2023
LiverHccSeg: A publicly available multiphasic MRI dataset with liver and HCC tumor segmentations and inter-rater agreement analysis
Gross M, Arora S, Huber S, Kücükkaya A, Onofrey J. LiverHccSeg: A publicly available multiphasic MRI dataset with liver and HCC tumor segmentations and inter-rater agreement analysis. Data In Brief 2023, 51: 109662. PMID: 37869619, PMCID: PMC10587725, DOI: 10.1016/j.dib.2023.109662.Peer-Reviewed Original ResearchTumor segmentation algorithmTumor segmentationSegmentation algorithmLiver segmentationManual segmentationTumor segmentation taskHigh-quality segmentationSegmentation taskSegmentation metricsSegmentation performanceAccurate segmentationRelevant metadataSegmentation agreementSegmentationMedical imagingFeature analysisExternal dataDatasetIntra-rater variabilityAlgorithmInnovative solutions
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 adjustmentIncremental Learning Meets Transfer Learning: Application to Multi-site Prostate MRI Segmentation
You C, Xiang J, Su K, Zhang X, Dong S, Onofrey J, Staib L, Duncan J. Incremental Learning Meets Transfer Learning: Application to Multi-site Prostate MRI Segmentation. Lecture Notes In Computer Science 2022, 13573: 3-16. PMID: 37415747, PMCID: PMC10323962, DOI: 10.1007/978-3-031-18523-6_1.Peer-Reviewed Original ResearchIncremental learningMedical image segmentation tasksMulti-site datasetImage segmentation tasksMedical image segmentationProstate MRI SegmentationComputation resourcesMedical datasetsSegmentation taskImage segmentationSegmentation frameworkEmbedding featuresBenchmark datasetsMRI segmentationTraining dataTarget domainLearning approachPractical deploymentDomain-specific expertiseCompetitive performanceDatasetTraining schemePrior workSegmentationSingle modelAtlas-Based Semantic Segmentation of Prostate Zones
Zhang J, Venkataraman R, Staib L, Onofrey J. Atlas-Based Semantic Segmentation of Prostate Zones. Lecture Notes In Computer Science 2022, 13435: 570-579. PMID: 38084296, PMCID: PMC10711803, DOI: 10.1007/978-3-031-16443-9_55.Peer-Reviewed Original ResearchSegmentation resultsSemantic segmentation frameworkSemantic segmentation resultsDice similarity coefficient valuesSemantic segmentationInference stageSegmentation frameworkSegmentation performanceExternal test datasetTest datasetRegion of interestSegmentationAnatomical atlasHyperparametersSimilarity coefficient valuesAnatomical informationGitHubUsersDatasetProstate zonesCodeFrameworkInformation
2018
Deep Learning Retinal Vessel Segmentation from a Single Annotated Example: An Application of Cyclic Generative Adversarial Neural Networks
Sadda P, Onofrey J, Papademetris X. Deep Learning Retinal Vessel Segmentation from a Single Annotated Example: An Application of Cyclic Generative Adversarial Neural Networks. Lecture Notes In Computer Science 2018, 11043: 82-91. DOI: 10.1007/978-3-030-01364-6_10.Peer-Reviewed Original ResearchGenerative adversarial neural networksAdversarial neural networkGround truth segmentationNeural networkTruth segmentationMedical image segmentation tasksImage segmentation tasksConvolutional neural networkDeep learning methodsRetinal vessel segmentationConvolutional networkSegmentation taskTraining examplesAnnotated examplesTraining dataLearning methodsVessel segmentationSegmentationSynthetic examplesNetworkLarge amountDatasetTaskExampleAccuracy