology, and histology. Among the investigator support procedures are Ficoll gradient isolation of peripheral blood mononuclear cells, platelet aggregation profiles, nonhuman primate lymphocyte proliferation assay, and flow cytometry (lymphocyte enumeration). Emergency generator power is accessible in each laboratory unit and for all major instrumentation and critical freezers. Animals: The center cares for approximately 360 chimpanzees and 5,500 New and Old World species of nonhuman primates. In addition to chimpanzees, the following species of nonhuman primates are being bred at the center: Vervet monkey (Chlorocebus aethiops), cynomolgus macaque (Macaca fascicularis), pigtailed macaque (M. nemestrina), rhesus macaque (M. mulatta). endoscopy, animal, assay, behavioral, biomedical, blood, cell, chemistry, chimpanzee, chlorocebus aethiops, cynomolgus, cytometry, development, hematology, histology, imagery, laboratory, laparoscopy, lymphocyte, macaca fascicularis, macaca mulatta, macaca nemestrina, macaque, microbiology, monkey, mononuclear, nonhuman, parasitology, peripheral, pharmacodynamic, pharmacokinetic, photo, pigtailed, platelet, primate, radiography, research, rhesus, science, testing, ultrasound, urinalysis, vaccine, vervet has parent organization: University of Louisiana; Louisiana; USA NCRR U42 RR01 5087;
NIH Office of the Director R24 OD010947
nif-0000-24364 SCR_008279 NIRC 2026-09-12 12:57:02 46
MultiPhase-SEG
 
Resource Report
Resource Website
MultiPhase-SEG (RRID:SCR_008275) data processing software, image analysis software, segmentation software, software application, software resource A segmentation software that employs the implementation of the active contours without edges level set based segmentation model. Its features include: segmentation of three-dimensional brain volumes into two or more regions (for example, regions could be WM, GM, and CSF), visualization of surfaces representing boundaries of different brain regions, and being written in Matlab with the ability to run on any platform with Matlab installed. segementation, visualization, 3D, software is related to: Laboratory of Neuro Imaging
is related to: MATLAB
has parent organization: University of Southern California; Los Angeles; USA
NIBIB 9P41EB015922-15;
NCRR 2-P41-RR-013642-15
Available for educational and research purposes only nif-0000-23319 http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=16 SCR_008275 2026-09-12 12:57:02 0
DualSurfaceMin
 
Resource Report
Resource Website
DualSurfaceMin (RRID:SCR_008278) DSM data processing software, image processing software, software application, software resource The DualSurfaceMin is a C++ implementation of the fully automatic dual surface minimization (DSM) algorithm for the optimization of deformable surfaces. The method is developed for automatic surface extraction from noisy volumetric images. Its features include: global DSM, DSM-OS, and DSM-IS algorithms for automatic surface extraction from volumetric images using deformable simplex meshes; support for the VRML and OFF formats; output pf both triangulated and simplex meshes; and support for the raw and Analyze 7.5 image formats. software, image processing, optimization, deformable surface, surface extraction is related to: Laboratory of Neuro Imaging
has parent organization: University of Southern California; Los Angeles; USA
NIBIB 9P41EB015922-15;
NCRR 2-P41-RR-013642-15
Available for educational and research purposes only nif-0000-23322 SCR_008278 2026-09-12 12:57:02 0
Sub-Volume Thresholding Analysis
 
Resource Report
Resource Website
Sub-Volume Thresholding Analysis (RRID:SCR_008272) SVT data analysis software, data processing software, software application, software resource Software tool for determining the statistically significant regions of activation in single or multi-subject human brain functional studies. It can be also applied to structural brain data for analyzing developmental, dementia and other changes of anatomy over time. This package was originally developed to work on Sun SPARC and SGI stations using the "C" language compiler provided by Sun/SGI as part of the standard system software. data processing, data analysis, functional magnetic resonance imaging, fMRI, software, brain, brain functional studies is related to: Laboratory of Neuro Imaging
has parent organization: University of Southern California; Los Angeles; USA
NIBIB 9P41EB015922-15;
NCRR 2-P41-RR-013642-15
Available for educational and research purposes only nif-0000-23314 SCR_008272 2026-09-12 12:57:02 0
New England Primate Research School
 
Resource Report
Resource Website
New England Primate Research School (RRID:SCR_008290) data or information resource, disease-related portal, portal, research forum portal, topical portal THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. A center that focuses on performing bio-medical research on nonhuman primates to aid in human health research. The center also focuses on training young scientists for professional careers in bio-medical research and primate biology. One of the New England Primate Research School's main accomplishments was the creation of an animal model for AIDS that first demonstrated that vaccine protection could be possible. Recent research has led to the development of novel agents for brain imaging that will aid in the diagnosis and treatment of Parkinson's disease. aids, biology, biomedical, disease, parkinson's, primate, protection, research, scientific, smoking, training, treatment, vaccine has parent organization: Harvard University; Cambridge; United States NCRR THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-24357 SCR_008290 NEPRC 2026-09-12 12:57:02 0
ResearchMatch
 
Resource Report
Resource Website
100+ mentions
ResearchMatch (RRID:SCR_006387) ResearchMatch community building portal, data or information resource, patient registry, people resource, portal Free and secure registry to bring together two groups of people who are looking for one another: (1) people who are trying to find research studies, and (2) researchers who are looking for people to participate in their studies. It has been developed by major academic institutions across the country who want to involve you in the mission of helping today''''s studies make a real difference for everyone''''s health in the future. Anyone can join ResearchMatch. Many studies are looking for healthy people of all ages, while some are looking for people with specific health conditions. ResearchMatch can help ''''match'''' you with any type of research study, ranging from surveys to clinical trials, always giving you the choice to decide what studies may interest you. recruit, volunteer, clinical research, clinical, recruitment registry, registry, patient, clinical study, clinical trial, survey is related to: Clinical and Translational Science Awards Consortium
has parent organization: Vanderbilt University; Tennessee; USA
Healthy, Specific health condition NIH ;
NCATS UL1TR000445;
NCRR 1U54RR032646-01
PMID:22104055 nlx_152168 SCR_006387 Research Match 2026-09-12 12:56:39 214
CTSA-IP
 
Resource Report
Resource Website
CTSA-IP (RRID:SCR_006380) CTSA-IP community building portal, data or information resource, database, portal Database that aggregates and markets technologies from CTSA institutions as well as those of the National Institutes of Health, with the goal of enhancing research activity and private partnerships across the CTSA consortium. Regular, automatic updating with a standardized template facilitates broad participation by CTSA consortium members. Currently, there are over a dozen CTSAs contributing information on their technologies to the site. CTSA-IP Mission * Intellectual Property information exchange * Links publicly available licensing opportunities from CTSI Institutions in an easily searchable format that connects providers & users. * Aim of creating a consortium view of IP, licensing & sponsored research opportunities. * Stimulus to collaboration and partnering with and between CTSA member institutions. technology, intellectual property, partnership, aggregator, licensing opportunity is related to: Clinical and Translational Science Awards Consortium
has parent organization: University of Rochester; New York; USA
NCRR UL1 RR024160 PMID:22029803 Open access nlx_152160 SCR_006380 Clinical and Translational Sciences Award Intellectual Property 2026-09-12 12:56:39 0
Comparative Toxicogenomics Database (CTD)
 
Resource Report
Resource Website
1000+ mentions
Comparative Toxicogenomics Database (CTD) (RRID:SCR_006530) CTD analysis service resource, data analysis service, data or information resource, database, production service resource, service resource A public database that enhances understanding of the effects of environmental chemicals on human health. Integrated GO data and a GO browser add functionality to CTD by allowing users to understand biological functions, processes and cellular locations that are the targets of chemical exposures. CTD includes curated data describing cross-species chemical–gene/protein interactions, chemical–disease and gene–disease associations to illuminate molecular mechanisms underlying variable susceptibility and environmentally influenced diseases. These data will also provide insights into complex chemical–gene and protein interaction networks. environment, chemical, disease, gene, pathway, protein, interaction, animal model, ontology, annotation, toxin, ontology or annotation browser, FASEB list is used by: DisGeNET
is used by: NIF Data Federation
is listed by: 3DVC
is listed by: Gene Ontology Tools
is related to: PharmGKB Ontology
is related to: Gene Ontology
is related to: BioRAT
is related to: Integrated Gene-Disease Interaction
is related to: OMICtools
is related to: Integrated Manually Extracted Annotation
has parent organization: Mount Desert Island Biological Laboratory
has parent organization: North Carolina State University; North Carolina; USA
is parent organization of: Interaction Ontology
American Chemistry Council ;
NCRR P20 RR016463;
NIEHS ES014065;
NIEHS R01 ES019604;
NIEHS U24 ES033155;
Pfizer
PMID:16902965
PMID:16675512
PMID:14735110
PMID:12760826
Free, Freely available OMICS_01578, nif-0000-02683, r3d100011530 http://ctd.mdibl.org, https://doi.org/10.17616/R3KS7N SCR_006530 CTD - Comparative Toxicogenomics Database 2026-09-12 12:56:41 1901
Pharmabase - an open content cheminformatics resource linking physiology with pharmacology
 
Resource Report
Resource Website
Pharmabase - an open content cheminformatics resource linking physiology with pharmacology (RRID:SCR_002462) Pharmabase data or information resource, database, image collection THIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2015. Open content cheminformatics database linking physiology with pharmacology, it targets the action and use of pharmacological compounds in modifying protein function, while revealing molecular relationships and linking out to related databases and sites. Pharmabase has been developed as a research tool, a resource for students, and an ongoing interactive forum on the use of pharmacological compounds in cellular research. It has several navigational routes, including a graphics browser (shows graphics of cell types and pathways) and membrane transport, which also illustrates the diversity of mechanisms that are covered. Users have access to detailed compound records with interactive features, and a form to send comments to the editor. Investigators are encouraged to alert the editors to mistakes, omissions or new compound information available from their reading and research. function, cell, compound, graphic, illustration, membrane, molecular, pharmacological, pharmacology, protein, transport, metabolism, intracellular messenger, cell signaling, disease, tissue, cell type, pathway, pharmacology, channel, pump, carriers, protein transporter, membrane transport has parent organization: BioCurrents Research Center NCRR P41 RR001395 PMID:18428760 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-21324 SCR_002462 2026-09-12 12:55:41 0

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