IMOD
Resource Report
Resource Website
1000+ mentions
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IMOD (RRID:SCR_003297)
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IMOD
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image analysis software, image processing software, data processing software, software application, software resource, source code
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A free, cross-platform set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD 4.1.8 Is Now Available for Linux, Windows, and Mac OS X
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electron microscopy, magnetic resonance, tomographic reconstruction, reconstruction, segmentation, 3d volume
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is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: SoftCite
has parent organization: University of Colorado Boulder; Colorado; USA
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NCRR ;
NIGMS ;
NIBIB |
PMID:27444392 |
Free, Available for download, Freely available |
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nif-0000-31686 |
http://www.nitrc.org/projects/imod |
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SCR_003297 |
IMOD - 3D Reconstruction and Analysis |
2026-08-15 11:22:28 |
1685 |
NeuroImaging Tools and Resources Collaboratory (NITRC)
Resource Report
Resource Website
100+ mentions
|
NeuroImaging Tools and Resources Collaboratory (NITRC) (RRID:SCR_003430)
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NITRC
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data repository, storage service resource, software repository, portal, data or information resource, software resource, community building portal, service resource
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Software repository for comparing structural (MRI) and functional neuroimaging (fMRI, PET, EEG, MEG) software tools and resources. NITRC collects and points to standardized information about structural or functional neuroimaging tool or resource.
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collaboration, information, resource, structural, functional, neuroimaging, MRI, fMRI, EEG, MEG, PET
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is used by: NIF Data Federation
is used by: Consortium for Reliability and Reproducibility
is used by: DataLad
is recommended by: National Library of Medicine
lists: Dipy
lists: 3DMeshMetric
lists: MPScope
lists: VectorValuedHistogramNormalizer
lists: Faceted Search Based Ontology Visualizer
lists: Morphometry BIRN
lists: Colin 3T/7T High-resolution Atlas
lists: CMFreg
lists: BrainFX
lists: dinifti
lists: Center for Computational Biology at UCLA
lists: Convert MNI coordinates to or from XYZ
lists: Licensing issues in software and data
lists: Local Binary Pattern Analysis Tools for MR Brain Images
lists: MIView
lists: uManager
lists: Penn Hippocampus Atlas
lists: RapidArt
lists: Scribe
lists: ShapeWorks
lists: Vervet Probabilistic Atlas
lists: Talairach Daemon
lists: ADHD-200 Preprocessed Data
lists: LORIS - Longitudinal Online Research and Imaging System
lists: NVM
lists: Maps4Mipav (Exploratory JIST)
lists: Autism Tissue Program
lists: MEG Tools
lists: PyNIfTI
lists: LONI Visualization Tool
lists: Mind Research Network - COINS
lists: OpenElectrophy
lists: CIFTI Connectivity File Format
lists: 3DSlicerLupusLesionModule
lists: BrainNetworkConstructionAnalysisPlatform
lists: COMPARE
lists: Data Format Tools
lists: GesTr
lists: I/OWA
lists: MINC Example files
lists: cbiNifti: Matlab/Octave Nifti library
lists: BRAINSCut
lists: C-PAC
lists: Connectir
lists: DicomBrowser
lists: Hitachi Optical Topography System
lists: Net Station API
lists: imcalc: SPM batch image calculator
lists: BRAINSCortex
lists: Insight Segmentation and Registration Toolkit
lists: LONI Debabeler
lists: LONI Pipeline Processing Environment
lists: NiLearn
lists: MRI Studio
lists: BraVa
lists: Brede Wiki
lists: Center for Functional Neuroimaging Technologies
lists: Philips Users Community
lists: medInria
lists: Beijing: Eyes Open Eyes Closed Study
lists: vIST/e
lists: Camino
lists: Diffusion Tensor Imaging ToolKit
lists: TORTOISE
lists: NIDAG: Neuroimaging Data Access Group
lists: MRI CVPR
lists: vuTools
lists: Medical Image Processing and Visualization in Virtual Environments
lists: Brainstorm
lists: Atlas3D
lists: FMRISTAT - A general statistical analysis for fMRI data
lists: FreeSurfer
lists: Rosetta Bit
lists: Laboratory of Neuro Imaging
lists: Group ICA of fMRI Toolbox
lists: Hierarchical Attribute Matching Mechanism for Elastic Registration
lists: Internet Brain Segmentation Repository
lists: Neural ElectroMagnetic Ontologies (NEMO) Project
lists: Wavelet-based Image Fusion
lists: ITK-SNAP
lists: Internet Brain Volume Database
lists: Statistical non-Parametric Mapping
lists: VoxBo
lists: NITRC Computational Environment
lists: Spatially Constrained Parcellation
lists: Cluster reporter
lists: Cluster Extent Correction
lists: 4D Atlases Construction
lists: CIGAL
lists: CleanLine
lists: Computational Morphometry Toolkit
lists: Cognitive Paradigm Ontology
lists: aBEAT
lists: MR Connectome Automated Pipeline
lists: International Neuroinformatics Coordinating Facility
lists: Functional Regression Analysis of DTI Tract Statistics
lists: MCIC
lists: MGDM: Multi Geometric Deformable Model
lists: MIAS Registration Toolkit
lists: Medical Image Visualization and Analysis
lists: Microstructural correlation toolbox
lists: MisterI
lists: MriWatcher
lists: Multiple Correlation Function Tool
lists: NITRC Community Conferences Workshops and Meetings
lists: BRAINSFit
lists: INCF Software Center
lists: BrainVision Analyzer
lists: COGNISION
lists: DPARSF
lists: GLIRT
lists: MINC
lists: Group Level Imputation of Statistic Maps
lists: MRIcron
lists: Inter-Group Registration Toolbox
lists: MCML and CONV
lists: MEGSIM
lists: MIRIAD
lists: MRI Defacer
lists: MS lesion segmentation challenge 2008
lists: Measure Projection Toolbox
lists: Mindboggle
lists: Mindboggle-101 atlases
lists: ModelGUI
lists: Multi-Modal MRI Reproducibility Resource
lists: MultiTracer
lists: Multicomponent T2 estimation with stimulated echo correction
lists: NCANDA: Data Integration Component
lists: NFT
lists: Net Station EEG Software
lists: Network Based Statistic Toolbox
lists: NeuroScope
lists: Numerical Fibre Generator
lists: PSTNet: MRI Simulator
lists: cortex
lists: iBEAT
lists: M3
lists: Group ICA Of EEG Toolbox
lists: 4D-PARSeR Pathological Anatomy Regression via Segmentation and Registration
lists: Automatic Segmentation Tool Adapter
lists: DTI-TEMPLATE-RHESUS-MACAQUES
lists: LONI Provenance Editor
lists: MNI N3
lists: MRI Digital Projection System
lists: NIDB - Neuroinformatics Database
lists: NIPY
lists: NIRAL Utilities
lists: NIRx NIRS Neuroimaging
lists: NIRx2nirs: A NIRx to .nirs data converter
lists: NITRC Enhanced Services
lists: NITRC GForge Extensions
lists: NPTK
lists: NeuroImaging Analysis Kit (NIAK)
lists: NiBabel
lists: NiftyRec
lists: Nipype
lists: Nirfast
lists: Nitime
lists: Non-Rigid Image Registration Evaluation Project
lists: Normative Independent Component Analysis
lists: OEI: fMRI compatible olfactometer
lists: ORS Visual SI
lists: OpenMEEG
lists: PANDA
lists: PESTICA fMRI Physio Detection/Correction
lists: PHYCAA+: adaptive physiological noise correction for BOLD fMRI
lists: ParaView
lists: Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR)
lists: Presentation
lists: PySurfer
lists: Pythagorean Displacement and Motion Regressors
lists: Quantitative Diffusion Tools
lists: R-package for adaptive DWI analysis
lists: R-package for adaptive fMRI analysis
lists: REX
lists: RFT FDR
lists: ROBEX
lists: RT Image
lists: Resource Ontology Discussion Group
lists: Rodent Brain Extraction Tool
lists: Rodent Cortical Thickness Analysis
lists: S-rep Fitting Statistics and Segmentation
lists: SCIRun
lists: SCRalyze
lists: SOCK
lists: SPHARM-MAT
lists: SPHARM-PDM Toolbox
lists: SRI24 Atlas: Normal Adult Brain Anatomy
lists: Seg3D
lists: ShapeComplexAtlas
lists: Signed Differential Mapping
lists: Sleuth
lists: Slice:Drop
lists: Slicer3 Example Modules
lists: Source Information Flow Toolbox
lists: Spanish Resting State Network
lists: Spatial Analysis 3D
lists: Stereoscopic Atlas of Intrinsic Brain Networks
lists: UNC Infant 0-1-2 Atlases
lists: UNC Primate Brain Atlas
lists: XCEDE Schema
lists: peak nii
lists: pydicom
lists: pyxnat
lists: scikit-learn
lists: shapeAnalysisMANCOVA - SPHARM tools
lists: VMTK in 3D Slicer
lists: 3D Interactive Chemical Shift Imaging
lists: BRAINSSurfaceStats
lists: Brain lesion segmentation tool using SVM
lists: Diffusion Tractography with Kalman Filter
lists: Fast Nonlocal Means for MRI denoising
lists: Monte Carlo Simulation Software: tMCimg
lists: Web Interfaces for Multiscale Images
lists: STAPLE
lists: Segmentation Validation Engine
lists: Spatial Statistical Parametric Mapping
lists: SpineSegmentation module for 3DSlicer
lists: Stochastic Tractography System
lists: Subject Library
lists: TAPIR
lists: TARQUIN
lists: Template Image Processing Library
lists: TetraMetrix
lists: TractoR: Tractography with R
lists: Triangle BioSystems
lists: TumorSim
lists: TurtleSeg
lists: UNC Human Brain Atlas
lists: VR Worlds 2
lists: Vaa3D
lists: ValMap: simple statistical mapping tool
lists: WFU Biological Parametric Mapping Toolbox
lists: WFU Pipeline
lists: Working Memory Trainer
lists: vis: SPM Visualized Statistics toolbox
lists: Synchronized Histological Image Viewing Architecture
lists: LONI ShapeViewer
lists: LONI ShapeTools
lists: FFT Library
lists: Automated recognition of brain region mentions in neuroscience literature.
lists: NUTMEG
lists: Cognitive Atlas
lists: Mouse BIRN Atlasing Toolkit
lists: Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat
lists: FSL
lists: LEAD-DBS
lists: Brainscape
lists: EONS
lists: BioImage Suite
lists: ADNI - Alzheimer's Disease Neuroimaging Initiative
lists: MindSeer
lists: XNAT - The Extensible Neuroimaging Archive Toolkit
lists: brainmap.org
lists: ImageJ
lists: Neuroimaging Informatics Technology Initiative
lists: IMOD
lists: Statistics Online Computational Resource
lists: signalml.org
lists: Mouse Biomedical Informatics Research Network
lists: NIH MRI Study of Normal Brain Development
lists: MGH-USC Human Connectome Project
lists: Fusion ICA Toolbox
lists: Corpus Callosum Thickness Profile Analysis Pipeline
lists: ABIDE
lists: Mouse Connectome Project
lists: NITRC-IR
lists: Open Connectome Project
lists: neurodebian
lists: NIMH Data Archive
lists: ANTS - Advanced Normalization ToolS
lists: XNAT Extras
lists: TrackVis
lists: Brain Connectivity Toolbox
lists: FieldTrip
lists: LONI Inspector
lists: BrainLiner
lists: OpenNeuro
lists: Biomedical Informatics Research Network
lists: McConnell Brain Imaging Center MNI Macaque Atlas
lists: SINOMO
lists: DONE: Detection of Outlier NEurons
lists: Neuro Bureau
lists: ADHD-200 Sample
lists: 1000 Functional Connectomes Project
lists: PubBrain
lists: CBRAIN
lists: ENIGMA: Enhancing Neuro Imaging Genetics Through Meta-Analysis
lists: Bisque
lists: 3D Slicer
lists: Internet Analysis Tools Registry
lists: Neuromorphometrics
lists: Analysis of Functional NeuroImages
lists: Automated Image Registration
lists: BASH4RfMRI
lists: MNE software
lists: Object-Oriented Development Interface for NMR
lists: NYU CSC TestRetest
lists: Optseq - fMRI Event Scheduler
lists: TOADS-CRUISE Brain Segmentation Tools
lists: MouseTracker
lists: Hammer And WML Modules for 3D Slicer
lists: ABC (Atlas Based Classification)
lists: Allen Brain Atlas API
lists: Viking Viewer for Connectomics
lists: ARCTIC
lists: ArtRepair for robust fMRI
lists: Automatic Registration Toolbox
lists: Artifact Detection Tools
lists: Segmentation of Hippocampus Subfields
lists: ASL data processing tool box
lists: Bioelectromagnetism Matlab Toolbox
lists: PyMVPA
lists: Human Imaging Database
lists: BrainImage Software
lists: Brede Toolbox
lists: Computerized Anatomical Reconstruction and Editing Toolkit
lists: BrainColor: Collaborative Open Labeling Online Resource
lists: Registry Builder Data Harmonization and Aggregation Tool
lists: PsychoPy
lists: NiftySim
lists: NiftyReg
lists: Neurobiological Image Management System
lists: BRAINSTools
lists: MeshValmet: Validation Metric for Meshes
lists: BrainSuite
lists: DW-MRI Random Walk Simulator
lists: Web Game for Collaborative Labeling
lists: BrainVoyager Brain Tutor
lists: POLGUI - Matlab Polhemus Interface
lists: BrainVoyager Brain Viewer
lists: NeuroPub Visualizer
lists: NODDI Matlab Toolbox
lists: MITK Diffusion
lists: Federal Interagency Traumatic Brain Injury Research Informatics System
lists: BrainMaps.org
lists: PRoNTo
lists: Scalable Brain Atlas
lists: NIH Human Connectome Project
lists: Mesh-based Monte Carlo (MMC)
lists: Matlab Neuroshare Library
lists: MRtrix
lists: MABMIS: Multi-Atlas Based Multi-Image Segmentation
lists: Monte Carlo eXtreme
lists: Whole Brain Catalog
lists: BCILAB
lists: ABSORB: Atlas Building by Self-Organized Registration and Bundling
lists: VAMCA
lists: SPM
lists: Low Resolution Electromagnetic Tomography
lists: SurfStat
lists: Cambridge Brain Activation
lists: CLEAVE
lists: CoCoMac
lists: fMRI Data Center
lists: Function BIRN
lists: EEGLAB
lists: BrainVISA / Anatomist
lists: MIPAV: Medical Image Processing and Visualization
lists: NeuroLens
lists: WFU PickAtlas
lists: Open Access Series of Imaging Studies
lists: BioSig: An Imaging Bioinformatics System for Phenotypic Analysis
lists: xjView: A Viewing Program For SPM
lists: Human Connectome Coordination Facility
lists: ASL spm8
lists: Integrated Manually Extracted Annotation
lists: JIST: Java Image Science Toolkit
lists: Functional Analysis of Diffusion Tensor
lists: AHEAD
lists: ANTsR
lists: 3DBar
lists: Cancer Imaging Archive (TCIA)
lists: Pediatric Imaging Neurocognition and Genetics
lists: Atlasing of the basal ganglia
lists: cmrep
lists: 3D DTI Atlas of the Rat Brain In Postnatal Day 5 14 and Adulthood
lists: AutoSeg
lists: BXH/XCEDE Tools
lists: Baby Brain Toolkit
lists: Best Practices for Software Development
lists: Brain Catalogue
lists: Draw3D and Meshinator
lists: Brain Segmentation Testing Protocol
lists: BrainNet Viewer
lists: BrainSolution
lists: Brainvox
lists: C8: Corpus Callosum Computations
lists: CAMINO-TRACKVIS
lists: CANDI Share: Schizophrenia Bulletin 2008
lists: CBS High-Res Brain Processing Tools
lists: CCSeg - Corpus Callosum Segmentation
lists: Cerebral Blood Flow Database and Analysis Pipeline
lists: Create DWI Atlas
lists: DFBIdb
lists: DIAMOND
lists: DICOM UploadGUI
lists: DOTS WM tract segmentation
lists: DTI Fiber Tract Statistics
lists: DW-MRI registration in FSL
lists: DbGaP Cleaner
lists: DentalTools
lists: Diffusion MRI - In-vivo and Phantom Data
lists: Diffusion MRI at DKFZ Heidelberg
lists: Diffusion Warp
lists: Disease State Prediction
lists: EEG human categorization data
lists: Epsilon Radial Networks
lists: FBIRN Image Processing Scripts
lists: FSL extensions
lists: False Discovery Rate Weighted
lists: Fiber Tracking Tool
lists: Fiber-tracking based on Finsler distance
lists: FiberViewerLight
lists: Finsler tractography module for Slicer
lists: Fluid Registration and Atlas Toolkit
lists: Framework for Open Programmatic Access
lists: Functional Connectivity Community
lists: Functional ROI Atlas
lists: Functional and Structural Neuroimaging Journals Listing
lists: GAMBIT
lists: GAMMA
lists: BRAINSMush
lists: GPU based affine registration
lists: GRETNA
lists: Generalized Covariance Analysis
lists: Generalized PPI Toolbox
lists: Group Information Guided ICA
lists: Groupwise Image Registration Toolbox
lists: HD Neuro-Informatics
lists: Hitachi2nirs
lists: IDeA Lab brain image processing suite
lists: INCF Neuroimaging Data Sharing
lists: INIA19 Primate Brain Atlas
lists: JHU Proj. in Applied Medical Imaging
lists: JIST Resources for Algorithm Development
lists: BRAINSROIAuto
lists: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI
lists: Landman NeuroImaging Tools
lists: Local Label Learning Segmentation
lists: MASI Label Fusion
lists: MASIMatlab
lists: MATLAB Tutorial on Diffusion Tensor MRI
lists: Multi-Echo Independent Component Regression Group-Level Connectivity Dataset
lists: Multi-fiber Reconstruction from DW-MRI
lists: NITRC Books
lists: Network Modification Tool Lite
lists: Non-rigid groupwise registration method
lists: Rockland Download Link Script
lists: Subject Order-Independent Group ICA
lists: Task Independent Fluctuations Discussion
lists: UNC Human DTI Brain Atlas
lists: BRAINSTestData
lists: cPPI Toolbox for fMRI
lists: fMRI Classification in R
lists: fMRI-CPCA
lists: fNIRS Data Analysis Environment
lists: factory t1 dti
lists: BRAINSDemonWarp
lists: AMILab
lists: ADJUST
lists: ALVIN
lists: Age Related Atrophy Dataset
lists: B0 and eddy current correction for DTI
lists: BESA
lists: BSMac
lists: BVQXtools
lists: BioMesh3D
lists: BrainBrowser
lists: BrainGraph Editor
lists: BrainMagix SPM Viewer
lists: BrainMask Volume Processing Tool
lists: Brainsight
lists: Brainwaver
lists: CANDI Neuroimaging Access Point
lists: CBFBIRN
lists: CDF-HC PointSetReg
lists: GIMIAS
lists: CURRY
lists: CalaTK
lists: CoCoMac-Paxinos3D viewer
lists: INVIZIAN
lists: CONN
lists: Connectome File Format
lists: Connectome Viewer
lists: Cytoseg
lists: DICCCOL predictor
lists: DRAMMS
lists: DSI Studio
lists: Level-set Segmentation for Slicer3
lists: DTI BrainImageScope
lists: DTI-Reg
lists: DTIProcess ToolKit
lists: DWI/DTI Quality Control Tool: DTIPrep
lists: Diffusional Kurtosis Estimator
lists: Distributome
lists: ImageVis3D
lists: E-Prime
lists: E-Prime Extensions for fMRI
lists: EEGVIS
lists: EEProbe
lists: EMSE Suite
lists: LONI Brain Parser
lists: EPILAB
lists: ERPLAB
lists: FIV
lists: FMRIpower
lists: Fiber Optic Button Response System
lists: Free-D
lists: GIFTI
lists: GMAC: A Matlab toolbox for spectral Granger causality analysis of fMRI data
lists: HAMMER Suite
lists: HERMES
lists: HI-SPEED Software Packets
lists: Homer2
lists: IIT Human Brain Atlas
lists: JIP Analysis Toolkit
lists: Jim
lists: LDDMM
lists: LIBEEP
lists: LIMO EEG
lists: LONI De-identification Debablet
lists: Waxholm Space
lists: Lipsia
lists: Lumina LP- 400 Response System
lists: MRI Dataset for Hippocampus Segmentation
lists: MaCH-Admix
lists: Mach2dat
lists: Mag Design and Engineering
lists: MagVenture: MagPro Magnetic Stimulator
lists: SR Research EyeLink Eye Trackers
lists: Mango
lists: Manually Labeled MRI Brain Scan Database
lists: MarsBaR region of interest toolbox for SPM
lists: MazeSuite
lists: MoTrak Head Motion Tracking System
lists: NCIGT Fast Imaging Library
lists: NeuroWeb - NeuroImaging Database
lists: Neuroimaging Made Easy Blog
lists: Neurophysiological Biomarker Toolbox
lists: SVV
lists: Slicer3 Module Rician noise filter
lists: UNC/Utah NAMIC DTI Fiber Analysis Framework
lists: caGWAS
lists: eConnectome
lists: elastix
lists: fMRI Artefact rejection and Sleep Scoring Toolbox
lists: MACH
lists: fMRI Grocer
lists: fNIR Devices
lists: fanDTasia Java Applet: DT-MRI Processing
lists: g.BSanalyze
lists: iTools
lists: iView X MRI-LR - Eye Tracking for fMRI
lists: map3d
lists: NICE-SIGN
lists: NIRS-SPM
lists: NITRC Community
lists: NordicNeuroLab
lists: PICSL Multi-Atlas Segmentation Tool
lists: Paradigm
lists: Pipeline Neuroimaging VirtualEnvironment
lists: Pipeline System for Octave and Matlab
lists: ProbabilisticBiasCorrection
lists: Program for optimal design of blocked fMRI experiments
lists: QCQP
lists: REST: a toolkit for resting-state fMRI
lists: Robust Biological Parametric Mapping
lists: SPM SS - fMRI functional localizers
lists: Solar Eclipse Imaging Genetics tools
lists: VPixx: VIEWPixx /3D
lists: resting-state pediatric imaging template
lists: DATAPixx
lists: GTRACT
lists: Wisconsin White Matter Hyperintensities Segmentation Toolbox
lists: COBRE
lists: AngioCalc Cerebral Aneurysm Calculator
lists: USC Multimodal Connectivity Database
lists: BRAINSConstellationDetector
lists: ASA - Advanced Source Analysis
lists: BRAINSTracer
lists: EYE-EEG (combined eye-tracking & EEG)
lists: BrainVoyager
lists: Mean Machine
lists: ERP PCA Toolkit
lists: LiverSegm
lists: GSA-SNP
lists: FastICA
lists: DTI Atlas Builder
lists: Neuroimaging in Python
lists: Brain Decoder Toolbox
lists: iso2mesh
lists: CUDA-SPHERE-FWD-MEEG
lists: BrainCSI
lists: BrainVisa Morphology extensions
lists: VPixx: VIEWPixx
lists: VPixx: PROPixx
lists: GenGen
lists: MACH 1.0
lists: PennCNV
lists: SumsDB
lists: Integrated Software
lists: NeuroLex
lists: Parkinson's Progression Markers Initiative
lists: NeuroSynth
lists: Textpresso
lists: ANNOVAR
lists: Graphtools
lists: Grantees Meeting for NITRC
lists: FP-CIT SPECT brain template in MNI space
lists: Brain Computer Interface 2000 Software Package
lists: BEAST
lists: Brian Simulator
lists: Connectome Workbench
lists: ConnectomeDB
lists: DIAN - Dominantly Inherited Alzheimer Network
lists: NKI-RS Enhanced Sample
lists: EPILEPSIE database
lists: GEneral NEural SImulation System: The Neurospaces Project
lists: Hippocampome.org
lists: Kitware
lists: Kymata Atlas
lists: L-Measure
lists: MDR
lists: neuroConstruct
lists: Neurolucida
lists: NeuroMorpho.Org
lists: NEURON
lists: NeuronJ: An ImageJ Plugin for Neurite Tracing and Quantification
lists: NeuroVault
lists: National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS)
lists: NINDS Repository
lists: NKI/Rockland Sample
lists: ODIN
lists: OBART
lists: Open Science Framework
lists: PLINK
lists: MBF BioScience: Stereo Investigator
lists: studyforrest.org
lists: Virtual brain
lists: TREES toolbox
lists: APERTURE
lists: 3dsvm
lists: 7T Structural MRI scans ATAG
lists: Atlases of amygdala and hippocampus for pediatric populations
lists: BetA-Series COrrelation
lists: bic-mni-models
lists: BiofilmQuant
lists: Biomag Discussion Group on Yahoo
lists: Brain Entropy in space and time (BEst)
lists: Brainnetome Atlas Viewer
lists: Brainnetome fMRI toolkit
lists: BROCCOLI
lists: C-MIND Database
lists: CARLsim: a GPU-accelerated SNN Simulator
lists: Clinical Toolbox for SPM
lists: CMIND PY
lists: COST
lists: dcm2nii
lists: DICOMConvert
lists: Displacement Field Viewer
lists: DTI denoising
lists: Efficient Longitudinal Upload of Depression in the Elderly (ELUDE)
lists: Efficient Permutation Testing
lists: DTI-TK
lists: ERPwavelab
lists: ExPosition Packages
lists: Fast T2 relaxation data analysis with stimulated echo correction and non-local spatial regularisation
lists: Forward: Accurate finite element electromagnetic head models
lists: freesurfR
lists: Functional Connectivity Analysis Tool for near-infrared spectroscopy data
lists: GazeReader
lists: gCCA
lists: Generation R Pediatric MRI Resources
lists: GIMME
lists: GLMdenoise: a fast, automated technique for denoising task-based fMRI data
lists: GraphVar: A toolbox for comprehensive graph analyses of functional brain connectivity
lists: HAMMER: Deformable Registration
lists: HBM Hackathon
lists: HDBIG
lists: High-quality diffusion-weighted imaging of Parkinsons disease
lists: MGA - Multimodal Glioma Analysis
lists: Image Synthesis Tools
lists: Imeka Tractography Service
lists: International Imaging Genetics Conference
lists: Intrinsic Unscented Kalman Filter (IUKF) Tractography Software v1.0
lists: Iterative dual-regression with sparse prior
lists: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI
lists: KWScene: MRML-based Atlas and Scene Builder/Reader/Writer
lists: L-Neuron
lists: Laplace Beltrami Filter on QuadEdge Meshes
lists: libSBML
lists: Lightweight Data Pipeline
lists: Longitudinal MS Lesion Imaging Archive
lists: MARS (Multi-Atlas Robust Segmentation)
lists: minc-toolkit
lists: minc-toolkit-testsuite
lists: MISST - Microstructure Imaging Sequence Simulation ToolBox
lists: MRI Neuroanatomy Labeling Services
lists: MRIcroS
lists: Multivariate General Linear Models (MGLM) on Riemannian Manifolds
lists: Neoseg
lists: NeoSegPipeline
lists: NeuriteTracer
lists: NeuroElf
lists: Neuron-C
lists: NIH Pediatric MRI Data Repository
lists: NIH-CIDI Lung Segmentation Tool
lists: NiiStat
lists: Northwestern University Schizophrenia Data and Software Tool (NUSDAST)
lists: Notion ResearchPACS
lists: NTU-DSI-122: a DSI template in ICBM-152 space
lists: OpenViBE
lists: OpenWalnut
lists: Orientation Distribution Function in Constant Solid Angle (CSA-ODF)
lists: Parkinsons Disease Discovery Database
lists: Prediction and Diagnosis for Depression and Schizophrenia
lists: Preprocessed Connectomes Project
lists: Principal Components Analysis of Scalar, Vector, and Mesh Vertex Data
lists: Ruby NIfTI
lists: SCORE
lists: SFMProject
lists: ShapePopulationViewer
lists: Simulated DW-MRI Brain Data Sets for Quantitative Evaluation of Estimated Fiber Orientations
lists: SPIKECOR: fMRI tool for automated correction of head motion spikes
lists: Spinal Cord Toolbox
lists: Stark Cross-Sectional Aging
lists: Brain Coactivation Map
lists: Multiscale Object Orientation Simulation Environment
lists: Striatal Subregional VOImap
lists: Topographica
lists: Turbo-BrainVoyager
lists: CRL Unbiased and Deformable Spatiotemporal Atlas of the Fetal Brain
lists: UNC-Wisconsin Neurodevelopment Rhesus MRI Database
lists: Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX)
lists: VMTK in 3D Slicer
lists: Wisconsin Cortical Thickness Analysis (CTA) Toolbox
lists: XFSL: An FSL toolbox
lists: XNBC
lists: YMDTI: Diffusion Tensor Images of Healthy Young Males
lists: BraTumIA (Brain Tumor Image Analysis)
lists: CAWorks
lists: Functional Real-time Interactive Endogenous Neuromodulation and Decoding (FRIEND)
lists: Graph Theory GLM (GTG) MATLAB Toolbox
lists: Functional Mixed Processes Models
lists: Papaya
lists: Parallel Stochastic Ion Channel Simulator
lists: Advanced Connectivity Analysis (ACA)
lists: International Imaging Genetics Conference
lists: Analyze Software System
lists: Optseq
lists: ENIGMA-DTI Pipeline
lists: Umea Brain Arteries
lists: MetaSearch
lists: BrainBox
lists: BluePyOpt
lists: MultiXplore
lists: Automatic Tractography-based Parcellation Pipeline
lists: Epilepsy T1 and Hippocampal Segmentation Datasets
lists: Mixed Effect Model of Genetic-Set and Environment Interaction
lists: masked ICA (mICA) Toolbox
lists: Altered States Database
lists: User Friendly Functional Connectivity - UF²C
lists: Intra- and inter-scanner reliability of RS-fMRI BOLD and ASL with eyes closed vs. eyes open
lists: Region to Region
lists: Waxholm Space Atlas of the Sprague Dawley Rat Brain
lists: Nutil - Neuroimaging utilities
lists: MeshView
lists: vini: A viewer for fMRI data
lists: brainGraph
lists: Diffusion Toolkit
lists: Neurodocker
lists: HeuDiConv: a heuristic-centric DICOM converter
lists: Knowing what you know (kwyk) - Bayesian Brain Parcellation
lists: Rhesus Macaque Brain Atlases
lists: MIITRA atlas
lists: MonkeyCBP
lists: ReproNim/containers
lists: ReproMan
lists: ABCD-ReproNim Course
lists: Ventricular Morphometry Analysis System
lists: ONPRC18 Multimodal MRI Atlas
lists: volBrain
lists: Waxholm Space
is affiliated with: Manual Align RTS2000
is related to: University of California; San Diego;National Center for Microscopy and Imaging Research - NCMIR
has parent organization: Harvard University; Cambridge; United States
has parent organization: NIH Blueprint for Neuroscience Research
is parent organization of: Licensing issues in software and data
is parent organization of: NITRC Enhanced Services
is parent organization of: Resource Ontology Discussion Group
is parent organization of: NITRC-IR
is parent organization of: 1000 Functional Connectomes Project
is parent organization of: NYU CSC TestRetest
is parent organization of: NITRC Books
is parent organization of: NITRC Community
is parent organization of: ABIDE
is parent organization of: COBRE
is parent organization of: Group Sparse Canonical Correlation Analysis
is parent organization of: Challenge Competitions Collection
is parent organization of: 1000 Functional Connectomes Project
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NIH Blueprint for Neuroscience Research ;
NIMH ;
NIDA ;
NIBIB U24 EB023398;
NINDS R44 NS074540 |
PMID:26044860
PMID:18999128 |
Free, Freely available |
|
nif-0000-00202, r3d100010784, r3d100011515 |
https://doi.org/10.17616/R3W32N |
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SCR_003430 |
Neuroimaging Informatics Tools and Resources Clearinghouse, , NeuroImaging Tools and Resources Collaboratory, Neuroimaging Informatics Tools Resources Clearinghouse, NITRC - Neuroimaging Informatics Tools and Resources Clearinghouse, NITRC - Neuroimaging Informatics Tools Resources Clearinghouse |
2026-08-15 11:22:30 |
374 |
University of Colorado Boulder; Colorado; USA
Resource Report
Resource Website
1+ mentions
|
University of Colorado Boulder; Colorado; USA (RRID:SCR_003114)
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university
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Public university that offers degrees in the sciences, humanities, and social sciences.
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university, research university, public university, colorado, degree
|
is related to: Beta Cell Biology Consortium
is related to: ELOKA
has parent organization: University of Colorado; Colorado; USA
is parent organization of: University of Colorado at Boulder Labs and Facilities
is parent organization of: Community Surface Dynamics Modeling System
is parent organization of: National Snow and Ice Data Center
is parent organization of: IMOD
is parent organization of: University of Colorado at Boulder, Department of Neuroscience
is parent organization of: NeuraLinksPlus
is parent organization of: Emergent
is parent organization of: Standalone hamming
is parent organization of: CU Boulder Electron Microprobe Laboratory
is parent organization of: CU Boulder Institute for Behavioral Genetics
is parent organization of: SeqTrace
is parent organization of: QIIME
is parent organization of: Colorado University at Boulder Shared Instrumentation in Nanofabrication and Characterization Core Facility
is parent organization of: Colorado University at Boulder JILA Keck Lab and Fabrication Core Facility
is parent organization of: Colorado University at Boulder Biochemistry Shared Instruments Pool Core Facility
is parent organization of: Colorado University at Boulder Center for Infrastructure, Energy, and Space Testing Core Facility
is parent organization of: Colorado University at Boulder Light Microscopy Core Facility
is parent organization of: Colorado University at Boulder EM Services Core Facility
is parent organization of: Colorado University at Boulder Green Labs Core Facility
is parent organization of: Colorado University at Boulder Central Analytical Mass Spectrometry Core Facility
is parent organization of: Colorado University at Boulder Intermountain Neuroimaging Consortium Core Facility
is parent organization of: Colorado University at Boulder Green Labs Core Facility
is parent organization of: Colorado University at Boulder BioChemistry Krios Electron Microscopy Core Facility
is parent organization of: University of Colorado Boulder Chemical and Bio. Engineering instrument and electronics Core Facility
is parent organization of: University of Colorado Boulder High Performance Computing PetaLibrary Core Facility
is parent organization of: University of Colorado Boulder Earth Systems Stable Isotope Lab Core Facility
is parent organization of: University of Colorado Boulder Organic Geochemistry Laboratory Core Facility
is parent organization of: University of Colorado Boulder BioCore Core Facility
is parent organization of: University of Colorado Boulder CU Thermochronology Research and Instrumentation Lab Core Facility
is parent organization of: Colorado University at Boulder Soft Materials Research Center X-Ray Diffraction Facility Core Facility
is parent organization of: University of Colorado Boulder Raman Microspectroscopy Lab Core Facility
is parent organization of: Colorado University at Boulder Facility for Electron Microscopy of Materials Core Facility
is parent organization of: Colorado University at Boulder Materials Instrumentation and Multimodal Imaging Core Facility
is parent organization of: Colorado University at Boulder BioFrontiers Next-Gen Sequencing Facility Core Facility
is parent organization of: Colorado University at Boulder Flow Cytometry Shared Core Facility
is parent organization of: Colorado University at Boulder Macromolecular X-ray Crystallography Core Facility
is parent organization of: University of Colorado Anschutz Medical Campus ImmunoMicro Flow Cytometry Core Facility
is parent organization of: Colorado University at Boulder High Throughput Screening Core Facility
is parent organization of: University of Colorado Boulder Polymeric and Optical Materials Characterization Shared Core Facility
is parent organization of: SHARCQ
is parent organization of: University of Colorado Boulder Geomicrobiology Lab Core Facility
is parent organization of: University of Colorado Boulder Intermountain Neuroimaging Consortium Core Facility
is parent organization of: University of Colorado Boulder Biochemistry Nuclear Magnetic Resonance Core Facility
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Free, Freely available |
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nlx_10266 |
https://ror.org/02ttsq026 |
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SCR_003114 |
CU Boulder, UC Boulder, University of Colorado Boulder, CU-Boulder |
2026-08-15 11:22:24 |
3 |
SoftCite
Resource Report
Resource Website
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SoftCite (RRID:SCR_024411)
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project portal, portal, data or information resource, software resource, knowledge base
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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.
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Gold standard dataset, software mentions, research publications, annotated software mentions, full text academic literature,
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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 |
2026-08-15 11:27:55 |
0 |
