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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NeuroScope Resource Report Resource Website 50+ mentions |
NeuroScope (RRID:SCR_002455) | NeuroScope | software application, data visualization software, software resource, data processing software | An advanced viewer for electrophysiological and behavioral data: it can display local field potentials (EEG), neuronal spikes, behavioral events, as well as the position of the animal in the environment. It also features limited editing capabilities. | eeg, meg, electrocorticography, behavior, neuronal spike, behavioral event, edit |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Buzsaki Lab |
PMID:16580733 | Free, Freely available | nlx_155828 | SCR_002455 | 2026-08-10 09:31:43 | 88 | |||||||
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Variant Reporter Software Resource Report Resource Website 50+ mentions |
Variant Reporter Software (RRID:SCR_002329) | data analysis software, software application, software resource, sequence analysis software, data processing software |
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 28, 2017. Software that performs comparative sequencing, also known as direct sequencing, medical sequencing, PCR sequencing and resequencing with DNA sequencing files. The software is designed for reference based and non-reference based analysis such as mutation detection and analysis, SNP discovery and validation and sequence confirmation. |
comparative sequencing, mutation detection, snp discovery, sequence confirmation |
is listed by: OMICtools is listed by: Thermo Fisher Scientific has parent organization: Life Technologies |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01818 | http://www.lifetechnologies.com/order/catalog/product/4385261 | SCR_002329 | 2026-08-10 09:31:41 | 85 | ||||||||
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MNI N3 Resource Report Resource Website 10+ mentions |
MNI N3 (RRID:SCR_002484) | N3 | software application, data processing software, image processing software, software resource | The perl script nu_correct implements a novel approach to correcting for intensity non-uniformity in MR data that achieves high performance without requiring supervision. By making relatively few assumptions about the data, the method can be applied at an early stage in an automated data analysis, before a tissue intensity or geometric model is available. Described as Non-parametric Non-uniform intensity Normalization (N3), the method is independent of pulse sequence and insensitive to pathological data that might otherwise violate model assumptions. To eliminate the dependence of the field estimate on anatomy, an iterative approach is employed to estimate both the multiplicative bias field and the distribution of the true tissue intensities. Preprocessing of MR data using N3 has been shown to substantially improve the accuracy of anatomical analysis techniques such as tissue classification and cortical surface extraction. | magnetic resonance, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McConnell Brain Imaging Center |
Free, Available for download, Freely available | nlx_155878 | http://www.nitrc.org/projects/nu_correct | SCR_002484 | MNI N3 Software Package, MNI_N3, Non-parametric Non-uniform intensity Normalization, N3 - MINC B0 nonuniformity correction, MNI_N3 Software Package | 2026-08-10 09:31:44 | 11 | ||||||
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Human Brain Project EU Resource Report Resource Website 50+ mentions |
Human Brain Project EU (RRID:SCR_002241) | HBP EU, HBP, European HBP, | data or information resource, organization portal, portal, funding resource | Global, collaborative effort for neuroscience, medicine and computing to understand brain, its diseases and its computational capabilities. Goal is to obtain access to research, data sources, platforms and infrastructures offered by other organisations, and enabling organizations outside HBP to use HBP platforms to pursue their own research. Coordinating these activities is the responsibility of the European Research Programme. | brain, ethics, neuroscience, medicine, computing, treatment, brain disease, neuroinformatics, software development, computational modeling, software, connectomics |
is related to: BigBrain is related to: Julich-Brain Cytoarchitectonic Atlas is parent organization of: subcellular application is parent organization of: Subcellular App |
Restricted | nlx_155553 | SCR_002241 | European Human Brain Project | 2026-08-10 09:31:40 | 69 | |||||||
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NIDB - Neuroinformatics Database Resource Report Resource Website 1+ mentions |
NIDB - Neuroinformatics Database (RRID:SCR_002488) | NIDB | data or information resource, software application, database, data management software, software resource | Neuroimaging database designed to allow simple importing, searching, and sharing of imaging data. NIDB also provides automated pipelining with importing of results back into NIDB which can be searched along with imaging meta data. | connectome file format, clinical neuroinformatics, computational neuroscience, computed tomography, imaging genomics, interfile, javascript, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
PMID:25888923 | Free, Available for download, Freely available | nlx_155882 | http://www.nitrc.org/projects/nidb | http://nidb.sourceforge.net/ | SCR_002488 | Neuroinformatics Database | 2026-08-10 09:31:44 | 2 | ||||
|
PHYCAA+: adaptive physiological noise correction for BOLD fMRI Resource Report Resource Website 1+ mentions |
PHYCAA+: adaptive physiological noise correction for BOLD fMRI (RRID:SCR_002514) | PHYCAA+ | software application, data processing software, image processing software, software resource | Software algorithm that automatically estimates and removes physiological noise in BOLD fMRI data, including the effects of heartbeat and respiration. This algorithm (1) masks out high-variance CSF and vascular tracts that may otherwise confound analyses, and (2) regresses out noise timeseries in grey matter tissue, using an adaptive multivariate component decomposition (Canonical Autocorrelations Analysis). PHYCAA+ is an efficient, automated procedure that does NOT require external measures of physiology, nor does it require the user to manually identify noise components. Based on the peer-reviewed article: Churchill & Strother (2013). PHYCAA+: An Optimized, Adaptive Procedure for Measuring and Controlling Physiological Noise in BOLD fMRI. NeuroImage 82: 306-325 | algorithm, matlab, magnetic resonance, nifti, os independent, fmri, bold, bold fmri, multivariate, physiological noise |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Toronto; Ontario; Canada |
PMID:23727534 | GNU Lesser General Public License | nlx_155913 | SCR_002514 | 2026-08-10 09:31:44 | 7 | |||||||
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DNA DataBank of Japan (DDBJ) Resource Report Resource Website 500+ mentions |
DNA DataBank of Japan (DDBJ) (RRID:SCR_002359) | DDBJ | data or information resource, data repository, database, service resource, storage service resource | Maintains and provides archival, retrieval and analytical resources for biological information. Central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: DDBJ Omics Archive and BioProject. DOR is archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides organizational framework to access metadata about research projects and data from projects that are deposited into different databases. | nucleotide sequence, genome, dna, dna database, dna research, nucleotide, phylogenetics, protein, sequence, protein binding, gene expression, gene, genetics, nucleoid, genomics, protein binding, gold standard, bio.tools, FASEB list |
is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: INSDC is related to: GenBank is related to: INSDC is related to: European Nucleotide Archive (ENA) is related to: GenBank is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Worldwide Protein Data Bank (wwPDB) is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: PDBe - Protein Data Bank in Europe is related to: PDBe - Protein Data Bank in Europe is related to: European Nucleotide Archive (ENA) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: NCBI Assembly Archive Viewer has parent organization: National Institute of Genetics; Shizuoka; Japan is parent organization of: DDBJ Omics Archive is parent organization of: BodyMap-Xs is parent organization of: DDBJ Sequence Read Archive is parent organization of: CIBEX: Center for Information Biology gene EXpression database is parent organization of: Japanese Genotype-phenotype Archive (JGA) |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:26578571 PMID:25477381 |
Free, Freely available, | OMICS_01644, biotools:ddbj, nif-0000-02740, r3d100010218 | https://bio.tools/ddbj, https://doi.org/10.17616/R3M01R | SCR_002359 | DNA DataBank of Japan (DDBJ), DNA DataBank of Japan, DDBJ, DNA Data Bank of Japan, DDBJ - DNA Data Bank of Japan | 2026-08-10 09:31:42 | 709 | ||||
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NCBI Genome Resource Report Resource Website 500+ mentions |
NCBI Genome (RRID:SCR_002474) | Genome | data or information resource, data repository, database, service resource, storage service resource | Database that organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations in six major organism groups: Archaea, Bacteria, Eukaryotes, Viruses, Viroids, and Plasmids. Genomes of over 1,200 organisms can be found in this database, representing both completely sequenced organisms and those for which sequencing is in progress. Users can browse by organism, and view genome maps and protein clusters. Links to other prokaryotic and archaeal genome projects, as well as BLAST tools and access to the rest of the NCBI online resources are available. | chromosome, organelle, plasmid, viroid, virus, genome, sequence, map, assembly, annotation, gene mapping, dna, blast, protein cluster, gold standard |
is listed by: re3data.org is related to: MapViewer is related to: UniProt Proteomes is related to: CaspBase has parent organization: NCBI works with: nTrackAnnotator |
Free, Freely avaialble | nif-0000-02802, r3d100010785 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome, https://doi.org/10.17616/R3R89S | SCR_002474 | Entrez Genomes, Entrez Genome, NCBI, Genome, Genome Database, Genome: Information by genome sequence | 2026-08-10 09:31:44 | 618 | ||||||
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iBEAT Resource Report Resource Website 10+ mentions |
iBEAT (RRID:SCR_002470) | iBEAT | software application, software toolkit, software resource, image analysis software, image processing software, data processing software | A toolbox with graphical user interfaces for processing infant brain MR images. Longitudinal (or single-time-point) multimodality (including T1, T2, and FA) (or single-modality) data can be processed using the toolbox. Main functions of the software (step by step) include image preprocessing, brain extraction, tissue segmentation and brain labeling. Linux operating system (64 bit) is required. A workstation or server with memory >8G is recommended for processing many images simutaneously. The graphical user interfaces and overall framework of the software are implemented in MATLAB. The image processing functions are implemented with the combination of C/C++, MATLAB, Perl and Shell languages. Parallelization technologies are used in the software to speed up image processing. | atlas application, atlas data, data resource, image display, information resource, magnetic resonance, registration, segmentation, spatial transformation, visualization, warping, mri, infant, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA |
PMID:23055044 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155851 | http://www.nitrc.org/projects/ibeat | SCR_002470 | Infant Brain Extraction and Analysis Toolbox, LIBRA, iBEAT: Infant Brain Extraction and Analysis Toolbox | 2026-08-10 09:31:44 | 39 | |||||
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Non-Rigid Image Registration Evaluation Project Resource Report Resource Website 1+ mentions |
Non-Rigid Image Registration Evaluation Project (RRID:SCR_002505) | NIREP | data or information resource, database, narrative resource, standard specification, software resource | Project to develop software tools and provide shared image validation databases for rigorous testing of non-rigid image registration algorithms. NIREP will extend the scope of prior validation projects by developing evaluation criteria and metrics using large image populations, using richly annotated image databases, using computer simulated data, and increasing the number and types of evaluation criteria. The goal of this project is to establish, maintain, and endorse a standardized set of relevant benchmarks and metrics for performance evaluation of nonrigid image registration algorithms. Furthermore, these standards will be incorporated into an exportable computer program to automatically evaluate the registration accuracy of nonrigid image registration algorithms. | magnetic resonance, registration software |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Iowa; Iowa; USA |
NIBIB R33 EB004126 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155904 | http://www.nitrc.org/projects/nirep | SCR_002505 | Non-Rigid Image Registration Evaluation Project, Non-Rigid Image Registration Evaluation Project (NIREP) | 2026-08-10 09:31:44 | 7 | |||||
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SCRalyze Resource Report Resource Website 10+ mentions |
SCRalyze (RRID:SCR_002542) | SCRalyze | software application, software resource, data analysis software, data processing software | A powerful software for model-based analysis of peripheral psychophysiology (e.g. skin conductance, heart rate, pupil size etc.). General linear modelling and dynamic causal modelling of these signals provide for inference on neural states/processes. SCRalyze includes flexible data import and display, statistical inference and results display and export. Easy programming of add-ons for new data formats, signal channels, and models. | eeg, meg, electrocorticography, matlab, modeling, os independent, quantification, time domain analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
Free, Available for download, Freely available | nlx_155950 | http://www.nitrc.org/projects/scralyze | SCR_002542 | SCRalyze - A matlab environment for model-based psychophysiology | 2026-08-10 09:31:45 | 17 | ||||||
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Cancer Genomics Hub Resource Report Resource Website 100+ mentions |
Cancer Genomics Hub (RRID:SCR_002657) | CGHub | data or information resource, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A secure repository for storing, cataloging, and accessing cancer genome sequences, alignments, and mutation information from the Cancer Genome Atlas (TCGA) consortium and related projects. CGHub gives scientific researchers the statistical power of large cancer genome datasets to attack the molecular complexity of cancer. | genome, genome sequence, alignment, mutation | has parent organization: University of California at Santa Cruz; California; USA | Cancer | PMID:25267794 | THIS RESOURCE IS NO LONGER IN SERVICE. | r3d100011174, nlx_156095 | https://doi.org/10.17616/R3F919 | SCR_002657 | 2026-08-10 09:31:47 | 179 | |||||
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PySurfer Resource Report Resource Website 10+ mentions |
PySurfer (RRID:SCR_002524) | PySurfer | software application, data visualization software, software toolkit, software library, software resource, data processing software | Software Python tool for visualization and interaction with cortical surface representations of neuroimaging data from Freesurfer. It extends Mayavi powerful visualization engine with interface for working with MRI and MEG data. PySurfer offers command-line interface designed to broadly replicate Freesurfer program as well as Python library for writing scripts to explore complex datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | eeg, meg, electrocorticography, magnetic resonance, mri, python, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: FreeSurfer |
Free, Available for download, Freely available | nlx_155930 | http://www.nitrc.org/projects/pysurfer, https://sources.debian.org/src/python3-surfer/ | SCR_002524 | 2026-08-10 09:31:45 | 29 | |||||||
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ShotGun Resource Report Resource Website 10+ mentions |
ShotGun (RRID:SCR_002529) | data analysis software, software application, simulation software, software resource, sequence analysis software, data processing software | Software for short read simulating in order to facilitate sequencing-based study designs. | sequence based study design, short read stimulation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:23357921 | Free, Available for download, Freely available | biotools:abcd, OMICS_00255 | https://bio.tools/abcd | SCR_002529 | ShotGun: a Flexible Short Read Simulator to Facilitate Sequencing-based Study Designs | 2026-08-10 09:31:45 | 35 | ||||||
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ConTrack Resource Report Resource Website 10+ mentions |
ConTrack (RRID:SCR_002681) | ConTrack | software application, data processing software, image processing software, software resource | An algorithm for identifying pathways that are known to exist between two regions within DTI data of anisotropic tissue, e.g., muscle, brain, spinal cord. The ConTrack algorithms use knowledge of DTI scanning physics and apriori information about tissue architecture to identify the location of connections between two regions within the DTI data. Assuming a course of connection or pathway between these two regions is known to exist within the measured tissue, ConTrack can be used to estimate properties of these connections in-vivo. | diffusion tensor imaging, tractography, brain connectivity, mri, software, source code, pathway, fiber tractography, tissue analysis |
is listed by: Biositemaps has parent organization: Simtk.org |
NIH Roadmap for Medical Research ; NIGMS U54 GM072970; NEI EY015000 |
PMID:18831651 | Free, Available for download, Freely available | nif-0000-23303 | SCR_002681 | Connectivity Tracking, Connectivity Tracking (ConTrack) | 2026-08-10 09:31:47 | 13 | |||||
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CRE Driver Network Resource Report Resource Website 1+ mentions |
CRE Driver Network (RRID:SCR_002720) | CRE Driver Network | material resource, organism supplier, biomaterial supply resource | Project to provide Neuroscience Community with mouse strains that are suitable for tissue and cell-type-specific perturbation of gene function in nervous system. NIH Neuroscience Blueprint has established three centers in the USA for generation of genetically modified mice expressing CRE recombinases in nervous system on the C57BJ/6 genetic background. Mouse lines are generated at Cold Spring Harbor Lab, at Scripps Research Institute, and at Baylor College of Medicine. | cre-recombinase, expression, neuroscience, mutant mouse strain, knock out mouse, phenotype, expression profile, image collection, microarray, electrophysiology, atlas, morphology, cell, annotation |
is related to: JAX Cre Repository is related to: Recombinase (cre) Activity has parent organization: NIH Blueprint for Neuroscience Research is parent organization of: Mouse Neuronal Expression Database |
NIH Blueprint for Neuroscience Research ; NIH |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-23753 | SCR_002720 | Mouse Models for Neuroscience Research, CRE-driver Network, CRE-Driver Network, NIH Neuroscience Blueprint CRE Driver Network | 2026-08-10 09:31:48 | 9 | ||||||
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Slice:Drop Resource Report Resource Website 1+ mentions |
Slice:Drop (RRID:SCR_002557) | Slice:Drop | analysis service resource, source code, production service resource, service resource, software resource | A viewer for medical imaging data that supports a variety of scientific file formats out-of-the-box (see https://github.com/xtk/X/wiki/X:Fileformats for a complete list). We think that the best way to render your files is without any necessary conversions. Just drop'em on a website and they are ready to render. Just drag'n'drop some medical imaging files on this website or try one of the four examples in the right corner. Then, play with the panels on the left and click, drag and rotate the 3d content. Slice:Drop uses WebGL and HTML5 Canvas to render the data in 2D and 3D. We use our own open-source toolkit to perform the rendering, called XTK ( http://goxtk.com ). | ascii, clinical neuroinformatics, computed tomography, dicom, javascript, mgh/mgz, magnetic resonance, nifti, nrrd, medical imaging, 3d, visualization, rendering | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155964 | http://www.nitrc.org/projects/slicedrop | SCR_002557 | 2026-08-10 09:31:45 | 5 | |||||||
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Gibbs Motif Sampler Resource Report Resource Website 1+ mentions |
Gibbs Motif Sampler (RRID:SCR_002550) | Gibbs Motif Sampler | analysis service resource, production service resource, service resource, software resource, data analysis service | Software to identify motifs, conserved regions, in DNA or protein sequences. | dna, protein, motif, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:gibbs_motif_sampler, OMICS_00496 | https://bio.tools/gibbs_motif_sampler | SCR_002550 | The Gibbs Motif Sampler | 2026-08-10 09:31:45 | 2 | ||||||
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Sleuth Resource Report Resource Website 100+ mentions |
Sleuth (RRID:SCR_002555) | data analysis software, software application, data visualization software, web application, software resource, data processing software | Software application that searches the BrainMap Database for papers of interest, reads their corresponding meta-data, and plots their results as coordinates on a standard glass brain in Talairach space. | brain map database, data visualization, neuroscience literature, talairach space, search software, meta-data analysis |
uses: MNI brain and the Talairach atlas uses: MNI brain and the Talairach atlas is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: brainmap.org |
Public, Account required, Available for download | nlx_155963 | http://www.nitrc.org/projects/brainmap | SCR_002555 | Sleuth Version 2.4 | 2026-08-10 09:31:45 | 224 | |||||||
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NCBI database of Genotypes and Phenotypes (dbGap) Resource Report Resource Website 500+ mentions |
NCBI database of Genotypes and Phenotypes (dbGap) (RRID:SCR_002709) | dbGaP | data or information resource, data repository, database, service resource, storage service resource | Database developed to archive and distribute clinical data and results from studies that have investigated interaction of genotype and phenotype in humans. Database to archive and distribute results of studies including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits. | clinical, trial, genotype, interaction, homology, cell, morphology, interaction, phenotype, molecular diagnosis, genetic recombination, gold standard, bio.tools |
is used by: International Genomics of Alzheimers Project is used by: NIDDK Inflammatory Bowel Disease Genetics Consortium is used by: NIH Heal Project is used by: Genomic Data Commons Data Portal (GDC Data Portal) is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: NIDDK Central Repository is related to: eMERGE Network: electronic Medical Records and Genomics is related to: Framingham Heart Study is related to: PhenoExplorer is related to: Chronic Renal Insufficiency Cohort Study is related to: DbGaP Cleaner is related to: Psychiatric Genomics Consortium is related to: ISCA Consortium is related to: Allen Institute for Brain Science has parent organization: NCBI is parent organization of: Resource for Genetic Epidemiology Research on Adult Health and Aging |
NLM | PMID:24297256 PMID:17898773 |
Restricted | nif-0000-23342, OMICS_00263, biotools:dbgap, r3d100010788 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=gap, https://bio.tools/dbgap, https://doi.org/10.17616/R3GS4K | SCR_002709 | database of Genotypes and Phenotypes (dbGaP), dbGaP, NCBI, Database of Genotypes and Phenotypes | 2026-08-10 09:31:48 | 736 |
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