2024
Modeling intra‐individual inter‐trial EEG response variability in autism
Dong M, Telesca D, Guindani M, Sugar C, Webb S, Jeste S, Dickinson A, Levin A, Shic F, Naples A, Faja S, Dawson G, McPartland J, Şentürk D. Modeling intra‐individual inter‐trial EEG response variability in autism. Statistics In Medicine 2024, 43: 3239-3263. PMID: 38822707, DOI: 10.1002/sim.10131.Peer-Reviewed Original Research
2023
Magnetic resonance imaging quality in the context of a knee-spanning external fixator placed inside the MR bore: a literature review
Marcel A, Green J, Porrino J, Katz L, Medvecky M. Magnetic resonance imaging quality in the context of a knee-spanning external fixator placed inside the MR bore: a literature review. Skeletal Radiology 2023, 53: 629-636. PMID: 37955679, DOI: 10.1007/s00256-023-04505-2.Peer-Reviewed Original ResearchKnee-spanning external fixatorExternal fixatorNoise ratioMR boreSoft tissue repairDevice compositionKnee injury patientsLimb-threatening injuriesSoft tissue injuriesUtility of MRIMagnetic resonance imagingMagnetic field strengthImage qualityField strengthKnee dislocationInjury patientsTissue injuryAnatomical assessmentUseful diagnostic informationResonance imagingLigamentous structuresFixatorMRIEmergent assessmentMRI sequencesBrain imaging with portable low-field MRI
Kimberly W, Sorby-Adams A, Webb A, Wu E, Beekman R, Bowry R, Schiff S, de Havenon A, Shen F, Sze G, Schaefer P, Iglesias J, Rosen M, Sheth K. Brain imaging with portable low-field MRI. Nature Reviews Bioengineering 2023, 1: 617-630. PMID: 37705717, PMCID: PMC10497072, DOI: 10.1038/s44222-023-00086-w.Peer-Reviewed Original ResearchSparse k-space dataK-space dataImage reconstructionUseful diagnostic imagesReconstruction algorithmLow power requirementsNew applicationsLF-MRIDiagnostic imagesNew approachNew opportunitiesHardwareConventional systemMachineOngoing developmentPower requirementsAlgorithmImagesTechnological innovationFurther innovationNoise cancellationNoise ratioTechnologyRequirementsInformationCharacterization of GafchromicTM EBT4 film with clinical kV/MV photons and MeV electrons
Guan F, Chen H, Draeger E, Li Y, Aydin R, Tien C, Chen Z. Characterization of GafchromicTM EBT4 film with clinical kV/MV photons and MeV electrons. Precision Radiation Oncology 2023, 7: 84-91. DOI: 10.1002/pro6.1204.Peer-Reviewed Original ResearchX-ray beamMeV electron beamMV photon beamElectron beamMV photonsBeam energyMeV electronsPhoton beamsEnergy dependenceKilovoltage x-ray beamsMinimal energy dependenceClinical photonPhotonsBeamRadiation typesMeVElectronsDependence experimentsFilmsDose-response dependenceResponse dependenceDependenceEnergyNoise ratioEBT3Enhanced characterization of breast cancer phenotypes using Raman micro-spectroscopy on stainless steel substrate
Thomas G, Fitzgerald S, Gautam R, Chen F, Haugen E, Rasiah P, Adams W, Mahadevan-Jansen A. Enhanced characterization of breast cancer phenotypes using Raman micro-spectroscopy on stainless steel substrate. Analytical Methods 2023, 15: 1188-1205. PMID: 36799369, DOI: 10.1039/d2ay01764d.Peer-Reviewed Original ResearchConceptsStainless steel substratesStainless steelSteel substrateRaman spectroscopySteelRaman signalRaman signal intensityCalcium fluoride substratesLaser powerFluoride substratesSignal qualityFundamental understandingStrong Raman signalNoise ratioSubstrateCost-effective alternativeEnhanced characterizationRaman spectraSignals
2022
Translator: A Transfer Learning Approach to Facilitate Single-Cell ATAC-Seq Data Analysis from Reference Dataset
Xu S, Skarica M, Hwang A, Dai Y, Lee C, Girgenti MJ, Zhang J. Translator: A Transfer Learning Approach to Facilitate Single-Cell ATAC-Seq Data Analysis from Reference Dataset. Journal Of Computational Biology 2022, 29: 619-633. PMID: 35584295, PMCID: PMC9464368, DOI: 10.1089/cmb.2021.0596.Peer-Reviewed Original ResearchConceptsGraphic Processing Units ParallelismComplex feature interactionsDeep learning frameworkFree software packageFeature interactionsUltra-high dimensionalityLearning frameworkSoftware packageComputational efficiencySeq data analysisScATAC-seq dataDatasetReference datasetReference dataData analysisDownstream analysisCell representationRepresentationParallelismLow signalTranslatorsClusteringDimensionalityNoise ratioNonlinear relationship
2021
Assessing the utility of low resolution brain imaging: treatment of infant hydrocephalus
Harper JR, Cherukuri V, O’Reilly T, Yu M, Mbabazi-Kabachelor E, Mulando R, Sheth KN, Webb AG, Warf BC, Kulkarni AV, Monga V, Schiff SJ. Assessing the utility of low resolution brain imaging: treatment of infant hydrocephalus. NeuroImage Clinical 2021, 32: 102896. PMID: 34911199, PMCID: PMC8646178, DOI: 10.1016/j.nicl.2021.102896.Peer-Reviewed Original ResearchConceptsDeep learning enhancementLow-quality imagesDeep learningQuality imagesDeep learning algorithmsEnhanced imageRole of machineLearning enhancementImage qualityLearning algorithmAcceptable image qualityReconstruction errorImage resolutionImagesAlgorithmCT imagesLearningCT counterpartsNoise ratioTreatment planningPlanningNew standardStructural errorsExperienced pediatric neurosurgeonsMachineReal-time threshold determination of auditory brainstem responses by cross-correlation analysis
Wang H, Li B, Lu Y, Han K, Sheng H, Zhou J, Qi Y, Wang X, Huang Z, Song L, Hua Y. Real-time threshold determination of auditory brainstem responses by cross-correlation analysis. IScience 2021, 24: 103285. PMID: 34765914, PMCID: PMC8571499, DOI: 10.1016/j.isci.2021.103285.Peer-Reviewed Original ResearchShape-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 ratioUltrahigh-speed point scanning two-photon microscopy using high dynamic range silicon photomultipliers
Ching-Roa VD, Olson EM, Ibrahim SF, Torres R, Giacomelli MG. Ultrahigh-speed point scanning two-photon microscopy using high dynamic range silicon photomultipliers. Scientific Reports 2021, 11: 5248. PMID: 33664354, PMCID: PMC7933192, DOI: 10.1038/s41598-021-84522-0.Peer-Reviewed Original ResearchConceptsMaximum imaging rateSilicon photomultipliersAdvanced detection technologyPhoton detection rateDetection electronicsDetection technologyTwo-photon microscopyHigh sensitivityPhotomultiplier tubeDynamic rangeMicroscopyTwo-photon microscopeNoise ratioImaging rateOrders of magnitudeTwo-photonIntegration timeDetector designElectronicsPhotomultipliersMicroscopeConfocal microscopyTubeTechnologyDetection rate
2020
Simultaneous Denoising and Motion Estimation for Low-Dose Gated PET Using a Siamese Adversarial Network with Gate-to-Gate Consistency Learning
Zhou B, Tsai Y, Liu C. Simultaneous Denoising and Motion Estimation for Low-Dose Gated PET Using a Siamese Adversarial Network with Gate-to-Gate Consistency Learning. Lecture Notes In Computer Science 2020, 12267: 743-752. DOI: 10.1007/978-3-030-59728-3_72.Peer-Reviewed Original ResearchMotion estimationMotion estimation networkRobust motion estimationMotion correction methodRespiratory motion blurringEstimation networkNoise ratioMotion correctionMotion blurringImage volumesCorrection methodCorrection stepMotion vectorsGateSimultaneous denoisingImage qualityEstimationAdversarial network
2015
Three-dimensional, three-vector-component velocimetry of cilia-driven fluid flow using correlation-based approaches in optical coherence tomography
Huang BK, Gamm UA, Bhandari V, Khokha MK, Choma MA. Three-dimensional, three-vector-component velocimetry of cilia-driven fluid flow using correlation-based approaches in optical coherence tomography. Biomedical Optics Express 2015, 6: 3515-3538. PMID: 26417520, PMCID: PMC4574676, DOI: 10.1364/boe.6.003515.Peer-Reviewed Original ResearchDigital particle image velocimetryFluid flowVelocimetry measurementsParticle image velocimetryImage velocimetryFlow performanceFlow velocity measurementsVelocimetryVelocity measurementsLow-dimensional measurementsDimensional measurementsS regimeFlowNoise ratioCilia-driven fluid flowMeasurementsFlow imagingCorrelation-based approach
2014
Electron cloud density measurements in accelerator beam-pipe using resonant microwave excitation
Sikora J, Carlson B, Duggins D, Hammond K, De Santis S, Tencate A. Electron cloud density measurements in accelerator beam-pipe using resonant microwave excitation. Nuclear Instruments And Methods In Physics Research Section A Accelerators Spectrometers Detectors And Associated Equipment 2014, 754: 28-35. DOI: 10.1016/j.nima.2014.03.063.Peer-Reviewed Original ResearchBeam-pipeElectron cloudPositively charged beamsResonant microwave excitationLow-energy electronsCloud densityAccelerated beamCharged beamsEnergy electronsMicrowave excitationImproved signal-to-noise ratioCoupling microwaveResonance techniquesElectronSignal-to-noise ratioResonant frequencyBeamElectron cloud densityMicrowaveDensityAccelerationDensity measurementsExcitationCloudNoise ratioTof-Pet Ordered Subset Reconstruction Using Non-Uniform Separable Quadratic Surrogates Algorithm
Kim K, Ye J, Cheng L, Ying K, Fakhri G, Li Q. Tof-Pet Ordered Subset Reconstruction Using Non-Uniform Separable Quadratic Surrogates Algorithm. 2014, 963-966. DOI: 10.1109/isbi.2014.6868032.Peer-Reviewed Original ResearchSignal-to-noise ratioQuadratic surrogatesTOF-basedAlgorithm timeNoise ratioReconstruction algorithmReconstructed imagesAlgorithmConvergence rateImage qualityPET reconstructionTransmission reconstructionComputer simulationsTOF PET reconstructionTOF-PETEmission reconstructionAccurate imagingImagesSmall regionConvergenceComputerReconstructionNon-uniformityOSEM
2012
Optimal noise reduction in 3D reconstructions of single particles using a volume-normalized filter
Sindelar CV, Grigorieff N. Optimal noise reduction in 3D reconstructions of single particles using a volume-normalized filter. Journal Of Structural Biology 2012, 180: 26-38. PMID: 22613568, PMCID: PMC3498508, DOI: 10.1016/j.jsb.2012.05.005.Peer-Reviewed Original ResearchConceptsParticle mapsOptimal noise reductionWiener filterError reduction schemeConventional Wiener filterNoise reductionNovel filterInversion methodNew filterHigh noise levelsParticle densityParticle volumeFilterParticlesNoise ratioNoise levelTheoretical analysisSingle particleAccurate implementationSpectral signalsSSNRInterior regionImage dataSignalsFourier inversion methodPhosphorus-31 MRI of hard and soft solids using quadratic echo line-narrowing
Frey MA, Michaud M, VanHouten JN, Insogna KL, Madri JA, Barrett SE. Phosphorus-31 MRI of hard and soft solids using quadratic echo line-narrowing. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 5190-5195. PMID: 22431609, PMCID: PMC3325667, DOI: 10.1073/pnas.1117293109.Peer-Reviewed Original Research
2011
An adaptation of the Wiener filter suitable for analyzing images of isolated single particles
Sindelar CV, Grigorieff N. An adaptation of the Wiener filter suitable for analyzing images of isolated single particles. Journal Of Structural Biology 2011, 176: 60-74. PMID: 21757012, PMCID: PMC3184790, DOI: 10.1016/j.jsb.2011.06.010.Peer-Reviewed Original ResearchConceptsWiener filterConventional Wiener filterCryo-EM applicationsNew filterFourier ring correlationParticle areaEstimation schemeFilterLeast-squares senseEstimation methodNoise ratioSpecific applicationsSingle particleParticlesImage fieldError reductionNumeric testsApplicationsImaging conditionsSimulated dataInput data
2009
Using Perturbation theory to reduce noise in diffusion tensor fields
Bansal R, Staib LH, Xu D, Laine AF, Liu J, Peterson BS. Using Perturbation theory to reduce noise in diffusion tensor fields. Medical Image Analysis 2009, 13: 580-597. PMID: 19540791, PMCID: PMC2782748, DOI: 10.1016/j.media.2009.05.001.Peer-Reviewed Original ResearchConceptsTensor fieldsDiffusion tensor fieldsPerturbation theoryMarkov random fieldPrior termDifferent spatial directionsRandom fieldsSymmetric tensorsRiemannian distanceSpatial directionsWhite matter fiber bundlesSmoothed fieldsLikelihood termEigenvaluesOriginal fieldEigenvectorsTensorReal-world datasetsDTI datasetsHomogeneous regionsTheoryLow signalNoiseNoise ratioFine structure
2008
Voltage Sensitive Dye Imaging System for Awake and Freely Moving Animals
Park J, Culurciello E, Kim D, Verhagen J, Gautam S, Pieribone V. Voltage Sensitive Dye Imaging System for Awake and Freely Moving Animals. 2008, 89-92. DOI: 10.1109/biocas.2008.4696881.Peer-Reviewed Original ResearchInflow quantification in three‐dimensional cardiovascular MR imaging
Nezafat R, Herzka D, Stehning C, Peters DC, Nehrke K, Manning WJ. Inflow quantification in three‐dimensional cardiovascular MR imaging. Journal Of Magnetic Resonance Imaging 2008, 28: 1273-1279. PMID: 18972337, DOI: 10.1002/jmri.21493.Peer-Reviewed Original Research
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