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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MASIMatlab Resource Report Resource Website 1+ mentions |
MASIMatlab (RRID:SCR_009506) | MASIMatlab | software resource | This repository stores and provides opportunities for collaboration through Matlab code, libraries, and configuration information for projects in early stage development. The MASI research laboratory concentrates on analyzing large-scale cross-sectional and longitudinal neuroimaging data. Specifically, they are interested in population characterization with magnetic resonance imaging (MRI), multi-parametric studies (DTI, sMRI, qMRI), and shape modeling. | magnetic resonance, matlab, population characterization, mri, dti, smri, qmri, shape modeling |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Vanderbilt University; Tennessee; USA |
nlx_155655 | SCR_009506 | 2026-08-01 12:04:09 | 4 | |||||||||
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iView X MRI-LR - Eye Tracking for fMRI Resource Report Resource Website 1+ mentions |
iView X MRI-LR - Eye Tracking for fMRI (RRID:SCR_009627) | iView X MRI-LR | software resource | A non-invasive, long-range eye tracking system for use in the fMRI environment. Some features of the system include: * Elaborate faraday shielding and fiber optics to avoid noise in high-field magnets. * Includes stimulus presentation software ?Experiment Center? and is compatible with 3rd party products such as ?Presentation? by NeuroBS. * Utilizes mirror box customized for large field of view. * Includes powerful analysis software ?BeGaze2? for graphical and statistical analysis of eye movements. * Includes fixation, saccade and blink detection, and area-of-interest based statistics * Real-time data available via digital or analog output | magnetic resonance, fmri, meg, eye, eye tracking, mri, eye tracking device | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commerical | nlx_155853 | http://www.nitrc.org/projects/iviewx_mri-lr | SCR_009627 | 2026-08-01 12:03:45 | 3 | |||||||
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MASI Label Fusion Resource Report Resource Website 1+ mentions |
MASI Label Fusion (RRID:SCR_009505) | MASI Label Fusion | software resource | Tool that provides a unified framework for testing and applying statistical and voting label fusion techniques. The project will include implementations of several different voting techniques including majority vote, weighted voting, and regionally weighted voting. Additionally, multiple statistical fusion methods will be included, notably, STAPLE, Spatial STAPLE, STAPLER and COLLATE. In addition to the fusion algorithms, code for running specialized simulations and various tools and utilities to test the efficacy of the algorithms will be provided. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Vanderbilt University; Tennessee; USA |
GNU Lesser General Public License | nlx_155654 | SCR_009505 | 2026-08-01 12:03:43 | 3 | ||||||||
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BRAINSROIAuto Resource Report Resource Website |
BRAINSROIAuto (RRID:SCR_009501) | BRAINSROIAuto | software resource | Automatically creates a mask based on the "foreground" of an anatomical scan volume. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: BRAINSTools |
BRAINS License | nlx_155703 | http://www.nitrc.org/projects/brainsroiauto | SCR_009501 | 2026-08-01 12:04:00 | 0 | |||||||
|
SCALCE Resource Report Resource Website |
SCALCE (RRID:SCR_009658) | SCALCE | software resource | A FASTQ compression tool that uses locally consistent parsing to obtain better compression rate. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00969 | SCR_009658 | Boosting Sequence Compression Algorithms using Locally Consistent Encoding | 2026-08-01 12:03:45 | 0 | |||||||||
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JHU Proj. in Applied Medical Imaging Resource Report Resource Website |
JHU Proj. in Applied Medical Imaging (RRID:SCR_009499) | JHU Proj. in Applied Medical Imaging | software resource | This project is used for students enrolled in courses using the JIST framework. Content in this CVS is freely available, but it is not intended for any specific purpose. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: JIST: Java Image Science Toolkit has parent organization: Johns Hopkins University; Maryland; USA |
Free | nlx_155647 | SCR_009499 | 2026-08-01 12:03:43 | 0 | ||||||||
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iMir Resource Report Resource Website 10+ mentions |
iMir (RRID:SCR_009496) | iMir | software resource | A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, DE analysis, target prediction by integrating multiple open source modules and resources in an automated workflow. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24330401 | Apache License | OMICS_00358, biotools:imir | https://bio.tools/imir | SCR_009496 | 2026-08-01 12:04:09 | 11 | ||||||
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SpliceMap Resource Report Resource Website 10+ mentions |
SpliceMap (RRID:SCR_009650) | SpliceMap | software resource | A de novo splice junction discovery and alignment tool. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:25577377 PMID:20371516 |
OMICS_01252, biotools:splicemap | https://bio.tools/splicemap | SCR_009650 | 2026-08-01 12:04:10 | 21 | |||||||
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DATAPixx Resource Report Resource Website 10+ mentions |
DATAPixx (RRID:SCR_009648) | DATAPixx | commercial organization | Supplies a complete multi-function data and video processing USB peripheral for vision research. In addition to a dual-display video processor, the DATAPixx includes an array of peripherals which often need to be synchronized to video during an experiment, including a stereo audio stimulator, a button box port for precise reaction-time measurement, triggers for electrophysiology equipment, and even a complete analog I/O subsystem. Because we implemented the video controller and peripheral control on the same circuit board, you can now successfully synchronize all of your subject I/O to video refresh with microsecond precision. | eeg, eeg, meg, electrocorticography, experiment control, hardware, magnetic resonance, physiological recording, response monitoring, stimulus presentation, vision | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial license | nlx_155989 | http://www.nitrc.org/projects/vpixx | SCR_009648 | 2026-08-01 12:03:45 | 15 | |||||||
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Robust Biological Parametric Mapping Resource Report Resource Website 1+ mentions |
Robust Biological Parametric Mapping (RRID:SCR_009642) | Robust Biological Parametric Mapping | software resource | To enable widespread application of the Biological parametric mapping (BPM) approach, they introduce robust regression and non-parametric regression in the neuroimaging context of application of the general linear model. Biological parametric mapping (BPM) has extended the widely popular statistical parametric approach to enable application of the general linear model to multiple image modalities (both for regressors and regressands) along with scalar valued observations. This approach offers great promise for direct, voxelwise assessment of structural and functional relationships with multiple imaging modalities. However, as presented, the biological parametric mapping approach is not robust to outliers and may lead to invalid inferences (e.g., artifactual low p-values) due to slight mis-registration or variation in anatomy between subjects. | magnetic resonance, neuroimaging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU Lesser General Public License | nlx_155944 | SCR_009642 | 2026-08-01 12:04:10 | 3 | ||||||||
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Connectome File Format Resource Report Resource Website |
Connectome File Format (RRID:SCR_009551) | CFF | software resource | A container format for multi-modal neuroimaging data. It comprises connectome objects of type: CMetadata, CNetwork, CVolume, CSurface, CTrack, CScript, CData, CTimeseries, CImagestack. The Python library cfflib provides read/write functionality. | file format, gifti, information resource, information specification, magnetic resonance, nifti, portable document format, python, neuroimaging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155731 | http://www.nitrc.org/projects/cff | SCR_009551 | Connectome File Format (CFF) | 2026-08-01 12:03:43 | 0 | ||||||
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CDF-HC PointSetReg Resource Report Resource Website |
CDF-HC PointSetReg (RRID:SCR_009544) | CDF-HC PointSetReg | software resource | A Matlab demo for group wise point set registration using a novel CDF-based Havrda-Charvat Divergence, which is based on the paper: Ting Chen, Baba C. Vemuri, Anand Rangarajan and Stephan J. Eisenschenk, Group-wise Point-set registration using a novel CDF-based Havrda-Charvat Divergence. In IJCV : International Journal of Computer Vision, 86(1):111-124, January, 2010. | matlab | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:20221321 | GNU General Public License | nlx_155723 | http://www.nitrc.org/projects/cdfhc2010 | SCR_009544 | 2026-08-01 12:04:01 | 0 | ||||||
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Oregon Health and Science University; Oregon; USA Resource Report Resource Website 1+ mentions |
Oregon Health and Science University; Oregon; USA (RRID:SCR_009665) | OHSU | university | As the state''s only health and research university, OHSU brings together patient care, research, education of the next generation of health care providers and scientists and community service to improve the health and well-being of all Oregonians. |
is related to: Alzheimers Disease Genetics Consortium is related to: International AMD Genetics Consortium is related to: Beta Cell Biology Consortium is related to: Clinical and Translational Science Awards Consortium is parent organization of: OHSU MRI Support Core Laboratory is parent organization of: MCML and CONV is parent organization of: Neuron Registry Annotated Corpus is parent organization of: OHSU Biolibrary is parent organization of: Sterol and Isoprenoid Research Consortium is parent organization of: CTSAconnect is parent organization of: CTSA ShareCenter is parent organization of: OHSU Layton Aging and Alzheimer's Disease Center is parent organization of: Clinical Outcomes Research Initiative is parent organization of: OHSU Investigator Support and Integration Services is parent organization of: OHSU Advanced Computing Center Core Facility is parent organization of: OHSU Advanced Imaging Research Center Core Facility is parent organization of: OHSU Advanced Light Microscopy Core Facility is parent organization of: OHSU Assisted Reproductive Technologies and Embryonic Stem Cell Laboratory is parent organization of: OHSU Bioanalytical Shared Resource Pharmacokinetics Core Facility is parent organization of: OHSU Biochemical Genetics Laboratory is parent organization of: Oregon Clinical and Translational Research Institute Biomedical Informatics Program is parent organization of: OHSU Biomedical Informatics Shared Resource is parent organization of: OHSU Clinical Cytogenetics Laboratory is parent organization of: OHSU DNA Services Core Facility is parent organization of: Oregon Health and Science University Multiscale Microscopy Core Facility is parent organization of: OHSU Electronics and Instrumentation Design Core Resource is parent organization of: OHSU Endocrine Technology Support Core Laboratory is parent organization of: OHSU Flow Cytometry and Monoclonal Antibody Shared Resource Core Facility is parent organization of: OHSU Gene Profiling Shared Resource Core Facility is parent organization of: OHSU Lipid-Atherosclerosis Laboratory is parent organization of: OHSU Histopathology Shared Resource Core Facility is parent organization of: OHSU Imaging and Morphology Support Core Laboratory is parent organization of: OHSU Immuno Electron Microscopy Core is parent organization of: OHSU Immunology Support Core Cellular Immunology Unit is parent organization of: OHSU Immunology Support Core Flow Cytometry Unit is parent organization of: OHSU In Vivo Optical Imaging Center is parent organization of: OHSU Massively Parallel Sequencing Shared Resource Core Facility is parent organization of: OHSU Methamphetamine Abuse Research Center Animal Core Component is parent organization of: OHSU Molecular and Cellular Biology Core Laboratory is parent organization of: OHSU Monoclonal Antibody Core Laboratory is parent organization of: OHSU Neuropathology Core is parent organization of: OHSU Nuclear Magnetic Resonance Core Facility is parent organization of: OHSU Proteomics Shared Resource Core Facility is parent organization of: OHSU Research Cytogenetics Core Laboratory is parent organization of: OHSU Animal Model Support Core Facility is parent organization of: Oregon Clinical and Translational Research Institute Bionutrition Unit is parent organization of: OHSU Oregon Clinical and Translational Research Center Core Facility is parent organization of: Oregon Stem Cell Center Monoclonal Antibody Core is parent organization of: OSHU Gene Microarray Shared Resource is parent organization of: Oregon Health and Science University Labs and Facilities is parent organization of: OHSU DNA Services Core Facility is parent organization of: OHSU Molecular Virology Support Core is parent organization of: Oregon Health and Science University School of Medicine; Oregon; USA is parent organization of: Zebra Finch Expression Brain Atlas is parent organization of: Oregon Brain Bank is parent organization of: Research Network in Early Experience and Brain Development is parent organization of: Eagle I is parent organization of: Oregon Health and Science University Integrated Genomics Laboratory Core Facility is parent organization of: Oregon Health and Science University Multiscale Microscopy Core Facility is parent organization of: Oregon Health and Science University Elemental Analysis Core Facility is parent organization of: Oregon Health and Science University Center for Radiochemistry Research Core Facility is parent organization of: Oregon Health and Science University Biophysics Core Facility is parent organization of: Oregon Health and Science University Small Animal Research Imaging Core Facility is parent organization of: Oregon Health and Science University Biostatistics and Design Program Core Facility is parent organization of: Oregon Health and Science University Medicinal Chemistry Core Facility is parent organization of: Oregon Health and Science University Bioinformatics and Biostatistics Core Facility is parent organization of: MONARCH Initiative is parent organization of: Oregon Health and Science University Primate Genetics Core Facility is parent organization of: OHSU Monoclonal Antibody Shared Resource Core Facility |
nlx_80843, grid.5288.7, Crossref funder ID:100006668, Wikidata:Q282097, ISNI:0000 0000 9758 5690 | https://ror.org/009avj582 | SCR_009665 | Oregon Health & Science University; Oregon; USA, Oregon Health & Science University, Oregon Health University | 2026-08-01 12:04:10 | 1 | ||||||||
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U.S. Department of Commerce Resource Report Resource Website 1+ mentions |
U.S. Department of Commerce (RRID:SCR_009859) | Commerce.gov | institution | Executive department of the federal government concerned with promoting economic growth. Among its tasks are gathering economic and demographic data for business and government decision-making, and helping to set industrial standards. | Government granting agency |
is parent organization of: NIST - National Institute of Standards and Technology is parent organization of: National Oceanic and Atmospheric Administration is parent organization of: U.S. Census Bureau |
Crossref funder ID: 100000190, grid.239119.1, ISNI: 0000 0004 0478 6426, Wikidata: Q503577, nlx_144074 | https://ror.org/04chq2495 | SCR_009859 | United States Department of Commerce | 2026-08-01 12:04:11 | 2 | |||||||
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U.S. Geological Survey Resource Report Resource Website 100+ mentions |
U.S. Geological Survey (RRID:SCR_010168) | USGS | institution | Scientific agency of the United States government. The scientists of the USGS study the landscape of the United States, its natural resources, and the natural hazards that threaten it. The organization's work spans the disciplines of biology, geography, geology, and hydrology. | Government granting agency | nlx_157935, grid.2865.9, ISNI: 121546924, Crossref funder ID: 100000203, Wikidata: Q193755 | https://ror.org/035a68863 | SCR_010168 | United States Geological Survey | 2026-08-01 12:04:05 | 342 | ||||||||
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AllSeq Resource Report Resource Website |
AllSeq (RRID:SCR_010053) | AllSeq | service resource | Free online tools to find the best Sequencing Service provider for your project. | is listed by: OMICtools | Free | OMICS_01726 | SCR_010053 | 2026-08-01 12:04:11 | 0 | |||||||||
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University of Lyon; France Resource Report Resource Website |
University of Lyon; France (RRID:SCR_010178) | university | University of Lyon, located in Lyon and Saint-Étienne, France, is a center for higher education and research comprising 11 members and 24 associated institutions. | is parent organization of: I3-CRB: Interoperable IT Infrastructure for Biological Resources Centres / Biobanks - France | nlx_30442 | http://www.univ-lyon2.fr/international-/ | SCR_010178 | 2026-08-01 12:03:46 | 0 | ||||||||||
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San Diego State University; California; USA Resource Report Resource Website 1+ mentions |
San Diego State University; California; USA (RRID:SCR_009874) | SDSU | university | Public research university in San Diego, California. Founded in 1897 as San Diego Normal School, it is the third-oldest university in the 23-member California State University system. | is parent organization of: PRINSEQ | nlx_156724, Wikidata:Q913861, ISNI:0000 0001 0790 1491, Crossref funder ID:100007099, grid.263081.e | https://ror.org/0264fdx42 | SCR_009874 | San Diego State University | 2026-08-01 12:03:46 | 1 | ||||||||
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IsoEM Resource Report Resource Website 10+ mentions |
IsoEM (RRID:SCR_009993) | IsoEM | software resource | Software package that can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Connecticut; Connecticut; USA |
biotools:isoem, OMICS_01278 | https://bio.tools/isoem | SCR_009993 | 2026-08-01 12:04:05 | 10 | ||||||||
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Centre for Reviews and Dissemination Resource Report Resource Website 10+ mentions |
Centre for Reviews and Dissemination (RRID:SCR_010267) | CRD | institution | A research department of the University of York provides research-based information about the effects of health and social care interventions via their databases. The institute undertakes systematic reviews evaluating research evidence on health and public health questions of national and international importance. | evidence review, research review, public health, evidence synthesis, FASEB list | is related to: PROSPERO | National Institute for Health Research UK | Public, Available to the research community | nlx_156926 | http://www.york.ac.uk/ | SCR_010267 | University of York Centre for Reviews and Dissemination | 2026-08-01 12:04:07 | 40 |
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