2024
A Flow-based Truncated Denoising Diffusion Model for super-resolution Magnetic Resonance Spectroscopic Imaging
Dong S, Cai Z, Hangel G, Bogner W, Widhalm G, Huang Y, Liang Q, You C, Kumaragamage C, Fulbright R, Mahajan A, Karbasi A, Onofrey J, de Graaf R, Duncan J. A Flow-based Truncated Denoising Diffusion Model for super-resolution Magnetic Resonance Spectroscopic Imaging. Medical Image Analysis 2024, 99: 103358. PMID: 39353335, DOI: 10.1016/j.media.2024.103358.Peer-Reviewed Original ResearchDenoising diffusion modelsDeep learning-based super-resolution methodsLearning-based super-resolution methodsMulti-scale super-resolutionGenerative modelSuper-resolution methodsDeep learning modelsHigh-resolution magnetic resonance spectroscopic imagingHigh-quality imagesPost-processing approachSuper-resolutionFlow-based networksLearning modelsLow resolutionTruncation stepLow-resolution dataSharpness adjustmentNetworkSensitivity restrictionsUncertainty estimationDiffusion modelImagesCapabilitySampling processSpectroscopic imagingHigh‐resolution extracellular pH imaging of liver cancer with multiparametric MR using Deep Image Prior
Dong S, Shewarega A, Chapiro J, Cai Z, Hyder F, Coman D, Duncan J. High‐resolution extracellular pH imaging of liver cancer with multiparametric MR using Deep Image Prior. NMR In Biomedicine 2024, 37: e5145. PMID: 38488205, DOI: 10.1002/nbm.5145.Peer-Reviewed Original ResearchDeep Image PriorU-NetUnsupervised deep learning techniquesU-Net parametersDeep learning techniquesHigh-resolution ground truthU-Net architectureSuper-resolution imagingImage priorsSuper-resolutionGround truthMean absolute errorDeepSpatial resolutionPostprocessing methodDeep imagingAbsolute errorImagesAnatomical MR imagesMR spectroscopic imagingAnatomical informationSpectroscopic imagingInformationAcquisition timeError
2022
Flow-Based Visual Quality Enhancer for Super-Resolution Magnetic Resonance Spectroscopic Imaging
Dong S, Hangel G, Chen E, Sun S, Bogner W, Widhalm G, You C, Onofrey J, de Graaf R, Duncan J. Flow-Based Visual Quality Enhancer for Super-Resolution Magnetic Resonance Spectroscopic Imaging. Lecture Notes In Computer Science 2022, 13609: 3-13. DOI: 10.1007/978-3-031-18576-2_1.Peer-Reviewed Original ResearchAdversarial networkVisual qualityDeep learning-based super-resolution methodsLearning-based super-resolution methodsFlow-based modelImage visual qualityGenerative adversarial networkHigh visual qualitySuper-resolution methodSuper-resolved imagesGenerative modelHigh-resolution imagesImage modalitiesFlow-based methodNetworkLow spatial resolutionUncertainty estimationImagesPromising resultsEnhancer networkAnatomical informationHigh fidelityEssential toolDatasetQuality adjustment
2021
MDPET: 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 qualityImagesEstimationMulti-frame Attention Network for Left Ventricle Segmentation in 3D Echocardiography
Ahn SS, Ta K, Thorn S, Langdon J, Sinusas AJ, Duncan JS. Multi-frame Attention Network for Left Ventricle Segmentation in 3D Echocardiography. Lecture Notes In Computer Science 2021, 12901: 348-357. PMID: 34729554, PMCID: PMC8560213, DOI: 10.1007/978-3-030-87193-2_33.Peer-Reviewed Original ResearchPerformance of segmentationLeft ventricle segmentationVentricle segmentationMedical image segmentation modelsSpatiotemporal featuresAttention networkImage segmentation modelSequence of imagesAttention mechanismSegmentation modelTedious taskTarget imageSegmentationEchocardiography imagesExperimental resultsImagesNetworkAnatomy-Constrained Contrastive Learning for Synthetic Segmentation Without Ground-Truth
Zhou B, Liu C, Duncan J. Anatomy-Constrained Contrastive Learning for Synthetic Segmentation Without Ground-Truth. Lecture Notes In Computer Science 2021, 12901: 47-56. DOI: 10.1007/978-3-030-87193-2_5.Peer-Reviewed Original ResearchSegmentation networkContrastive learningManual segmentationSuperior segmentation performanceObject of interestSynthetic SegmentationManual effortSegmentation performanceTraining dataUnsupervised adaptationImaging dataSource modalitySegmentationNetworkPrevious methodsLearningLarge amountSuccessful applicationPET imaging dataImagesObjectsCodeDataNew imaging modalityShape-Regularized Unsupervised Left Ventricular Motion Network With Segmentation Capability In 3d+ Time Echocardiography
Ta K, Ahn SS, Stendahl JC, Sinusas AJ, Duncan JS. Shape-Regularized Unsupervised Left Ventricular Motion Network With Segmentation Capability In 3d+ Time Echocardiography. 2011 IEEE International Symposium On Biomedical Imaging: From Nano To Macro 2021, 00: 536-540. PMID: 34168721, PMCID: PMC8221369, DOI: 10.1109/isbi48211.2021.9433888.Peer-Reviewed Original ResearchConvolutional neural networkAccurate motion estimationCardiac motion patternsMotion estimation performanceDense displacement fieldB-mode echocardiography imagesSegmentation masksMedical imagesMotion estimationNeural networkSegmentation capabilityTarget imageUnsupervised estimationImportant taskSegmentationMotion patternsDisplacement fieldNetworkEchocardiography imagesEstimation performanceImagesLow signalAdditional challengesMotion networkNoise ratio
2020
Layer Embedding Analysis in Convolutional Neural Networks for Improved Probability Calibration and Classification
Zhang F, Dvornek N, Yang J, Chapiro J, Duncan J. Layer Embedding Analysis in Convolutional Neural Networks for Improved Probability Calibration and Classification. IEEE Transactions On Medical Imaging 2020, 39: 3331-3342. PMID: 32356739, PMCID: PMC7606489, DOI: 10.1109/tmi.2020.2990625.Peer-Reviewed Original ResearchConceptsConvolutional neural networkNeural networkClassification taskProbability calibrationTissue classification tasksImage representationBaseline methodsPublic datasetsModel performanceRandom forest modelNetworkBetter performanceForest modelDatasetClassificationTaskCT imagesImagesOriginal model outputMR imagesModel outputInstitutional datasetPerformanceEmbeddingOutputUnsupervised motion tracking of left ventricle in echocardiography
Ahn SS, Ta K, Lu A, Stendahl JC, Sinusas AJ, Duncan JS. Unsupervised motion tracking of left ventricle in echocardiography. Proceedings Of SPIE--the International Society For Optical Engineering 2020, 11319: 113190z-113190z-7. PMID: 32994659, PMCID: PMC7521020, DOI: 10.1117/12.2549572.Peer-Reviewed Original ResearchMotion trackingGround truth displacement fieldsConvolutional neural networkAccurate motion trackingDense displacement fieldB-mode echocardiography imagesU-NetNeural networkTracking frameworkNon-rigid registration algorithmTarget imageRegistration algorithmTarget frameSource frameAlgorithmEchocardiography imagesFavorable performanceDatasetImagesTrackingDisplacement estimationLarge amountEchocardiographic imagesSegmentationNetwork
2018
Liver Tissue Classification Using an Auto-context-based Deep Neural Network with a Multi-phase Training Framework
Zhang F, Yang J, Nezami N, Laage-gaupp F, Chapiro J, De Lin M, Duncan J. Liver Tissue Classification Using an Auto-context-based Deep Neural Network with a Multi-phase Training Framework. Lecture Notes In Computer Science 2018, 11075: 59-66. PMID: 32432233, PMCID: PMC7236808, DOI: 10.1007/978-3-030-00500-9_7.Peer-Reviewed Original ResearchNeural networkNovel deep convolutional neural networkStandard neural network approachesTraining frameworkDeep convolutional neural networkU-Net-like architectureTissue classificationConvolutional neural networkDeep neural networksNeural network approachSegmentation masksBenchmark methodsNetwork approachPatch-based strategyLearning spacesLiver tissue classificationMagnetic resonance imagesPromising resultsNetworkImagesPredictive modelClassificationFrameworkResonance imagesArchitecture2-Channel Convolutional 3D Deep Neural Network (2CC3D) for FMRI Analysis: ASD Classification and Feature Learning
Li X, Dvornek NC, Papademetris X, Zhuang J, Staib LH, Ventola P, Duncan JS. 2-Channel Convolutional 3D Deep Neural Network (2CC3D) for FMRI Analysis: ASD Classification and Feature Learning. 2011 IEEE International Symposium On Biomedical Imaging: From Nano To Macro 2018, 2018: 1252-1255. PMID: 32983370, PMCID: PMC7519578, DOI: 10.1109/isbi.2018.8363798.Peer-Reviewed Original ResearchConvolutional neural networkNeural networkCNN convolutional layerSpatial featuresASD classificationDeep neural networksMean F-scoreTraditional machineFeature learningConvolutional layersInput formatF-scoreClassification modelTemporal informationNetworkWindow parametersImagesClassificationConvolutionalTemporal statisticsMachineLearningFeaturesFormatScheme
2016
Machine learning–based 3‐D geometry reconstruction and modeling of aortic valve deformation using 3‐D computed tomography images
Liang L, Kong F, Martin C, Pham T, Wang Q, Duncan J, Sun W. Machine learning–based 3‐D geometry reconstruction and modeling of aortic valve deformation using 3‐D computed tomography images. International Journal For Numerical Methods In Biomedical Engineering 2016, 33 PMID: 27557429, PMCID: PMC5325825, DOI: 10.1002/cnm.2827.Peer-Reviewed Original ResearchConceptsHuman expertsGeometry reconstructionHuman errorMean discrepancyPreoperative planning systemComputational modeling processReconstructed geometryFinite element model generationModel generationPatient-specific computational modelingCardiac imagesComputational modeling methodsFast feedbackComputational modeling frameworkModeling processMesh correspondencePlanning systemModeling methodMachineModeling frameworkAortic valveImagesDisease diagnosisLarge patient cohortIndividual patient needsTowards patient-specific modeling of mitral valve repair: 3D transesophageal echocardiography-derived parameter estimation
Zhang F, Kanik J, Mansi T, Voigt I, Sharma P, Ionasec RI, Subrahmanyan L, Lin BA, Sugeng L, Yuh D, Comaniciu D, Duncan J. Towards patient-specific modeling of mitral valve repair: 3D transesophageal echocardiography-derived parameter estimation. Medical Image Analysis 2016, 35: 599-609. PMID: 27718462, DOI: 10.1016/j.media.2016.09.006.Peer-Reviewed Original ResearchConceptsMitral valve modelingTemporal informationPatient-specific modelingImage acquisitionEuclidean distanceValve modelingComputational frameworkExtended Kalman filterImage analysisModeling frameworkKalman filterFrameworkAverage errorMitral valve geometryTEE imagesInformationMachineParameter estimationClosed mitral valveLeaflet material propertiesSubjective predictionModelingImagesRepresentationOptimization
2011
Segmentation of 3D radio frequency echocardiography using a spatio-temporal predictor
Pearlman PC, Tagare HD, Lin BA, Sinusas AJ, Duncan JS. Segmentation of 3D radio frequency echocardiography using a spatio-temporal predictor. Medical Image Analysis 2011, 16: 351-360. PMID: 22078842, PMCID: PMC3267850, DOI: 10.1016/j.media.2011.09.002.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsComputer SimulationDogsEchocardiography, Three-DimensionalHeart VentriclesImage EnhancementImage Interpretation, Computer-AssistedImaging, Three-DimensionalModels, CardiovascularModels, StatisticalPattern Recognition, AutomatedReproducibility of ResultsSensitivity and SpecificitySubtraction TechniqueConceptsLeft ventricular endocardial boundarySpatio-temporal predictorsStandard level setRF dataSpatio-temporal coherenceNeighboring framesImage sequencesBoundary detectionMultiple framesImage inhomogeneitySegmentationEndocardial boundaryGeometric constraintsManual tracingRF ultrasoundAlgorithmLevel setsEchocardiographic imagesFrameConditional modelLinear predictorTrackingSpatial modelImagesRobustnessSegmentation of 3D RF Echocardiography Using a Multiframe Spatio-temporal Predictor
Pearlman PC, Tagare HD, Lin BA, Sinusas AJ, Duncan JS. Segmentation of 3D RF Echocardiography Using a Multiframe Spatio-temporal Predictor. Lecture Notes In Computer Science 2011, 22: 37-48. PMID: 21761644, DOI: 10.1007/978-3-642-22092-0_4.Peer-Reviewed Original ResearchConceptsLeft ventricular endocardial boundarySpatio-temporal predictorsStandard level setSpatio-temporal coherenceNeighboring framesImage sequencesBoundary detectionRF dataMultiple framesImage inhomogeneitySegmentationEndocardial boundaryGeometric constraintsManual tracingRF ultrasoundLevel setsConditional modelEchocardiographic imagesFrameLinear predictorAlgorithmTrackingSpatial modelImagesRobustness
2010
A coupled deformable model for tracking myocardial borders from real-time echocardiography using an incompressibility constraint
Zhu Y, Papademetris X, Sinusas AJ, Duncan JS. A coupled deformable model for tracking myocardial borders from real-time echocardiography using an incompressibility constraint. Medical Image Analysis 2010, 14: 429-448. PMID: 20350833, PMCID: PMC4318707, DOI: 10.1016/j.media.2010.02.005.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsArtificial IntelligenceComputer SystemsDogsEchocardiography, Three-DimensionalElasticity Imaging TechniquesHumansImage EnhancementImage Interpretation, Computer-AssistedPattern Recognition, AutomatedReproducibility of ResultsSensitivity and SpecificitySubtraction TechniqueConceptsDeformable modelImage-derived informationLV endocardial boundariesImage acquisition techniquesFinal segmentationAutomatic algorithmGround truthManual segmentationVolumetric imagesSegmentationSynthetic dataEndocardial boundaryNumber of effortsMyocardial bordersEpicardial boundariesAcquisition techniquesInstantaneous acquisitionConstraintsImagesEchocardiographic imagesSetSpeckle statisticsAlgorithmReal-time echocardiographyIntegrated Segmentation and Nonrigid Registration for Application in Prostate Image-Guided Radiotherapy
Lu C, Chelikani S, Chen Z, Papademetris X, Staib LH, Duncan JS. Integrated Segmentation and Nonrigid Registration for Application in Prostate Image-Guided Radiotherapy. Lecture Notes In Computer Science 2010, 13: 53-60. PMID: 20879214, DOI: 10.1007/978-3-642-15705-9_7.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsHumansImaging, Three-DimensionalMaleProstatic NeoplasmsRadiographic Image EnhancementRadiographic Image Interpretation, Computer-AssistedRadiotherapy, Computer-AssistedReproducibility of ResultsSensitivity and SpecificitySubtraction TechniqueSystems IntegrationTomography, X-Ray ComputedConceptsManual segmentationAutomatic segmentationImportant treatment parametersNonrigid registrationImage-guided radiotherapy systemReal patient dataNon-rigid registrationIntegrated SegmentationRegistration partRadiotherapy linear acceleratorSegmentationTreatment imagesImage qualityCone-beam CTTreatment parametersImagesPromising resultsPatient dataKey anatomical structuresLinear acceleratorRegistrationPrevious workRadiotherapy system3D Radio Frequency Ultrasound Cardiac Segmentation Using a Linear Predictor
Pearlman PC, Tagare HD, Sinusas AJ, Duncan JS. 3D Radio Frequency Ultrasound Cardiac Segmentation Using a Linear Predictor. Lecture Notes In Computer Science 2010, 13: 502-509. PMID: 20879268, PMCID: PMC3889143, DOI: 10.1007/978-3-642-15705-9_61.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsComputer SimulationDogsEchocardiography, Three-DimensionalImage EnhancementImage Interpretation, Computer-AssistedImaging, Three-DimensionalLinear ModelsModels, CardiovascularMyocardial InfarctionPattern Recognition, AutomatedRadio WavesReproducibility of ResultsSensitivity and SpecificityConceptsLeft ventricular endocardial boundaryStandard level setSpatio-temporal coherenceCardiac segmentationBoundary detectionImage inhomogeneityEndocardial boundarySegmentationGeometric constraintsManual tracingRadio frequency ultrasoundLinear predictorLevel setsRF dataEchocardiographic imagesB-mode dataTrackingImagesDataConstraintsSetDetectionNon-rigid Registration with Missing Correspondences in Preoperative and Postresection Brain Images
Chitphakdithai N, Duncan JS. Non-rigid Registration with Missing Correspondences in Preoperative and Postresection Brain Images. Lecture Notes In Computer Science 2010, 13: 367-374. PMID: 20879252, PMCID: PMC3031159, DOI: 10.1007/978-3-642-15705-9_45.Peer-Reviewed Original ResearchConceptsTypes of datasetsNon-rigid registration methodImage alignmentNon-rigid registrationMissing correspondencesSegmentation algorithmNon-rigid registration algorithmSimilarity metricCorrespondence problemValid correspondencesRegistration algorithmRegistration methodExpectation-maximization algorithmBrain imagesJoint registrationReal dataAlgorithmImagesRegistrationError kernel
2009
From medical image computing to computer‐aided intervention: development of a research interface for image‐guided navigation
Papademetris X, DeLorenzo C, Flossmann S, Neff M, Vives KP, Spencer DD, Staib LH, Duncan JS. From medical image computing to computer‐aided intervention: development of a research interface for image‐guided navigation. International Journal Of Medical Robotics And Computer Assisted Surgery 2009, 5: 147-157. PMID: 19301361, PMCID: PMC2796181, DOI: 10.1002/rcs.241.Peer-Reviewed Original ResearchConceptsResearch interfaceNavigation systemApplication programming interfaceDual computer systemComputer-aided interventionsSurgery navigation systemImage-guided navigation systemProgramming interfaceClient programNetwork interfacesMedical imagesImage-guided navigationResearch softwareReal timeViable solutionSoftwareImage analysis softwareTool positionVersatile linkAnalysis softwareImagesInterfaceNavigationSystemResearch techniques