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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
MRQy
 
Resource Report
Resource Website
1+ mentions
MRQy (RRID:SCR_025779) data analysis software, software resource, data processing software, software application Software quality assurance and checking tool for quantitative assessment of magnetic resonance imaging and computed tomography data. Used for quality control of MR imaging data. quantitative assessment, magnetic resonance imaging, computed tomography, imaging data, NCI U24CA199374;
NCI R01CA202752;
NCI R01CA208236;
NCI R01CA216579;
NCI R01CA220581;
NCI 1U01CA239055;
NCI 1F31CA216935;
NCI 1U01CA248226;
NHLBI R01HL15127701A1;
NIBIB 1R43EB028736;
NCRR 1C06RR12463
PMID:33176026 Free, Available for download, Freely available SCR_025779 2026-02-14 02:09:06 1
HCP Pipelines
 
Resource Report
Resource Website
10+ mentions
HCP Pipelines (RRID:SCR_026575) data processing software, software toolkit, software application, image processing software, software resource Software package as set of tools, primarily shell scripts, for processing multi-modal, high-quality MRI images for the Human Connectome Project. Minimal preprocessing pipelines for structural, functional, and diffusion MRI that were developed by the HCP to accomplish many low level tasks, including spatial artifact/distortion removal, surface generation, cross-modal registration, and alignment to standard space. Minimal preprocessing pipelines, Human Connectome Project, MRI images processing, MRI images, NIMH MH091657;
NIH Blueprint for Neuroscience Research ;
NIMH F30 MH097312;
NIMH ROI MH60974;
NCRR U24 RR021382;
NIBIB R01EB006758;
NIA R01AG008122;
NINDS R01 NS052585;
NINDS R21NS072652;
NINDS R01NS070963
PMID:23668970 Free, Available for download, Freely available https://www.humanconnectome.org/software/hcp-mr-pipelines SCR_026575 Human Connectome Project Pipelines 2026-02-14 02:09:43 20
Nested containment list
 
Resource Report
Resource Website
Nested containment list (RRID:SCR_027849) NCLS, NCList software resource, software library, software toolkit Software library for nested containment list data structure for interval overlap queries, like interval tree. It is a static interval-tree that is fast for both construction and lookups. nested containment list data structure, interval overlap queries, static interval-tree, construction and lookups, NCRR U54 RR021813;
NSF
PMID:17234640 Free, Available for download, Freely available SCR_027849 , Nested Containment List (NCList), Nested Containment List 2026-02-14 02:09:38 0
UCSF Chimera
 
Resource Report
Resource Website
1000+ mentions
UCSF Chimera (RRID:SCR_004097) Chimera software resource, d visualization software, data processing software, software application Software tool for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials. molecular modeling, electron microscopy, interactive visualization and analysis, molecular structures is used by: Structure-function linkage database
is listed by: 3DVC
is listed by: SoftCite
is related to: Integrative Modeling Platform
is related to: UCSF ChimeraX
is related to: UCSF ChimeraX
has parent organization: Resource for Biocomputing Visualization and Informatics
NIGMS P41 GM103311;
NCRR P41 RR001081
PMID:15264254 Restricted nlx_143560 http://plato.cgl.ucsf.edu/chimera/ SCR_004097 Chimera - an Extensible Molecular Modeling System, UCSF Chimera - an Extensible Molecular Modeling System 2026-02-14 02:00:40 2078
Velvet-SC
 
Resource Report
Resource Website
1+ mentions
Velvet-SC (RRID:SCR_004377) Velvet SC sequence analysis software, data processing software, data analysis software, software application, software resource Software package for short read data from single cells that improves assembly through use of progressively increasing coverage cutoff. Used for single cell Illumina sequences, allows variable coverage datasets to be utilized with assembly of E. coli and S. aureus single cell reads. Assembles single cell genome of uncultivated SAR324 clade of Deltaproteobacteria. genome, single, cell, short, read, assembly is listed by: OMICtools
is related to: Velvet
has parent organization: University of California at San Diego; California; USA
NHGRI R01 HG003647;
Sloan Foundation ;
NCRR P41 RR024851
PMID:21926975 Free, Available for download, Freely available OMICS_01504 SCR_004377 Velvet Single Cell 2026-02-14 02:00:56 5
MNE software
 
Resource Report
Resource Website
50+ mentions
MNE software (RRID:SCR_005972) MNE data visualization software, data processing software, data analysis software, software toolkit, software application, software resource 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
NIBIB R01 EB009048;
NIBIB P41 EB015896;
NCRR P41 RR014075;
NIDCD F32DC012456;
NSF 0958669;
NSF 1042134;
European Research Council (ERC) StG-263584
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 2026-02-14 02:01:03 97
ResearchMatch
 
Resource Report
Resource Website
100+ mentions
ResearchMatch (RRID:SCR_006387) ResearchMatch community building portal, people resource, portal, data or information resource, patient registry 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 2026-02-14 02:01:16 180
CTSA-IP
 
Resource Report
Resource Website
CTSA-IP (RRID:SCR_006380) CTSA-IP data or information resource, portal, database, community building 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 2026-02-14 02:01:16 0
Comparative Toxicogenomics Database (CTD)
 
Resource Report
Resource Website
1000+ mentions
Comparative Toxicogenomics Database (CTD) (RRID:SCR_006530) CTD data analysis service, analysis service resource, data or information resource, production service resource, service resource, database 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
Pfizer ;
American Chemistry Council ;
NIEHS ES014065;
NIEHS R01 ES019604;
NCRR P20 RR016463;
NIEHS U24 ES033155
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 2026-02-14 02:01:19 1188
eagle-i research resource ontology
 
Resource Report
Resource Website
1+ mentions
eagle-i research resource ontology (RRID:SCR_008784) ERO ontology, data repository, storage service resource, data or information resource, source code, service resource, controlled vocabulary, software application, software resource, database Ontology that models research resources such as instruments, protocols, reagents, animal models and biospecimens. It has been developed in the context of the eagle-i project (http://eagle-i.net/) and consists of over 3451 classes of which over 1200 were created within the ERO namespace, while the rest come from existent ontologies such as the Ontology for Biomedical Investigation (OBI), the uber-anatomy ontology (Uberon), VIVO, the Ontology for Clinical Research (OCRe), the Sequence Ontology (SO), the Software Ontology (SWO) and we include terms from the NCBI Taxonomy as well. The main ontology can be browsed in OntoBee. All purls resolve to OntoBee. research, resource, biomedical, owl is listed by: BioPortal
is related to: Ontobee
is related to: CTSA ShareCenter
has parent organization: Eagle I
has parent organization: Google Code
ARRA ;
NCRR U24RR029825
New BSD License nlx_144312 SCR_008784 2026-02-14 02:01:46 1
Slicer3 Module Rician noise filter
 
Resource Report
Resource Website
1+ mentions
Slicer3 Module Rician noise filter (RRID:SCR_009614) Slicer3:Module:Rician Noise Removal image processing software, software resource, data processing software, software application Two Slicer3 modules removing rician noise in diffusion tensor MRI c++, console (text based), linux, magnetic resonance, posix/unix-like, diffusion mri is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: 3D Slicer
NIH Roadmap for Medical Research ;
NIBIB U54 EB005149;
NCRR 2-P41-RR12553-07
PMID:17354881 GNU General Public License nlx_155836 http://www.nitrc.org/projects/dtiricianrem SCR_009614 2026-02-14 02:01:52 1
LONI Brain Parser
 
Resource Report
Resource Website
1+ mentions
LONI Brain Parser (RRID:SCR_009572) Brain Parser data processing software, software application, segmentation software, software resource, image analysis software Software that uses a novel statistical-learning technique to segment brain regions of interest (ROIs) based on a training set of data and generates 3D MRI volumes. The software comes pre-trained on a provided data set but can be retrained to work with your desired regions of interest. analyze, anatomic, application, c++, console (text based), labeling, linux, microsoft, magnetic resonance, posix/unix-like, region of interest, segmentation, sh/bash, unix shell, windows, windows nt/2000, windows vista, workflow is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Laboratory of Neuro Imaging
NIBIB 9P41EB015922-15;
NCRR 2-P41-RR-013642-15;
NCRR U54 RR021813
GNU General Public License, LONI Software License nlx_155783 http://www.nitrc.org/projects/brainparser SCR_009572 BrainParser 2026-02-14 02:01:53 3
map3d
 
Resource Report
Resource Website
1+ mentions
map3d (RRID:SCR_009628) map3d data visualization software, software resource, data processing software, software application 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 2026-02-14 02:01:42 3
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) 2026-02-14 02:01:34 60
Mouse Mutant Resource
 
Resource Report
Resource Website
1+ mentions
Mouse Mutant Resource (RRID:SCR_008367) MMR biomaterial supply resource, organism supplier, cell repository, material resource 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 2026-02-14 02:01:41 2
Alamogordo Primate Facility
 
Resource Report
Resource Website
Alamogordo Primate Facility (RRID:SCR_008376) APF biomaterial supply resource, organism supplier, material resource 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 2026-02-14 02:01:33 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, software application, segmentation software, software resource, image analysis software 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 2026-02-14 02:01:36 0
New Iberia Research Center
 
Resource Report
Resource Website
10+ mentions
New Iberia Research Center (RRID:SCR_008279) biomaterial supply resource, organism supplier, material resource 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 NIH Office of the Director R24 OD010947;
NCRR U42 RR01 5087
nif-0000-24364 SCR_008279 NIRC 2026-02-14 02:01:38 41
MultiPhase-SEG
 
Resource Report
Resource Website
MultiPhase-SEG (RRID:SCR_008275) data processing software, software application, segmentation software, software resource, image analysis software 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 2026-02-14 02:01:40 0
DualSurfaceMin
 
Resource Report
Resource Website
DualSurfaceMin (RRID:SCR_008278) DSM image processing software, software resource, data processing software, software application 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 2026-02-14 02:01:31 0

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