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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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Hardin MD Resource Report Resource Website |
Hardin MD (RRID:SCR_002364) | data or information resource, database, image collection | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2025. A medical database with lists, or directories, of information in health and medicine and images of medical conditions. Users may search Hardin MD, browse through the Medical picture gallery, and sort search results by disease or alphabetical letter. | disease, health, medicine, database, directory, gallery, image collection | has parent organization: University of Iowa; Iowa; USA | AIDS, Autoimmune disease, Childrens disease, Herpes, Infectious disease, Skin disease, Sexually transmitted disease, Cancer, Heart disease | THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-21186, r3d100011208 | https://doi.org/10.17616/R3G62Z | http://www.lib.uiowa.edu/hardin/md/ | SCR_002364 | SciCrunch Registry | Hardin Meta Directory | 2026-10-17 01:25:10 | 0 | |||||
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MNI N3 Resource Report Resource Website 10+ mentions |
MNI N3 (RRID:SCR_002484) | N3 | data processing software, image processing software, software application, 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 | SciCrunch Registry | MNI N3 Software Package, MNI_N3, Non-parametric Non-uniform intensity Normalization, N3 - MINC B0 nonuniformity correction, MNI_N3 Software Package | 2026-10-17 01:25:12 | 11 | ||||||
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COGNISION Resource Report Resource Website 1+ mentions |
COGNISION (RRID:SCR_002362) | COGNISION | software resource | A portable, highly integrated, internet-enabled, hardware / software platform and patient management system, which includes an online Patient Manager module which complies with the HIPAA Final Security Rule, an event-related potential (ERP) Viewer module to view and analyze raw and average ERP waves, and a Protocol Editor module to simplify the choice and administration of selected ERP protocols. It is also easy to train and administer with non-specialized personnel, and is designed to be used in an out-patient setting. COGNISION TM with auditory or visual event-related potential (ERP) technology, provides a direct physiologic measure of patients' cognitive processing (i.e., a cognitive biomarker). | eeg, eeg, meg, electrocorticography, event-related potentials, hardware, physiological recording, instrument, equipment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial License | nlx_155724 | http://www.nitrc.org/projects/neuronetrix | SCR_002362 | SciCrunch Registry | COGNISION (TM) System | 2026-10-17 01:25:23 | 2 | ||||||
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Relevance Voxel Machine Resource Report Resource Website |
Relevance Voxel Machine (RRID:SCR_002361) | RVoxM | software resource | A Bayesian image-based prediction algorithm that is based on the Relevance Vector Machine and Automatic Relevance Detection frameworks, which are popular approaches in Machine Learning. RVoxM adapts this framework to handle images and explicitly models the spatial smoothness in images. RVoxM can be used to learn to predict a binary or continuous variable from image data. | matlab, image, predict, spatial smoothness | PMID:23008245 | SciRes_000134 | SCR_002361 | SciCrunch Registry | 2026-10-17 01:25:10 | 0 | |||||||||
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Histology of Nervous Tissue Laboratory Course Resource Report Resource Website |
Histology of Nervous Tissue Laboratory Course (RRID:SCR_002367) | Histology of Nervous Tissue | data or information resource, narrative resource, training material | A website for a neuroscience lab class from the University of South Carolina that contains images of different parts of the nervous system and allows students to identify each part and answer questions about it. You should be able to (a) recognize nervous tissue in routine histological sections; (b) distinguish peripheral nerves from dense CT and smooth muscle; (c) recognize the morphological differences between myelinated and unmyelinated nerves at both the light microscopic and electron microscopic levels; (d) recognize nerve cell bodies and their component parts; (e) identify and differentiate dendrites and axons; (f) understand and identify various types of neuroglia, including Schwann cells; (g) understand and identify the structural relationship of the Schwann cell cytoplasm and plasma membrane enveloping axons; (h) understand the general features of nerve synapses. You should be able to draw nerves, cell bodies, Nodes of Ranvier, synapses etc. as they would appear under both the electron and light microscopes. | brain, class, histology, laboratory, material, nervous system, neuron, microscopy, neuroscience, peripheral nerve, light microscopy, electron microscopy, nerve cell, neuroglia, nervous tissue, image, glass slide, slide | has parent organization: University of South Carolina School of Medicine; South Carolina; USA | nif-0000-21192 | SCR_002367 | SciCrunch Registry | Histology of Nervous Tissue Laboratories 9 and 10 | 2026-10-17 01:25:23 | 0 | ||||||||
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University of Angers; Angers; France Resource Report Resource Website |
University of Angers; Angers; France (RRID:SCR_002400) | UA | university | Public institution of higher learning in western France that offers programs four major areas: law, economics and business; arts, letters and languages; human and social sciences; and sciences, technology and health. | french public university, public university, french research institute |
is parent organization of: University of Angers Plateforme SNP Transcriptome and Epigenomics is parent organization of: University of Angers Labs and Facilities |
Free | nlx_153965 | SCR_002400 | SciCrunch Registry | Universite d'Angers, University of Angers | 2026-10-17 01:25:11 | 0 | |||||||
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NIDB - Neuroinformatics Database Resource Report Resource Website 1+ mentions |
NIDB - Neuroinformatics Database (RRID:SCR_002488) | NIDB | data management software, data or information resource, database, software application, 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 | SciCrunch Registry | Neuroinformatics Database | 2026-10-17 01:25:12 | 2 | ||||
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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 | SciCrunch Registry | DNA DataBank of Japan (DDBJ), DNA DataBank of Japan, DDBJ, DNA Data Bank of Japan, DDBJ - DNA Data Bank of Japan | 2026-10-17 01:25:10 | 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 | SciCrunch Registry | Entrez Genomes, Entrez Genome, NCBI, Genome, Genome Database, Genome: Information by genome sequence | 2026-10-17 01:25:12 | 618 | ||||||
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Mason Resource Report Resource Website 100+ mentions |
Mason (RRID:SCR_002476) | simulation software, software application, software resource | Collection of software tools for simulating biological sequences, including simulations of genome fragment sampling, random genomic sequences, methylation levels, and NGS reads. | read simulating software, sequencing simulation, haplotype simulation | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_00252 | SCR_002476 | SciCrunch Registry | Mason2 | 2026-10-17 01:25:26 | 169 | ||||||||
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iBEAT Resource Report Resource Website 10+ mentions |
iBEAT (RRID:SCR_002470) | iBEAT | data processing software, image analysis software, image processing software, software application, software resource, software toolkit | 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 | SciCrunch Registry | Infant Brain Extraction and Analysis Toolbox, LIBRA, iBEAT: Infant Brain Extraction and Analysis Toolbox | 2026-10-17 01:25:25 | 39 | |||||
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Primate Cortical Connectivity Database Resource Report Resource Website |
Primate Cortical Connectivity Database (RRID:SCR_002468) | Primate Cortical Connectivity Database | bibliography, data or information resource | Bibliography for primate cortical connectivity. The page displays the articles by their year of publication and links to PubMed. | connectivity, cerebral cortex, monkey, primate | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21332 | SCR_002468 | SciCrunch Registry | 2026-10-17 01:25:12 | 0 | |||||||||
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S-rep Fitting Statistics and Segmentation Resource Report Resource Website |
S-rep Fitting Statistics and Segmentation (RRID:SCR_002540) | S-rep Fitting Statistics and Segmentation | data processing software, image analysis software, segmentation software, software application, software resource | Software to fit s-reps to segmented anatomic objects, to compute probability distributions on these s-reps, to train and to apply classifiers between two classes of anatomic objects, and to apply hypothesis testing to determine which geometric or physiological features vary significantly between two classes. Software for object segmentation from medical images may also be included. S-reps are skeletal models for anatomic objects especially suited for computing probability distributions from populations of these objects and for providing object-related coordinates for the interior of these objects. They allow classification and hypothesis testing using their geometric features and physiological features derived from medical images. They also allow the definition of shape spaces, probability-based geometric typicality functions, and appearance models used for segmentation or registration. A variety of successful applications to objects in neuroimages have already been performed. | computational neuroscience, computed tomography, domain independent, mr | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155948 | SCR_002540 | SciCrunch Registry | 2026-10-17 01:25:13 | 0 | ||||||||
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Grants.gov Resource Report Resource Website 10+ mentions |
Grants.gov (RRID:SCR_002661) | funding resource | A source to FIND and APPLY for federal grants. The U.S. Department of Health and Human Services is proud to be the managing partner for Grants.gov, an initiative that is having an unparalleled impact on the grant community. All discretionary grants offered by the 26 federal grant-making agencies can be found on Grants.gov. Grants.gov was established as a governmental resource named the E-Grants Initiative, part of the President's 2002 Fiscal Year Management Agenda to improve government services to the public. The concept has its origins in the Federal Financial Assistance Management Improvement Act of 1999, also known as Public Law 106-107. Public Law 106-107 has since sunset and is now known as the Grants Policy Committee (GPC). For more information on the Grants Policy Committee, click here. Today, Grants.gov is a central storehouse for information on over 1,000 grant programs and provides access to approximately $500 billion in annual awards. You may find information on *What is a Grant? *Who is Eligible for a Grant? *Program highlights and accomplishments *Grants.gov in the News (Articles, press releases, milestones and events) *Program Status (Detailed information about our relationship with partner federal agencies, financial contributions, grant opportunities, fiscal reports, planning strategies and statistics.) | grant, funding, award, database, opportunity |
is used by: NIF Data Federation is used by: Aging Portal is used by: NIDDK Information Network (dkNET) |
Free, Freely available | nif-0000-22393 | SCR_002661 | SciCrunch Registry | 2026-10-17 01:25:42 | 36 | |||||||||
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SCRalyze Resource Report Resource Website 10+ mentions |
SCRalyze (RRID:SCR_002542) | SCRalyze | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | SCRalyze - A matlab environment for model-based psychophysiology | 2026-10-17 01:25:28 | 17 | ||||||
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Resource Ontology Discussion Group Resource Report Resource Website |
Resource Ontology Discussion Group (RRID:SCR_002536) | Resource Ontology Discussion Group | data or information resource, discussion, knowledge environment, narrative resource | Project to discuss, debate, develop and deploy ontological practices for the fMRI community. | community, ontology, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Free, Available for download, Freely available | nlx_155943 | SCR_002536 | SciCrunch Registry | 2026-10-17 01:25:27 | 0 | ||||||||
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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 | SciCrunch Registry | 2026-10-17 01:25:15 | 179 | |||||
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Rodent Cortical Thickness Analysis Resource Report Resource Website |
Rodent Cortical Thickness Analysis (RRID:SCR_002539) | data processing software, image analysis software, image processing software, software application, software resource | An automatic cortical thickness measurement tool for rat brains. The pipeline consists of four steps: preprocessing to create binary mask and label map, thickness measurement which produces laplacian field and thickness map in order, run particle correspondence followed by statistical analysis resulting in mean thickness color map and t-test result. By running RodentThickness, you will need to fill in informations in a Graphical User Interface, and then compute. You can also run the tool in command line without using the GUI. Using the GUI, you will be able to save or load a dataset file or a configuration file. The tool needs these other tools to work, so be sure to have these installed on your computer: * ImageMath * measureThicknessFilter * GenParaMeshCLP * ParaToSPHARMMeshCLP * ShapeWorksRun * ShapeWorksGroom * SegPostProcessCLP * BinaryToDistanceMap * MeshPointsIntensitysampling | microscopy, magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155946 | http://www.nitrc.org/projects/rodentthickness | SCR_002539 | SciCrunch Registry | RodentThickness | 2026-10-17 01:25:13 | 0 | |||||||
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Rodent Brain Extraction Tool Resource Report Resource Website |
Rodent Brain Extraction Tool (RRID:SCR_002538) | rBET | data processing software, image processing software, software application, software resource | A modified version of the Brain Extraction Tool (BET) that can process rodent brains. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL has parent organization: King's College London; London; United Kingdom |
Free, Available for download, Freely available | nlx_155945 | http://www.nitrc.org/projects/rbet | SCR_002538 | SciCrunch Registry | 2026-10-17 01:25:40 | 0 | |||||||
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NiBabel Resource Report Resource Website 100+ mentions |
NiBabel (RRID:SCR_002498) | NiBabel | software resource | A Python package for reading and writing a variety of medical and neuroimaging file formats. This includes: ANALYZE (plain, SPM99, SPM2), NIfTI1, as well as MINC. NiBabel is the successor of PyNIfTI. | magnetic resonance, python, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: PyNIfTI is related to: MNE software has parent organization: Neuroimaging in Python |
Free, Available for download, Freely available | nlx_155896 | http://www.nitrc.org/projects/nibabel | SCR_002498 | SciCrunch Registry | NIPY File IO | 2026-10-17 01:25:40 | 142 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
