2019
Deep learning for liver tumor diagnosis part I: development of a convolutional neural network classifier for multi-phasic MRI
Hamm CA, Wang CJ, Savic LJ, Ferrante M, Schobert I, Schlachter T, Lin M, Duncan JS, Weinreb JC, Chapiro J, Letzen B. Deep learning for liver tumor diagnosis part I: development of a convolutional neural network classifier for multi-phasic MRI. European Radiology 2019, 29: 3338-3347. PMID: 31016442, PMCID: PMC7251621, DOI: 10.1007/s00330-019-06205-9.Peer-Reviewed Original ResearchAdultAgedBile Duct NeoplasmsBile Ducts, IntrahepaticCarcinoma, HepatocellularCholangiocarcinomaDeep LearningFemaleHumansImage Interpretation, Computer-AssistedLiver NeoplasmsMagnetic Resonance ImagingMaleMiddle AgedNeural Networks, ComputerReproducibility of ResultsROC CurveSensitivity and SpecificityUnited States
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 ResearchConceptsRecurrent 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
2013
Contour tracking in echocardiographic sequences via sparse representation and dictionary learning
Huang X, Dione DP, Compas CB, Papademetris X, Lin BA, Bregasi A, Sinusas AJ, Staib LH, Duncan JS. Contour tracking in echocardiographic sequences via sparse representation and dictionary learning. Medical Image Analysis 2013, 18: 253-271. PMID: 24292554, PMCID: PMC3946038, DOI: 10.1016/j.media.2013.10.012.Peer-Reviewed Original ResearchConceptsContour trackerSparse representationEchocardiographic sequencesRegion-based level set segmentationLevel set segmentationLocal image appearanceManual tracingExpert manual tracingsMultiscale sparse representationImage sequencesSegmentation resultsAppearance modelSpatiotemporal priorsFirst frameMultilevel informationHuman data setsEjection fraction estimatesLocal appearanceImage appearanceDictionary learningShape modelContour trackingManual resultsData setsContour estimationA Multiple Hypothesis Based Method for Particle Tracking and Its Extension for Cell Segmentation
Liang L, Shen H, Rompolas P, Greco V, De Camilli P, Duncan JS. A Multiple Hypothesis Based Method for Particle Tracking and Its Extension for Cell Segmentation. Lecture Notes In Computer Science 2013, 23: 98-109. PMID: 24683961, PMCID: PMC4122512, DOI: 10.1007/978-3-642-38868-2_9.Peer-Reviewed Original ResearchSegmentation of 4D Echocardiography Using Stochastic Online Dictionary Learning
Huang X, Dione DP, Lin BA, Bregasi A, Sinusas AJ, Duncan JS. Segmentation of 4D Echocardiography Using Stochastic Online Dictionary Learning. Lecture Notes In Computer Science 2013, 16: 57-65. PMID: 24505744, DOI: 10.1007/978-3-642-40760-4_8.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsArtificial IntelligenceData Interpretation, StatisticalDogsEchocardiography, Four-DimensionalImage EnhancementImage Interpretation, Computer-AssistedMyocardial InfarctionPattern Recognition, AutomatedReproducibility of ResultsSensitivity and SpecificityStochastic ProcessesSubtraction Technique
2012
Volumetric Intraoperative Brain Deformation Compensation: Model Development and Phantom Validation
DeLorenzo C, Papademetris X, Staib LH, Vives KP, Spencer DD, Duncan JS. Volumetric Intraoperative Brain Deformation Compensation: Model Development and Phantom Validation. IEEE Transactions On Medical Imaging 2012, 31: 1607-1619. PMID: 22562728, PMCID: PMC3600363, DOI: 10.1109/tmi.2012.2197407.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsBiomechanical PhenomenaBrainGame TheoryHumansImaging, Three-DimensionalModels, NeurologicalPhantoms, ImagingReproducibility of ResultsSkullSurgery, Computer-AssistedConceptsLinear elastic modelSurface displacementsElastic modelBrain deformationVolumetric brain deformationMaterial parametersMaterial propertiesRealistic brain phantomDeformationBiomechanical modelIntraoperative brainModel accuracyLocalization errorPhantom validationAccurate surgical guidanceModel solutionsModel developmentInitial estimationDisplacementModel sensitivityQuantitative validationPhantom resultsPreoperative imagesSurgical guidancePreliminary applicationSimultaneous Nonrigid Registration, Segmentation, and Tumor Detection in MRI Guided Cervical Cancer Radiation Therapy
Lu C, Chelikani S, Jaffray DA, Milosevic MF, Staib LH, Duncan JS. Simultaneous Nonrigid Registration, Segmentation, and Tumor Detection in MRI Guided Cervical Cancer Radiation Therapy. IEEE Transactions On Medical Imaging 2012, 31: 1213-1227. PMID: 22328178, PMCID: PMC3889159, DOI: 10.1109/tmi.2012.2186976.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsFemaleHumansImage EnhancementImage Interpretation, Computer-AssistedImaging, Three-DimensionalMagnetic Resonance ImagingPattern Recognition, AutomatedRadiotherapy, ConformalRadiotherapy, Image-GuidedReproducibility of ResultsSensitivity and SpecificitySubtraction TechniqueUterine Cervical NeoplasmsA Dynamical Appearance Model Based on Multiscale Sparse Representation: Segmentation of the Left Ventricle from 4D Echocardiography
Huang X, Dione DP, Compas CB, Papademetris X, Lin BA, Sinusas AJ, Duncan JS. A Dynamical Appearance Model Based on Multiscale Sparse Representation: Segmentation of the Left Ventricle from 4D Echocardiography. Lecture Notes In Computer Science 2012, 15: 58-65. PMID: 23286114, PMCID: PMC3889160, DOI: 10.1007/978-3-642-33454-2_8.Peer-Reviewed Original ResearchConceptsStatistical modelAppearance modelSparse representationIntensity modelPriorsShape predictionRepresentation methodMultiscale sparse representationSpatio-temporal coherenceSparse representation methodLocal appearanceImage sequencesModelRepresentationAppearance informationCoherenceRobustnessSegmentation accuracyPrecise Segmentation of Multiple Organs in CT Volumes Using Learning-Based Approach and Information Theory
Lu C, Zheng Y, Birkbeck N, Zhang J, Kohlberger T, Tietjen C, Boettger T, Duncan JS, Zhou SK. Precise Segmentation of Multiple Organs in CT Volumes Using Learning-Based Approach and Information Theory. Lecture Notes In Computer Science 2012, 15: 462-469. PMID: 23286081, DOI: 10.1007/978-3-642-33418-4_57.Peer-Reviewed Original ResearchConceptsMarginal Space LearningCT volumesChallenging segmentation problemInformation-theoretic schemesLearning-based approachComputer-aided diagnosisExcellent segmentation accuracyRobust boundary detectionInformation theoryPelvic organ segmentationSteerable featuresChallenging datasetArt solutionsOrgan segmentationSegmentation problemSpace learningSegmentation performanceSegmentation accuracyPrecise segmentationBoundary detectionJensen-Shannon divergenceTheoretic schemeInference processDiverse sourcesPrevious state
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 modelImagesRobustnessAn integrated approach to segmentation and nonrigid registration for application in image-guided pelvic radiotherapy
Lu C, Chelikani S, Papademetris X, Knisely JP, Milosevic MF, Chen Z, Jaffray DA, Staib LH, Duncan JS. An integrated approach to segmentation and nonrigid registration for application in image-guided pelvic radiotherapy. Medical Image Analysis 2011, 15: 772-785. PMID: 21646038, PMCID: PMC3164526, DOI: 10.1016/j.media.2011.05.010.Peer-Reviewed Original ResearchAlgorithmsBayes TheoremFemaleHumansImaging, Three-DimensionalMaleProstatic NeoplasmsRadiographic Image EnhancementRadiographic Image Interpretation, Computer-AssistedRadiotherapy, Computer-AssistedReproducibility of ResultsSensitivity and SpecificitySubtraction TechniqueSystems IntegrationTomography, X-Ray ComputedUterine Cervical Neoplasms3-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 ResearchConceptsEvanescent 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 curvatureSegmentation 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 modelImagesRobustnessA Unified Framework for Joint Segmentation, Nonrigid Registration and Tumor Detection: Application to MR-Guided Radiotherapy
Lu C, Chelikani S, Duncan JS. A Unified Framework for Joint Segmentation, Nonrigid Registration and Tumor Detection: Application to MR-Guided Radiotherapy. Lecture Notes In Computer Science 2011, 22: 525-537. PMID: 21761683, PMCID: PMC3889153, DOI: 10.1007/978-3-642-22092-0_43.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsArtificial IntelligenceComputer SimulationFemaleHumansImage EnhancementImage Interpretation, Computer-AssistedModels, BiologicalModels, StatisticalPattern Recognition, AutomatedRadiotherapy, Computer-AssistedReproducibility of ResultsSensitivity and SpecificitySubtraction TechniqueUterine Cervical NeoplasmsAn 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 ResearchNon-rigid Registration of Longitudinal Brain Tumor Treatment MRI
Chitphakdithai N, Chiang VL, Duncan JS. Non-rigid Registration of Longitudinal Brain Tumor Treatment MRI. Annual International Conference Of The IEEE Engineering In Medicine And Biology Society (EMBC) 2011, 2011: 4893-4896. PMID: 22255435, PMCID: PMC3753806, DOI: 10.1109/iembs.2011.6091212.Peer-Reviewed Original Research
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 echocardiographyImage-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 acquisitionErrorEstimationNon-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 kernel3D 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 dataTrackingImagesDataConstraintsSetDetection