2022
DuDoUFNet: Dual-Domain Under-to-Fully-Complete Progressive Restoration Network for Simultaneous Metal Artifact Reduction and Low-Dose CT Reconstruction
Zhou B, Chen X, Xie H, Zhou S, Duncan JS, Liu C. DuDoUFNet: Dual-Domain Under-to-Fully-Complete Progressive Restoration Network for Simultaneous Metal Artifact Reduction and Low-Dose CT Reconstruction. IEEE Transactions On Medical Imaging 2022, 41: 3587-3599. PMID: 35816532, PMCID: PMC9812027, DOI: 10.1109/tmi.2022.3189759.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsArtifactsHumansImage Processing, Computer-AssistedMetalsProstheses and ImplantsTomography, X-Ray ComputedSimCVD: Simple Contrastive Voxel-Wise Representation Distillation for Semi-Supervised Medical Image Segmentation
You C, Zhou Y, Zhao R, Staib L, Duncan JS. SimCVD: Simple Contrastive Voxel-Wise Representation Distillation for Semi-Supervised Medical Image Segmentation. IEEE Transactions On Medical Imaging 2022, 41: 2228-2237. PMID: 35320095, PMCID: PMC10325835, DOI: 10.1109/tmi.2022.3161829.Peer-Reviewed Original ResearchMeSH KeywordsDistillationImage Processing, Computer-AssistedSupervised Machine LearningTomography, X-Ray ComputedConceptsMedical image segmentationImage segmentationSemi-supervised medical image segmentationRobust Medical Image SegmentationMedical image analysisUnsupervised training strategyAtrial Segmentation ChallengeLearning-based approachMedical image synthesisAverage Dice scoreSemi-supervised approachPair-wise similarityContrastive objectiveData augmentationSegmentation challengePopular datasetsDice scoreSemantic informationDistillation frameworkSegmentation accuracyDownstream tasksImage synthesisPrevious best resultSupervised counterpartMedical dataDual-domain self-supervised learning for accelerated non-Cartesian MRI reconstruction
Zhou B, Schlemper J, Dey N, Mohseni Salehi SS, Sheth K, Liu C, Duncan JS, Sofka M. Dual-domain self-supervised learning for accelerated non-Cartesian MRI reconstruction. Medical Image Analysis 2022, 81: 102538. PMID: 35926336, DOI: 10.1016/j.media.2022.102538.Peer-Reviewed Original ResearchMeSH KeywordsHumansImage Processing, Computer-AssistedMagnetic Resonance ImagingMotionSupervised Machine LearningConceptsNon-Cartesian MRI reconstructionMRI reconstructionUndersampled dataPrevious baseline methodsSelf-supervised approachSelf-supervised learningHigh-quality reconstructionReconstruction networkAppearance consistencyDataset demonstrateBaseline methodsImage domainDisjoint partitionsSupervised trainingPractical adoptionReconstruction accuracyDomain partitionImproved image qualityImage qualityDDSSSampling patternK-spaceExperimental resultsNetworkMotion robustness
2021
DuDoDR-Net: Dual-domain data consistent recurrent network for simultaneous sparse view and metal artifact reduction in computed tomography
Zhou B, Chen X, Zhou SK, Duncan JS, Liu C. DuDoDR-Net: Dual-domain data consistent recurrent network for simultaneous sparse view and metal artifact reduction in computed tomography. Medical Image Analysis 2021, 75: 102289. PMID: 34758443, PMCID: PMC8678361, DOI: 10.1016/j.media.2021.102289.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsArtifactsHumansImage Processing, Computer-AssistedPhantoms, ImagingTomography, X-Ray ComputedConceptsRecurrent networksSevere streak artifactsRecurrent frameworkArtifact reductionSparse viewsImage domainReconstruction qualityCT metal artifact reductionX-ray projectionsMetal artifact reductionArtifact-free imagesMedical diagnosisPrevious methodsProjection dataConsistent layerExperimental resultsMDPET: A Unified Motion Correction and Denoising Adversarial Network for Low-Dose Gated PET
Zhou B, Tsai YJ, Chen X, Duncan JS, Liu C. MDPET: A Unified Motion Correction and Denoising Adversarial Network for Low-Dose Gated PET. IEEE Transactions On Medical Imaging 2021, 40: 3154-3164. PMID: 33909561, PMCID: PMC8588635, DOI: 10.1109/tmi.2021.3076191.Peer-Reviewed Original ResearchConceptsMotion estimationPyramid networkAdversarial networkAccurate motion estimationMotion correctionLow-noise reconstructionGated positron emission tomographyMotion correction methodMotion estimation networkGated PET dataEstimation networkRecurrent layersDenoising NetworkRespiratory motion blurringExperimental resultsLow-noise imagesMotion blurringNoise levelCorrection methodNetworkPET reconstructionPrevious methodsImage qualityImagesEstimationLimited View Tomographic Reconstruction Using a Cascaded Residual Dense Spatial-Channel Attention Network With Projection Data Fidelity Layer
Zhou B, Zhou S, Duncan JS, Liu C. Limited View Tomographic Reconstruction Using a Cascaded Residual Dense Spatial-Channel Attention Network With Projection Data Fidelity Layer. IEEE Transactions On Medical Imaging 2021, 40: 1792-1804. PMID: 33729929, PMCID: PMC8325575, DOI: 10.1109/tmi.2021.3066318.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsArtifactsImage Processing, Computer-AssistedNeural Networks, ComputerPhantoms, ImagingTomography, X-Ray ComputedConceptsAttention networkView reconstructionGrand challenge datasetLimited angle reconstructionHigh-quality reconstructionNeural network methodSparse-view reconstructionExperimental resultsLimited angle acquisitionArchitecture issuesSparse viewsChallenge datasetLimited view dataView dataNeural architectureQuality reconstructionNetwork methodTomographic reconstructionReconstructed imagesProjection viewsPrevious methodsAngle reconstructionDatasetNetworkAngle acquisitionAnatomy-guided multimodal registration by learning segmentation without ground truth: Application to intraprocedural CBCT/MR liver segmentation and registration
Zhou B, Augenfeld Z, Chapiro J, Zhou SK, Liu C, Duncan JS. Anatomy-guided multimodal registration by learning segmentation without ground truth: Application to intraprocedural CBCT/MR liver segmentation and registration. Medical Image Analysis 2021, 71: 102041. PMID: 33823397, PMCID: PMC8184611, DOI: 10.1016/j.media.2021.102041.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsCarcinoma, HepatocellularChemoembolization, TherapeuticCone-Beam Computed TomographyHumansImage Processing, Computer-AssistedLiver NeoplasmsSpiral Cone-Beam Computed TomographyConceptsMultimodal registrationLiver segmentationLarge-scale manual annotationGround truthMultimodal image registrationMultimodal registration methodSegmentation networkDomain adaptationManual annotationSource modalityImage registrationRegistration frameworkSegmentationImage-guided interventionsRegistration methodMedical imagingDiagnostic medical imagingCorrect transformationLimited FOVStructure informationIntraprocedural CBCTImage qualitySegmenterExperimental resultsPatient data
2020
Automated feature quantification of Lipiodol as imaging biomarker to predict therapeutic efficacy of conventional transarterial chemoembolization of liver cancer
Stark S, Wang C, Savic LJ, Letzen B, Schobert I, Miszczuk M, Murali N, Oestmann P, Gebauer B, Lin M, Duncan J, Schlachter T, Chapiro J. Automated feature quantification of Lipiodol as imaging biomarker to predict therapeutic efficacy of conventional transarterial chemoembolization of liver cancer. Scientific Reports 2020, 10: 18026. PMID: 33093524, PMCID: PMC7582153, DOI: 10.1038/s41598-020-75120-7.Peer-Reviewed Original ResearchConceptsConventional transarterial chemoembolizationLipiodol depositionTransarterial chemoembolizationLiver cancerPeripheral depositionLipiodol depositsTherapeutic efficacyNecrotic tumor areasBaseline MRITherapy optionsTumor responseTreatment responseTumor volumeLiver lesionsLipiodolH postTumor areaH-CTHounsfield unitsBiomarkersChemoembolizationHigh rateTumorsCancerImproved responseSparse Data–Driven Learning for Effective and Efficient Biomedical Image Segmentation
Onofrey JA, Staib LH, Huang X, Zhang F, Papademetris X, Metaxas D, Rueckert D, Duncan JS. Sparse Data–Driven Learning for Effective and Efficient Biomedical Image Segmentation. Annual Review Of Biomedical Engineering 2020, 22: 1-27. PMID: 32169002, PMCID: PMC9351438, DOI: 10.1146/annurev-bioeng-060418-052147.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsBrainDeep LearningDogsEchocardiographyHeart VentriclesHumansImage Processing, Computer-AssistedImaging, Three-DimensionalMachine LearningModels, TheoreticalNeural Networks, ComputerTomography, X-Ray Computed
2019
Flow network tracking for spatiotemporal and periodic point matching: Applied to cardiac motion analysis
Parajuli N, Lu A, Ta K, Stendahl J, Boutagy N, Alkhalil I, Eberle M, Jeng GS, Zontak M, O'Donnell M, Sinusas AJ, Duncan JS. Flow network tracking for spatiotemporal and periodic point matching: Applied to cardiac motion analysis. Medical Image Analysis 2019, 55: 116-135. PMID: 31055125, PMCID: PMC6939679, DOI: 10.1016/j.media.2019.04.007.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsDogsEchocardiographyImage Processing, Computer-AssistedImaging, Three-DimensionalMotionNeural Networks, ComputerVentricular Dysfunction, LeftConceptsDeformation/strainExcellent tracking accuracyEntire cardiac cycleTracking accuracyCardiac motion analysisAccurate estimationSurface pointsEchocardiographic image sequencesLV motionDisplacementMotion analysisImage sequencesCardiac cyclePoint matchingMotionConsecutive framesEstimationNetwork trackingImportant characteristicsSignificant promiseSchemeGood correlationFlow
2018
Learning Generalizable Recurrent Neural Networks from Small Task-fMRI Datasets
Dvornek NC, Yang D, Ventola P, Duncan JS. Learning Generalizable Recurrent Neural Networks from Small Task-fMRI Datasets. Lecture Notes In Computer Science 2018, 11072: 329-337. PMID: 30873514, PMCID: PMC6411297, DOI: 10.1007/978-3-030-00931-1_38.Peer-Reviewed Original ResearchMeSH KeywordsAutism Spectrum DisorderChildDeep LearningHumansImage Processing, Computer-AssistedMachine LearningMagnetic Resonance ImagingNeural Networks, ComputerReproducibility of ResultsSensitivity and SpecificityConceptsRecurrent neural networkNeural networkTask fMRI datasetsMedical image analysis problemsSuch deep networksImage analysis problemsTask fMRI scanTypical control subjectsDeep networkDeep learningTraining lossSmall datasetsLarge datasetsNumber of approachesAutism spectrum disorderAnalysis problemDatasetNetworkTraining runsImage analysisGeneralizable modelNon-imaging variablesSpectrum disorderFMRI analysisModel performance
2016
Pivotal response treatment prompts a functional rewiring of the brain among individuals with autism spectrum disorder
Venkataraman A, Yang D, Dvornek N, Staib LH, Duncan JS, Pelphrey KA, Ventola P. Pivotal response treatment prompts a functional rewiring of the brain among individuals with autism spectrum disorder. Neuroreport 2016, 27: 1081-1085. PMID: 27532879, PMCID: PMC5007196, DOI: 10.1097/wnr.0000000000000662.Peer-Reviewed Original ResearchMeSH KeywordsAutism Spectrum DisorderBayes TheoremBehavior TherapyBrainChildChild, PreschoolFemaleHumansImage Processing, Computer-AssistedMagnetic Resonance ImagingMaleNeural PathwaysOxygenConceptsPivotal Response TreatmentAutism spectrum disorderOccipital-temporal cortexAttentional systemResponse treatmentSpectrum disorderOrbitofrontal cortexPosterior cingulateHigh-level objectsBehavioral interventionsLearning mechanismPerception shiftProcessing areasNeural circuitsFunctional rewiringCortexTreatment regimenAutismInterventionNovel Bayesian frameworkCingulateFunctional changesIndividualsDisordersObjects
2014
Radial Basis Functions for Combining Shape and Speckle Tracking in 4D Echocardiography
Compas C, Wong EY, Huang X, Sampath S, Lin BA, Pal P, Papademetris X, Thiele K, Dione DP, Stacy M, Staib LH, Sinusas AJ, O'Donnell M, Duncan JS. Radial Basis Functions for Combining Shape and Speckle Tracking in 4D Echocardiography. IEEE Transactions On Medical Imaging 2014, 33: 1275-1289. PMID: 24893257, PMCID: PMC4283552, DOI: 10.1109/tmi.2014.2308894.Peer-Reviewed Original ResearchAlgorithmsAnimalsDogsEchocardiography, Four-DimensionalImage Processing, Computer-AssistedMaleMovementMyocardial InfarctionMyocardiumA Novel Multiple Hypothesis Based Particle Tracking Method for Clathrin Mediated Endocytosis Analysis Using Fluorescence Microscopy
Liang L, Shen H, De Camilli P, Duncan JS. A Novel Multiple Hypothesis Based Particle Tracking Method for Clathrin Mediated Endocytosis Analysis Using Fluorescence Microscopy. IEEE Transactions On Image Processing 2014, 23: 1844-1857. PMID: 24808351, PMCID: PMC4373089, DOI: 10.1109/tip.2014.2303633.Peer-Reviewed Original ResearchClathrinCytological TechniquesEndocytosisFluorescent DyesImage Processing, Computer-AssistedMicroscopy, FluorescenceMolecular ImagingParticle Size
2011
Targeted Imaging of the Spatial and Temporal Variation of Matrix Metalloproteinase Activity in a Porcine Model of Postinfarct Remodeling
Sahul ZH, Mukherjee R, Song J, McAteer J, Stroud RE, Dione DP, Staib L, Papademetris X, Dobrucki LW, Duncan JS, Spinale FG, Sinusas AJ. Targeted Imaging of the Spatial and Temporal Variation of Matrix Metalloproteinase Activity in a Porcine Model of Postinfarct Remodeling. Circulation Cardiovascular Imaging 2011, 4: 381-391. PMID: 21505092, PMCID: PMC3140564, DOI: 10.1161/circimaging.110.961854.Peer-Reviewed Original Research3-D Reconstruction of Microtubules from Multi-Angle Total Internal Reflection Fluorescence Microscopy Using Bayesian Framework
Yang Q, Karpikov A, Toomre D, Duncan JS. 3-D Reconstruction of Microtubules from Multi-Angle Total Internal Reflection Fluorescence Microscopy Using Bayesian Framework. IEEE Transactions On Image Processing 2011, 20: 2248-2259. PMID: 21324778, DOI: 10.1109/tip.2011.2114359.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsBayes TheoremCalibrationCell LineComputer SimulationImage Processing, Computer-AssistedImaging, Three-DimensionalMicroscopy, FluorescenceMicrotubulesPhantoms, ImagingPotoroidaeReproducibility of ResultsConceptsEvanescent fieldDifferent penetration depthsTIRF imagesPenetration depthSamples of microtubulesLaser beamTotal internal reflection fluorescence microscopyAxial resolutionReflection fluorescence microscopyLarge radiusIncident angleMulti-angle total internal reflection fluorescence microscopyElectron microscopy imagesTIRF dataSmall radiusTracking of microtubulesMicroscopy imagesFluorescence microscopyMicroscopyRadiusReconstruction resultsCurvilinear characteristicsZ-dimensionExperimental calibrationMicrotubule curvatureAn Expectation Maximization Based Method for Subcellular Particle Tracking Using Multi-angle TIRF Microscopy
Liang L, Shen H, De Camilli P, Toomre DK, Duncan JS. An Expectation Maximization Based Method for Subcellular Particle Tracking Using Multi-angle TIRF Microscopy. Lecture Notes In Computer Science 2011, 14: 629-636. PMID: 22003671, PMCID: PMC3648983, DOI: 10.1007/978-3-642-23623-5_79.Peer-Reviewed Original Research
2010
Image-Guided Intraoperative Cortical Deformation Recovery Using Game Theory: Application to Neocortical Epilepsy Surgery
DeLorenzo C, Papademetris X, Staib LH, Vives KP, Spencer DD, Duncan JS. Image-Guided Intraoperative Cortical Deformation Recovery Using Game Theory: Application to Neocortical Epilepsy Surgery. IEEE Transactions On Medical Imaging 2010, 29: 322-338. PMID: 20129844, PMCID: PMC2824434, DOI: 10.1109/tmi.2009.2027993.Peer-Reviewed Original ResearchConceptsDeformation estimationSurface deformationBrain surface deformationSurface deformation estimationPreoperative brain imagesCortical surface deformationSurface trackingCamera calibration parametersDisplacement errorStereo vision systemBrain deformationDeformationCalibration parametersBiomechanical modelIntraoperative brainCalibration errorsPhysical processesVision systemVivo casesCamera calibrationStereo systemInitial conditionsImage acquisitionErrorEstimation
2009
Segmentation of the Left Ventricle from Cardiac MR Images Using a Subject-Specific Dynamical Model
Zhu Y, Papademetris X, Sinusas AJ, Duncan JS. Segmentation of the Left Ventricle from Cardiac MR Images Using a Subject-Specific Dynamical Model. IEEE Transactions On Medical Imaging 2009, 29: 669-687. PMID: 19789107, PMCID: PMC2832728, DOI: 10.1109/tmi.2009.2031063.Peer-Reviewed Original ResearchConceptsSubject-specific dynamical modelGeneric dynamical modelDynamical modelStatistical modelSpecific dynamical modelRecursive Bayesian frameworkDynamic prediction algorithmStatic modelBayesian frameworkCardiac sequenceMotion modelActive Appearance Motion ModelsError propagationSpecific motion patternsPeriodic natureExperimental resultsPropagationCardiac shapeSegmentation resultsBackward directionSequential segmentationDynamicsModelMotion patternsOne-out
2004
Geometric strategies for neuroanatomic analysis from MRI
Duncan JS, Papademetris X, Yang J, Jackowski M, Zeng X, Staib LH. Geometric strategies for neuroanatomic analysis from MRI. NeuroImage 2004, 23: s34-s45. PMID: 15501099, PMCID: PMC2832750, DOI: 10.1016/j.neuroimage.2004.07.027.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsBrainBrain MappingCerebral CortexComputer SimulationDiffusion Magnetic Resonance ImagingHumansImage Processing, Computer-AssistedModels, StatisticalNerve FibersNeural PathwaysConceptsApplied mathematical approachWhite matter fiber tracksStatistical estimationMathematical approachFunction-structure analysisMagnetic resonance imagesEvolution strategyGeometric constraintsImage processingIntersubject registrationRich setGeometric strategyOngoing workData setsUse of levelsCommon spaceNeuroanatomic analysisSetRegistrationFiber tracksHuman brainResonance imagesInformationSegmentationEstimation