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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NIH Image Resource Report Resource Website 1000+ mentions |
NIH Image (RRID:SCR_003073) | NIH Image | image processing software, software resource, data processing software, software application, source code, image analysis software | Public image processing and analysis program for Macintosh. | image processing application, public image processing software, imagej |
is listed by: SoftCite is related to: ImageJ is related to: BrainImage Software is related to: Object-Image has parent organization: National Institutes of Health has parent organization: National Institute of Mental Health |
NINDS ; NIMH |
Free, download Freely available | nif-0000-30469 | https://imagej.net/nih-image/index.html | SCR_003073 | 2026-08-02 09:03:39 | 4412 | ||||||
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National Institute of Mental Health Resource Report Resource Website 100+ mentions |
National Institute of Mental Health (RRID:SCR_011431) | NIMH | government granting agency | National institute that is the largest scientific organization in the world dedicated to research focused on the understanding, treatment, and prevention of mental disorders and the promotion of mental health. NIMH envisions a world in which mental illnesses are prevented and cured. The mission of NIMH is to transform the understanding and treatment of mental illnesses through basic and clinical research, paving the way for prevention, recovery and cure. For the Institute to continue fulfilling this vital public health mission, it must foster innovative thinking and ensure that a full array of novel scientific perspectives are used to further discovery in the evolving science of brain, behavior, and experience. In this way, breakthroughs in science can become breakthroughs for all people with mental illnesses. In support of this mission, NIMH will generate research and promote research training to fulfill the following four objectives: * Promote discovery in the brain and behavioral sciences to fuel research on the causes of mental disorders * Chart mental illness trajectories to determine when, where, and how to intervene * Develop new and better interventions that incorporate the diverse needs and circumstances of people with mental illnesses * Strengthen the public health impact of NIMH-supported research To reach these goals, the NIMH divisions and programs are designed to emphasize translational research spanning bench, to bedside, to practice. For targeted priorities and funding initiatives, please visit our division websites |
lists: Neuroscience Information Framework has parent organization: NIH Blueprint for Neuroscience Research has parent organization: National Institutes of Health is parent organization of: NIMH Educational Resources is parent organization of: NIMH Multimedia is parent organization of: NIMH Image Library is parent organization of: NIMH Video is parent organization of: NIMH Clinical Trials is parent organization of: NIMH Resources for Research Training and Career Development is parent organization of: NIMH Director's Blog is parent organization of: NIMH Publications is parent organization of: RDoC is parent organization of: Neuroimaging Informatics Technology Initiative is parent organization of: Neurophysiology Imaging Facility is parent organization of: NIMH Data Archive is parent organization of: MRI Research Safety and Ethics is parent organization of: Analysis of Functional NeuroImages is parent organization of: NIMH Division of Intramural Research Programs is parent organization of: MicroSNiPer is parent organization of: NIH Image |
nlx_inv_1005109 | SCR_011431 | 2026-08-01 12:04:08 | 117 | ||||||||||
|
ImageJ Resource Report Resource Website 10000+ mentions |
ImageJ (RRID:SCR_003070) | software toolkit, software resource, image processing software, data processing software, software application, image analysis software | Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets. | image, data, processing, analysis, datasets, visualization, |
uses: NeuriteTracer is used by: Mouse Behavioral Analysis Toolbox is used by: Focinator is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: uManager is related to: Fiji is related to: NIH Image is related to: TrakEM2 is related to: BioVoxxel Toolbox is related to: Golddigger is related to: Analyze Complex Roots Tool is related to: Analyze Spheroid Cell Invasion In 3D Matrix is related to: PyImageJ has parent organization: Research Services Branch National Institutes of Mental Health has plug in: Diffusing Tensor Imaging in Java has plug in: OrientationJ has plug in: GRatio for ImageJ has plug in: BioVoxxel Toolbox has plug in: WormSizer has plug in: MultiStackReg has plug in: Iterative Deconvolve 3D has plug in: Thunder STORM has plug in: Whisker tracking macro has plug in: 3D Roi Manager has plug in: 3D Objects Counter has plug in: BoneJ has plug in: QuickFigures has plug in: ObjectJ has plug in: ADAPT has plug in: DHM Utilities has plug in: Sholl Analysis has plug in: nTracer has plug in: IHC Profiler has plug in: MicrobeJ has plug in: AccPbFRET has plug in: RiFRET has plug in: JaCoP has plug in: Cell Counter Plugin for ImageJ has plug in: Puncta Analyzer has plug in: SpinalJ has plug in: ColonyArea works with: Intensity Ratio Nuclei Cytoplasm Tool works with: 3D ImageJ Suite works with: Wound Healing Tool works with: MorphoLibJ |
NINDS ; NIGMS RC2 GM092519; Wellcome Trust Strategic Award 095931; the Laboratory for Optical and Computational Instrumentation ; the Morgridge Institute for Research ; NIH ; NIMH |
PMID:22930834 PMID:29187165 DOI:10.1038/nmeth.2089 |
Free, Available for download, Freely available | ascl:1206.013, rid_000070, Q1659584, 2012ascl.soft06013R, nif-0000-30467, SCR_018407 | https://imagej.net/ij/, http://rsbweb.nih.gov/ij, https://imagej.nih.gov/ij/download.html, https://imagej.nih.gov/ij/, https://sources.debian.org/src/imagej/, | https://imagej.nih.gov/ij/, http://www.nitrc.org/projects/incf_imagej, | SCR_003070 | Image J, ImageJ - Image Processing and Analysis in Java, ImageJ2, ImageJ | 2026-08-02 09:03:53 | 27070 | ||||
|
National Institutes of Health Resource Report Resource Website 1000+ mentions |
National Institutes of Health (RRID:SCR_011417) | NIH | institution | NIH is the nations medical research agency - making important medical discoveries that improve health and save lives. The National Institutes of Health (NIH), a part of the U.S. Department of Health and Human Services, is the primary Federal agency for conducting and supporting medical research. Helping to lead the way toward important medical discoveries that improve peoples health and save lives, NIH scientists investigate ways to prevent disease as well as the causes, treatments, and even cures for common and rare diseases. NIH research impacts: * child and teen health, * men's health, * minority health, * seniors' health, * women's health, and * wellness and lifestyle issues. Composed of 27 Institutes and Centers, the NIH provides leadership and financial support to researchers in every state and throughout the world. | granting agency, US Department of Health, medical research |
uses: ReadCube uses: Scizzle is related to: All About Grants Podcast is related to: Ranking Tables of NIH Funding to US Medical Schools in 2010 is related to: DMPTool has parent organization: United States Department of Health and Human Services granting agency is parent organization of: Human Genome Project Information is parent organization of: Cross Collaboration Initiatives at the NIH is parent organization of: GEOquery is parent organization of: Trans-Institute Angiogenesis Research Program is parent organization of: Collecting Duct Database is parent organization of: NIH Office of Research Services is parent organization of: ECRbase is parent organization of: NIH Worker Training Program is parent organization of: ACME is parent organization of: NIH Division of Nutrition Research Coordination is parent organization of: Research Services Branch National Institutes of Mental Health is parent organization of: NIH VideoCasting is parent organization of: Biositemaps is parent organization of: Neurofed is parent organization of: NeuronJ: An ImageJ Plugin for Neurite Tracing and Quantification is parent organization of: General Clinical Research Centers Program is parent organization of: Office of Intramural Training and Education is parent organization of: Mutant Mouse Resource and Research Center is parent organization of: NIH Image is parent organization of: Biomedical Information Science and Technology Initiative is parent organization of: NIH NeuroBioBank is parent organization of: NIH Human Pluripotent Stem Cell Registry is parent organization of: NIH MRI Study of Normal Brain Development is parent organization of: OppNet - Basic Behavioral and Social Science Opportunity Network is parent organization of: NIH Blueprint for Neuroscience Research is parent organization of: Kidney Health Initiative is parent organization of: Office of Rare Diseases Research is parent organization of: Center for Cancer Research is parent organization of: NIH Biospecimens Interest Group is parent organization of: NIH Neuroscience Microarray Consortium is parent organization of: Genomic Datasharing is parent organization of: Knockout Mouse Project is parent organization of: NIH Office of Science Education is parent organization of: BARD is parent organization of: StemCellDB is parent organization of: Jobs(at)NIH is parent organization of: Office of Extramural Research NIH is parent organization of: Office of Behavioral and Social Sciences Research is parent organization of: Prize4Life is parent organization of: NIH Pain Consortium is parent organization of: BRAIN Initiative is parent organization of: BTRIS: NIH Biomedical Translational Research Information System is parent organization of: NIH Human Connectome Project is parent organization of: Biowulf at the NIH is parent organization of: National Institutes of Neurological Disorders and Stroke Research Programs is parent organization of: REGARDS - REasons for Geographic and Racial Differences in Stroke is parent organization of: Model Organisms for Biomedical Research is parent organization of: Deltagen and Lexicon Knockout Mice and Phenotypic Data Resource is parent organization of: Brain Computer Interface 2000 Software Package is parent organization of: Cognitive and Emotional Health Project: The Healthy Brain is parent organization of: Cancer Chromosomes is parent organization of: X-linked SCID mutation database is parent organization of: Health Research Funding is parent organization of: Know Stroke Campaign is parent organization of: Comparative Vertebrate Sequencing is parent organization of: Phylogenetic Clusters of Orthologous Groups Ranking is parent organization of: PubMatrix is parent organization of: National Institutes of Health Stem Cell Tables is parent organization of: Allergen Database for Food Safety is parent organization of: Molecular Brain: Transcription Profiles of Mouse and Human Brains is parent organization of: Genetic and Rare Diseases Information Center is parent organization of: Molecular Libraries Program is parent organization of: BMAP - Brain Molecular Anatomy Project is parent organization of: CARDS Database is parent organization of: Office of logistics and acquisition operations is parent organization of: National Centers for Biomedical Computing is parent organization of: Center for Information Technology is parent organization of: Fogarty International Center is parent organization of: Genome association studies is parent organization of: National Cancer Institute is parent organization of: National Center for Complementary and Alternative Medicine is parent organization of: National Center for Research Resources is parent organization of: National Eye Institute (NEI) Commons is parent organization of: National Heart Lung and Blood Institute is parent organization of: National Human Genome Research Institute is parent organization of: National Institute of Biomedical Imaging and Bioengineering is parent organization of: National Institute of Child Health and Human Development is parent organization of: National Institute of Environmental Health Sciences is parent organization of: National Institute of Mental Health is parent organization of: National Institute of Nursing Research is parent organization of: National Institute on Aging is parent organization of: National Institute on Alcohol Abuse and Alcoholism is parent organization of: National Institute on Drug Abuse is parent organization of: National Institute on Minority Health and Health Disparities is parent organization of: National Library of Medicine is parent organization of: NIH Clinical Center is parent organization of: NIH Roadmap is parent organization of: Superfund basic research program is parent organization of: National Institute of Arthritis and Musculoskeletal and Skin Diseases is parent organization of: National Institute of Allergy and Infectious Diseases is parent organization of: NIH Office of the Director is parent organization of: NIH Common Fund is parent organization of: National Center for Advancing Translational Sciences is parent organization of: National Institute on Deafness and Other Communication Disorders is parent organization of: Office of research facilities development and operations is parent organization of: National Institute of General Medical Sciences is parent organization of: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is parent organization of: AIDSinfo Drug Database is parent organization of: Human Microbiome Project is parent organization of: National Institute of Neurological Disorders and Stroke is parent organization of: NIH electronic Research Materials catalogue is parent organization of: Center for Scientific Review is parent organization of: Ontology-based Knowledgebase for Human Cell Adhesion Molecules is parent organization of: Chronic Fatigue Syndrome is parent organization of: National Institute of Health Data Book is parent organization of: NIH-CIDI Lung Segmentation Tool is parent organization of: NIH Pediatric MRI Data Repository is parent organization of: DICOMConvert is parent organization of: Accelerating Medicines Partnership is parent organization of: Biospecimen Research Database |
Available to the research community | nlx_inv_1005116, ISNI: 0000 0001 2297 5165, grid.94365.3d, Wikidata: Q390551, Crossref funder ID: 100000002 | https://ror.org/01cwqze88 | SCR_011417 | National Institutes of Health | 2026-08-01 12:04:24 | 3944 | ||||||
|
SoftCite Resource Report Resource Website |
SoftCite (RRID:SCR_024411) | software resource, project portal, data or information resource, portal, knowledge base | Gold standard dataset of software mentions in research publications. Provides dataset of annotated software mentions from full text academic literature in biomedicine and economics directly converted from published PDFs with reproducible infrastructure. Includes provenance, and is formatted for immediately usefulness in NLP. Useful for supervised learning at scale. | Gold standard dataset, software mentions, research publications, annotated software mentions, full text academic literature, |
lists: ProteinPilot lists: ROCit lists: survivalROC lists: GIFT lists: PyWavelets lists: pRRophetic lists: GOplot lists: Rgdal lists: riskRegression lists: RNAfold lists: RNALocate lists: pyPCcazip lists: ScanProsite lists: RapGreen lists: ABySS lists: AMBER lists: ANNOVAR lists: ASAP lists: ASPicDB lists: AStalavista lists: ATSAS lists: Alien hunter lists: Adobe Photoshop lists: Affymetrix lists: Augustus lists: Argus lists: Adobe Illustrator lists: ART lists: AutoDock Vina lists: AutoDock lists: ANALYZE lists: BLASTClust lists: arrayQualityMetrics lists: BLASTN lists: BLASTX lists: BLASTP lists: Bowtie lists: Autogrid lists: BRB-ArrayTools lists: BEDTools lists: BWA lists: BioEdit lists: BRASS lists: Bioconductor lists: BioExtract lists: BaCelLo lists: BioMoby lists: Brain Extraction Tool lists: Bowtie 2 lists: BoxPlotR lists: biomaRt lists: BioPerl lists: CANGS lists: CFX Manager lists: CEAS lists: BlobFinder lists: CLC Genomics Workbench lists: BREAKDANCER lists: CASAVA lists: CLC Main Workbench lists: ClustalW lists: Clustal W2 lists: ComBat lists: CCP4 lists: Blender lists: Coot lists: CGView lists: COMSOL Multiphysics lists: CTFFIND lists: CalcuSyn lists: ChIPpeakAnno lists: Chimera lists: CVODE lists: DAVID lists: Cufflinks lists: caret lists: ClueGO lists: Cluster lists: Clocklab lists: DIANA-mirPath lists: Cytoscape lists: EMAN lists: E-Prime lists: DESeq2 lists: Definiens Developer XD lists: Eigensoft lists: EMBOSS lists: Ensembl lists: DIALIGN lists: Design-Expert lists: EndNote lists: CMAP lists: EEGLAB lists: CMap lists: Epi Info lists: FASTA lists: Ensembl Genome Browser lists: Epik lists: FACS lists: FCS Express lists: Flowlogic lists: FSL lists: FLASH lists: FATCAT lists: FastQC lists: G*Power lists: GOLD lists: FGENESH lists: FreeSurfer lists: FlowJo lists: GeneTools lists: Galaxy lists: GATK lists: ELDA lists: GraphPad lists: GRADEpro lists: Fiji lists: Gblocks lists: FigTree lists: GENIE lists: GBrowse lists: Gemma lists: GeneChip Operating Software lists: GeneMapper lists: GeneMarker lists: GenABEL lists: GenePattern lists: GraphPad Prism lists: GenePix Pro lists: Google lists: Genesis lists: Hologic lists: GeneSpring GX lists: GeneVenn lists: HaploReg lists: Google Scholar lists: HALO lists: Gwyddion lists: IMAGIC lists: HKL-2000 lists: Glide lists: Glimmer lists: I-TASSER lists: GenomeStudio lists: IMOD lists: Haploview lists: Hmmer lists: Hydra lists: IUPRED lists: HomeCageScan lists: Geneious lists: IGOR Pro lists: IMPUTE lists: Infernal lists: Image-Pro Plus lists: JASP lists: LSM Image Examiner lists: Imaris lists: Image Pro Plus lists: ImageQuant lists: ImageJ lists: Integrative Genomics Viewer lists: jcvi lists: InterProScan lists: KaleidaGraph lists: Ligprep lists: Heidelberg Eye Explorer lists: JMP lists: Ingenuity Pathways Knowledge Base lists: Leica QWin lists: JCB DataViewer lists: Jalview lists: LigandScout lists: Ingenuity Pathway Analysis lists: LabView lists: Kepler lists: MAFFT lists: Jmol lists: ImageScope lists: MACS lists: Maq lists: MUMmer lists: MATLAB lists: Mimics lists: MACH lists: MCODE lists: Mascot lists: Maestro lists: MSQuant lists: MediaWiki lists: MINC lists: MRIcron lists: MOE lists: ModFit LT lists: LIMMA lists: MassLynx lists: mitopred lists: MrBayes lists: MolProbity lists: MUSCLE lists: MutationAssessor lists: MaxQuant lists: Minitab lists: MODELLER lists: MetaboAnalyst lists: MedCalc lists: Origin lists: MPlus lists: MutationTaster lists: MuTect lists: Multi Gauge lists: NIA Array Analysis lists: NIH Image lists: Phenix lists: MycoBank lists: OpenClinica lists: Nexus lists: OMTools lists: NIS-Elements lists: PAST lists: NVivo lists: PRISM (Stanford database) lists: Metscape lists: PROCHECK lists: oligo lists: OpenEpi lists: Pathway Commons lists: Nanoparticle Tracking Analysis lists: Openlab lists: PLINK lists: PAUP lists: NONMEM lists: PREFAB lists: NetworkX lists: PeptideProphet lists: Primer Designer lists: PhyML lists: PASS lists: PyMOL lists: PSIPRED lists: PROFILER lists: PHYLIP lists: Phobius lists: Prime lists: Phyutility lists: Picard lists: ProteinProphet lists: Phaser lists: ProSAS lists: PostgreSQL lists: Primer-BLAST lists: ProteinLynx Global Server lists: QUANTO lists: Primer Express lists: Primer3Plus lists: ProtTest lists: ProbCons lists: Primer3 lists: Poretools lists: Protein preparation Wizard lists: QmRLFS-finder lists: PicTar lists: RevMan lists: Pipeline Pilot lists: QIIME lists: PRISMA lists: REDCap lists: RAxML lists: Proteome Discoverer lists: Research Randomizer lists: SPARTAN lists: SPSS lists: RNAstructure lists: Refmac lists: QuantPrime lists: Prodigal lists: RepeatModeler lists: Ringo lists: SQLite lists: SAGE lists: Rhinoceros lists: SAMTOOLS lists: SPAdes lists: RepeatMasker lists: SEDFIT lists: STATISTICA lists: RNAhybrid lists: SlideBook lists: STRUCTURE lists: SABmark lists: SPM lists: Stata lists: RStudio lists: SciPy lists: Scion Image lists: Simulink lists: TAGGER lists: TopHat lists: SAM lists: ShortRead lists: SIFT lists: SCAN lists: SignalP lists: Scopus lists: Strelka2 lists: Trans-ABySS lists: Statgraphics Centurion lists: T-Coffee lists: Statistical Analysis System lists: TargetScan lists: UCHIME lists: Sequencher lists: SigmaStat lists: UCSC Genome Browser lists: affy lists: Taverna lists: MBF BioScience: Stereo Investigator lists: Trimmomatic lists: Vmatch lists: WFU PickAtlas lists: SigmaPlot lists: X!Tandem lists: STAR lists: TASSEL lists: SyStat lists: WEBLOGO lists: UCSF Chimera lists: TreeView lists: pheatmap lists: WinWCP lists: microRNA.org lists: glmnet lists: Phenix.refine lists: BASE lists: beadarray lists: RMS lists: lumi lists: Web of Science lists: minfi lists: geNORM lists: WU-BLAST lists: WinBUGS lists: SPP lists: tRNAscan-SE lists: WebPlotDigitizer lists: qBasePLUS lists: Matplotlib lists: TreeBASE lists: pClamp lists: TBLASTN lists: igraph lists: V3D lists: survival lists: miRanda lists: piRNABank lists: topGO lists: NGmerge lists: OMNISEC lists: NOTUNG lists: OpenBUGS lists: Optimization Toolbox lists: ProgRes Capture Pro lists: Ocular lists: Umediation lists: Nano Measurer lists: PHYLDOG lists: VSEARCH lists: WinNonlin lists: WHONET lists: ToposPro lists: Treerecs lists: Agilent Seahorse Wave lists: SimPhy lists: TomoStudio lists: Mutation Assessor lists: Stem lists: SRAMP lists: CRISPResso2 lists: geepack lists: Evalue lists: DAGitty lists: FastMulRFS lists: ggridges lists: gamm4 lists: AutoRT lists: CopyKAT lists: Inference of CRISPR Edits lists: classInt lists: ASTRAL-Pro lists: maftools lists: mitml lists: CMplot lists: MetaPSICOV lists: LaCyTools lists: MADOKA lists: Kaplan Meier Plotter lists: IntFOLD lists: ModFOLD lists: lDDT has parent organization: University of Texas at Austin; Texas; USA |
Sloan Foundation | DOI:10.1002/asi.24454 | Free, Available for download, Freely available | https://github.com/softcite/softcite_dataset_v2, https://zenodo.org/record/7995565 | SCR_024411 | Software Citation | 2026-08-02 09:09:14 | 0 | ||||||
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Object-Image Resource Report Resource Website 10+ mentions |
Object-Image (RRID:SCR_015720) | software resource, image analysis software, data processing software, software application | Image analysis software package that allows non-destructive image marking, input for further image processing, and marking the results of automatic measurements. Object-Image integrates measurements, macros, graphical objects and image names in a closed unit called 'object file' so that it reduces file clutter. | image marking, non-destructive, image analysis, text editor, debugging software | is related to: NIH Image | Free, Available for download, Runs on Mac OS | simon.bio.uva.nl/Object-Image/object-image.html | SCR_015720 | 2026-08-02 09:07:13 | 18 | |||||||||
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BrainImage Software Resource Report Resource Website 1+ mentions |
BrainImage Software (RRID:SCR_006139) | BrainImage | image processing software, software resource, data processing software, software application, image analysis software | A multiplatform, highly modular image processing and visualization application which is under development by the Center for Interdisciplinary Brain Sciences Research. The goal of this project is provide a framework application for neuroimaging which facilitates the interchange of software tools developed by researchers. BrainImageJava can: * Delineate ROIs in slices along X, Y, or Z axes, with 3D feedback in the other axes. * Create and display triangular mesh surfaces from MRI volumes. * Draw Surfaces-of-Interest (SOIs) in 3D, and edit them in a planar display. * Set Talairach grid on a volume, export an AC/PC stack, and measure the values within each grid unit. This 3D image processing and analysis program for the Apple Macintosh PowerPC is based on the public domain application, NIH Image. It includes interactive procedures for 3D MRI quantification including semi-automated procedures for removing non-brain tissues from images, fuzzy segmentation of tissue compartments, global or local parcellation (based on the Talairach atlas), region-growing, etc. The last version of the software included multiplatform capability, volume visualization and advanced image analysis tools. | mri, segmentation, visualization, volume, neuroimaging, analyze, anatomic, application, artifact removal, image display, java, labeling, macos, mesh generation, microsoft, modeling, magnetic resonance, quantification, region of interest, rendering, spatial transformation, three dimensional display, volume measurement, volumetric analysis, volumetric analysis, windows, platform |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: NIH Image has parent organization: Stanford University School of Medicine; California; USA |
Human Brain Project | GNU General Public License | nif-0000-00272 | http://spnl.stanford.edu/tools/brainimage.htm | SCR_006139 | Brain Image, BrainImageJ, BrainImageJava | 2026-08-02 09:04:44 | 8 |
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