2025
The first complete 3D reconstruction and morphofunctional mapping of an insect eye
Makarova A, Chua N, Diakova A, Desyatirkina I, Gunn P, Pang S, Xu C, Hess H, Chklovskii D, Polilov A. The first complete 3D reconstruction and morphofunctional mapping of an insect eye. ELife 2025, 14: rp103247. PMID: 40310676, PMCID: PMC12045625, DOI: 10.7554/elife.103247.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCompound Eye, ArthropodEyeFemaleImaging, Three-DimensionalMicroscopy, ElectronWaspsClustering individuals using INMTD: a novel versatile multi-view embedding framework integrating omics and imaging data
Li Z, Windels S, Malod-Dognin N, Weinberg S, Marazita M, Walsh S, Shriver M, Fardo D, Claes P, Pržulj N, Van Steen K. Clustering individuals using INMTD: a novel versatile multi-view embedding framework integrating omics and imaging data. Bioinformatics 2025, 41: btaf122. PMID: 40119919, PMCID: PMC11978392, DOI: 10.1093/bioinformatics/btaf122.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsCluster AnalysisComputational BiologyGenomicsHumansImaging, Three-DimensionalSoftwareConceptsNonnegative matrix tri-factorizationMulti-view clustering methodsClustering methodMulti-view clusteringLow-rank embeddingDrivers of clusteringMatrix tri-factorizationBiologically meaningful interpretationSingle-view approachImage dataAdjusted Rand IndexEmbedding vectorsEmbedding frameworkFacial annotationsOmics dataSynthetic datasetsTri-factorizationRelevant embeddingsRand indexClusters of individualsOmicsComprehensive clusteringEmbeddingCluster individualsExternal qualityPatellar tilt calculation utilizing artificial intelligence on CT knee imaging
Sieberer J, Rancu A, Park N, Desroches S, Manafzadeh A, Tommasini S, Wiznia D, Fulkerson J. Patellar tilt calculation utilizing artificial intelligence on CT knee imaging. The Knee 2025, 54: 217-221. PMID: 40086415, DOI: 10.1016/j.knee.2025.02.019.Peer-Reviewed Original ResearchConceptsPatellar tiltDiagnosis of patellar instabilityMann-Whitney U testInterclass correlation coefficientKruskal-Wallis testCommercial AI algorithmsNo significant differenceCT scanPatellar instabilityMann-WhitneyU testAnatomical landmarksKruskal-WallisPatientsSignificant differencePatellofemoral diseaseConfidence intervalsBonferroni methodDislocation eventsCorrelation coefficientParallel detection of MRI and 1H MRSI for multi‐contrast anatomical and metabolic imaging
de Graaf R, Thomas M, De Feyter H. Parallel detection of MRI and 1H MRSI for multi‐contrast anatomical and metabolic imaging. Magnetic Resonance In Medicine 2025, 94: 497-507. PMID: 40079484, PMCID: PMC12140887, DOI: 10.1002/mrm.30501.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsBrainImage Processing, Computer-AssistedImaging, Three-DimensionalMagnetic Resonance ImagingPhantoms, ImagingProton Magnetic Resonance SpectroscopyRatsConceptsSmall frequency differenceRF pulsesFrequency-selective RF pulsesScan timePulse sequence modificationsWater suppressionFrequency differenceTotal scan timeRats in vivoOverall scan timeLine widthLong scan timesSpectral resolutionPhantom experimentsHigh-contrastMRSI studiesMetabolic imagingCombined MRINominal resolutionMRIMRSIPulseMulti-contrast MRIMulti-contrastScan durationVimentin filament transport and organization revealed by single-particle tracking and 3D FIB-SEM
Renganathan B, Moore A, Yeo W, Petruncio A, Ackerman D, Weigel A, Team T, Pasolli H, Xu C, Shtengel G, Hess H, Serpinskaya A, Zhang H, Lippincott-Schwartz J, Gelfand V. Vimentin filament transport and organization revealed by single-particle tracking and 3D FIB-SEM. Journal Of Cell Biology 2025, 224: e202406054. PMID: 40062969, PMCID: PMC11893169, DOI: 10.1083/jcb.202406054.Peer-Reviewed Original ResearchMeSH KeywordsHumansImaging, Three-DimensionalIntermediate FilamentsMicroscopy, Electron, ScanningMicrotubulesProtein TransportSingle Molecule ImagingVimentinVolume Electron MicroscopyThe development of an artificial intelligence auto-segmentation tool for 3D volumetric analysis of vestibular schwannomas
Jester N, Singh M, Lorr S, Tommasini S, Wiznia D, Buono F. The development of an artificial intelligence auto-segmentation tool for 3D volumetric analysis of vestibular schwannomas. Scientific Reports 2025, 15: 5918. PMID: 39966622, PMCID: PMC11836447, DOI: 10.1038/s41598-025-88589-x.Peer-Reviewed Original ResearchConceptsGround-truth datasetDice scoreVestibular schwannomaImage processing accuracyVolumetric analysisML-based algorithmsMeasuring tumor sizeMean dice scoreAuto-segmentation toolAccurate AIAI modelsTumor sizeTumor modelVS tumorsTumor growthTesting stageAI-LTumorImage processing softwareClinical practicePatient recruitmentProcessing softwareSchwannomaDatasetManual segmentationThree-dimensional Analysis of Patellar Instability: A Review of Current Concepts
Park N, Sieberer J, Manafzadeh A, Fulkerson J. Three-dimensional Analysis of Patellar Instability: A Review of Current Concepts. Sports Medicine And Arthroscopy Review 2025, 33: 7-13. PMID: 40145601, DOI: 10.1097/jsa.0000000000000420.Peer-Reviewed Original ResearchMeSH KeywordsHumansImaging, Three-DimensionalJoint InstabilityPatellaPatellar DislocationPatellofemoral JointTomography, X-Ray Computed
2024
Elucidating subcellular architecture and dynamics at isotropic 100-nm resolution with 4Pi-SIM
Ouyang Z, Wang Q, Li X, Dai Q, Tang M, Shao L, Gou W, Yu Z, Chen Y, Zheng B, Chen L, Ping C, Bi X, Xiao B, Yu X, Liu C, Chen L, Fan J, Huang X, Zhang Y. Elucidating subcellular architecture and dynamics at isotropic 100-nm resolution with 4Pi-SIM. Nature Methods 2024, 22: 335-347. PMID: 39715887, PMCID: PMC11810797, DOI: 10.1038/s41592-024-02515-z.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsHumansImaging, Three-DimensionalMiceMicroscopy, FluorescenceMicroscopy, InterferenceOrganellesTime-Lapse ImagingConceptsIsotropic optical resolutionThree-dimensional structured illumination microscopyStructured illumination microscopyWide-field microscopyDetected wavefrontSimultaneous imagingInterferometric microscopyDynamic behaviorOptical sectioningVolumetric imagesImage distortionOptical resolutionResolutionResolution resultsSANTO: a coarse-to-fine alignment and stitching method for spatial omics
Li H, Lin Y, He W, Han W, Xu X, Xu C, Gao E, Zhao H, Gao X. SANTO: a coarse-to-fine alignment and stitching method for spatial omics. Nature Communications 2024, 15: 6048. PMID: 39025895, PMCID: PMC11258319, DOI: 10.1038/s41467-024-50308-x.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsBreast NeoplasmsEmbryo, MammalianEpigenomicsFemaleGenomicsHumansImaging, Three-DimensionalMiceTranscriptomeTumor MicroenvironmentHead and neck tumor segmentation from [18F]F-FDG PET/CT images based on 3D diffusion model
Dong Y, Gong K. Head and neck tumor segmentation from [18F]F-FDG PET/CT images based on 3D diffusion model. Physics In Medicine And Biology 2024, 69: 155001. PMID: 38959909, PMCID: PMC11302413, DOI: 10.1088/1361-6560/ad5ef2.Peer-Reviewed Original ResearchMeSH KeywordsDiffusionFluorodeoxyglucose F18Head and Neck NeoplasmsHumansImaging, Three-DimensionalPositron Emission Tomography Computed TomographyConceptsTumor segmentationNetwork inputState-of-the-art techniquesState-of-the-artAccurate segmentation resultsSingle-modal dataPET/CT imagingCancer managementChallenge datasetSegmentation masksCT volumesUNet structureSegmentation resultsU-NetCT imagesDiffusion modelCT dataReversal processPrevalent typeTumor maskQuantitative metricsTumorProposed diffusion modelCTNoise volumeAccelerated 3D metabolite T1 mapping of the brain using variable‐flip‐angle SPICE
Zhao Y, Li Y, Guo R, Jin W, Sutton B, Ma C, Fakhri G, Li Y, Luo J, Liang Z. Accelerated 3D metabolite T1 mapping of the brain using variable‐flip‐angle SPICE. Magnetic Resonance In Medicine 2024, 92: 1310-1322. PMID: 38923032, PMCID: PMC12120684, DOI: 10.1002/mrm.30200.Peer-Reviewed Original ResearchConceptsLow-rank tensor modelGeneralized series modelMetabolite TExperimental resultsBrain metabolitesClinically acceptable scan timeEfficient encodingPhantom experimental resultsAcceptable scan timeNoisy dataSparse samplingImaging problemsData processingHealthy subject dataVariable flip angleFlip angleTensor modelSaturation effectsQuantitative metabolic imagingMRSI techniquePhantomScan timeData acquisitionMetabolic imagingT1 mappingSpach Transformer: Spatial and Channel-Wise Transformer Based on Local and Global Self-Attentions for PET Image Denoising
Jang S, Pan T, Li Y, Heidari P, Chen J, Li Q, Gong K. Spach Transformer: Spatial and Channel-Wise Transformer Based on Local and Global Self-Attentions for PET Image Denoising. IEEE Transactions On Medical Imaging 2024, 43: 2036-2049. PMID: 37995174, PMCID: PMC11111593, DOI: 10.1109/tmi.2023.3336237.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsHumansImage Processing, Computer-AssistedImaging, Three-DimensionalNeural Networks, ComputerPositron-Emission TomographySignal-To-Noise RatioConceptsMulti-head self-attentionConvolutional neural networkSelf-attentionSignal-to-noise ratioState-of-the-art deep learning architecturesGlobal self-attentionState-of-the-artLocal feature extractionDeep learning architectureLow signal-to-noise ratioImage denoisingChannel informationChannel-wiseLearning architectureFeature extractionNeural networkTransformation frameworkComputational costReceptive fieldsImage qualityQuantitative meritDenoisingFrameworkQuantitative resultsDatasetA novel approach to craniofacial analysis using automated 3D landmarking of the skull
Wilke F, Matthews H, Herrick N, Dopkins N, Claes P, Walsh S. A novel approach to craniofacial analysis using automated 3D landmarking of the skull. Scientific Reports 2024, 14: 12381. PMID: 38811771, PMCID: PMC11137148, DOI: 10.1038/s41598-024-63137-1.Peer-Reviewed Original ResearchMeSH KeywordsAnatomic LandmarksCone-Beam Computed TomographyFacial BonesFemaleHumansImaging, Three-DimensionalMaleReproducibility of ResultsSkullConceptsHuman skullCone-beam computed tomographyCentroid sizeCranial anatomyBone variationLandmark setsVault regionCraniofacial analysisSkullMorphological researchBone masksEvolutionary underpinningsIntraclass coefficientQuantification of variationCT imageryBone surfaceLandmarksCraniofacial structuresBone phenotypeLevel of concordanceManually placed landmarksShape analysisAutomatic landmarkingSkull scanIndependent observersVariations in the Anatomic Morphology of the Scapular Spine and Implications on Fracture After Reverse Shoulder Arthroplasty
Archambault S, Kakazu R, Jimenez A, Polisetty T, Cusano A, Berthold D, Muench L, Cote M, Slater M, Levy J, Mazzocca A. Variations in the Anatomic Morphology of the Scapular Spine and Implications on Fracture After Reverse Shoulder Arthroplasty. Journal Of The American Academy Of Orthopaedic Surgeons 2024, 32: 712-718. PMID: 38739868, DOI: 10.5435/jaaos-d-22-00557.Peer-Reviewed Original ResearchConceptsReverse shoulder arthroplastyIntraclass correlation coefficientShoulder arthroplastyFracture riskScapular spineIdentification of high-risk patientsScapular spine fracturesHigh-risk patientsIncreased fracture riskControl groupRegression analysisPilot study dataSpine fracturesSurgical indicationsFracture incidenceFracture groupControl cohortAverage agePatientsScapular measurementsStudy dataSpineAnatomical morphologyType IAcromionMotion of VAPB molecules reveals ER–mitochondria contact site subdomains
Obara C, Nixon-Abell J, Moore A, Riccio F, Hoffman D, Shtengel G, Xu C, Schaefer K, Pasolli H, Masson J, Hess H, Calderon C, Blackstone C, Lippincott-Schwartz J. Motion of VAPB molecules reveals ER–mitochondria contact site subdomains. Nature 2024, 626: 169-176. PMID: 38267577, PMCID: PMC10830423, DOI: 10.1038/s41586-023-06956-y.Peer-Reviewed Original ResearchConceptsContact sitesExchange of signaling moleculesInterorganelle communicationOrganelle tetheringEukaryotic cellsSingle-molecule imagingCellular physiologyThree-dimensional electron microscopyMembrane curvatureSignaling moleculesExchange of moleculesDynamic subdomainsNanoscale organizationProtein BMetabolic needsSubdomainsCellsSitesMutationsMoleculesRemodelingSites1,2HomeostasisCommunication hubRegulationEditorial Commentary: Magnetic Resonance Imaging May Underestimate Hip Femoral Version Versus Computed Tomography Scan: Both May Be Optimized Using 3-Dimensional Imaging
Moran J, Jimenez A. Editorial Commentary: Magnetic Resonance Imaging May Underestimate Hip Femoral Version Versus Computed Tomography Scan: Both May Be Optimized Using 3-Dimensional Imaging. Arthroscopy The Journal Of Arthroscopic And Related Surgery 2024, 40: 2411-2412. PMID: 38253294, DOI: 10.1016/j.arthro.2024.01.011.Peer-Reviewed Original ResearchMeSH KeywordsArthroscopyFemoracetabular ImpingementFemurHip JointHumansImaging, Three-DimensionalMagnetic Resonance ImagingTomography, X-Ray ComputedConceptsMagnetic resonance imagingComputed tomographyPreoperative planningTreatment of femoroacetabular impingement syndromeGold standardComputed tomography scanFemoral version measurementsFemoral versionFemoroacetabular impingement syndromeTomography scanPatient positioningLow dosesHip arthroscopyCT imagesImpingement syndromeResonance imagingOptimal outcomesVersion measurementsPatientsIncreased femoral anteversionThree-dimensional imagesImage qualitySyndromeFemoral anteversionDose
2023
Performance and reliability assessment of a lower dose, task-based scoliosis radiography protocol in pediatric patients
Al-Dasuqi K, Taylor E, Ehrlich L, Cooperman D, Socci A, Tuason D, Hoerner M, Staib L, Silva C. Performance and reliability assessment of a lower dose, task-based scoliosis radiography protocol in pediatric patients. Pediatric Radiology 2023, 54: 146-153. PMID: 38010426, DOI: 10.1007/s00247-023-05812-5.Peer-Reviewed Original ResearchMeSH KeywordsChildFemaleHumansImaging, Three-DimensionalMaleRadiographyReproducibility of ResultsRetrospective StudiesScoliosisConceptsDose area productPatient heightAdequate image qualityEffective doseExposure indexMedian effective doseLower radiation exposureComparison of proportionsChi-squared testIntraclass correlation coefficientBland-Altman plotsConsecutive patientsPediatric patientsIncident air kermaDose reductionLow doseSkeletal maturityRadiographsPatientsAir kermaRadiation exposureScoliosis radiographyStatistical significanceDoseSpinal curvatureThree-dimensional reconstructions of mechanosensory end organs suggest a unifying mechanism underlying dynamic, light touch
Handler A, Zhang Q, Pang S, Nguyen T, Iskols M, Nolan-Tamariz M, Cattel S, Plumb R, Sanchez B, Ashjian K, Shotland A, Brown B, Kabeer M, Turecek J, DeLisle M, Rankin G, Xiang W, Pavarino E, Africawala N, Santiago C, Lee W, Xu C, Ginty D. Three-dimensional reconstructions of mechanosensory end organs suggest a unifying mechanism underlying dynamic, light touch. Neuron 2023, 111: 3211-3229.e9. PMID: 37725982, PMCID: PMC10773061, DOI: 10.1016/j.neuron.2023.08.023.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsImaging, Three-DimensionalIon ChannelsMammalsMechanoreceptorsMechanotransduction, CellularMerkel CellsAn atlas of healthy and injured cell states and niches in the human kidney
Lake B, Menon R, Winfree S, Hu Q, Melo Ferreira R, Kalhor K, Barwinska D, Otto E, Ferkowicz M, Diep D, Plongthongkum N, Knoten A, Urata S, Mariani L, Naik A, Eddy S, Zhang B, Wu Y, Salamon D, Williams J, Wang X, Balderrama K, Hoover P, Murray E, Marshall J, Noel T, Vijayan A, Hartman A, Chen F, Waikar S, Rosas S, Wilson F, Palevsky P, Kiryluk K, Sedor J, Toto R, Parikh C, Kim E, Satija R, Greka A, Macosko E, Kharchenko P, Gaut J, Hodgin J, Eadon M, Dagher P, El-Achkar T, Zhang K, Kretzler M, Jain S. An atlas of healthy and injured cell states and niches in the human kidney. Nature 2023, 619: 585-594. PMID: 37468583, PMCID: PMC10356613, DOI: 10.1038/s41586-023-05769-3.Peer-Reviewed Original ResearchMeSH KeywordsCase-Control StudiesCell NucleusGene Expression ProfilingHumansImaging, Three-DimensionalKidneyKidney DiseasesSingle-Cell AnalysisTranscriptomeConceptsCellular statesCell typesMulti-omics approachComplexity of cell typesMultiple single-cellCell atlasTranscriptome profilingBiological pathwaysHuman kidneyCell statesCellular atlasRegulatory factorsSpatial transcriptomicsSingle-cellActive immune responseMolecular signaturesEpithelial repairKidney injuryDiseased human kidneysKidney functionNephron segmentsKidney diseaseImmune responseMolecular profilingCell populationsThree-dimensional imaging of vascular development in the mouse epididymis.
Damon-Soubeyrand C, Bongiovanni A, Chorfa A, Goubely C, Pirot N, Pardanaud L, Piboin-Fragner L, Vachias C, Bravard S, Guiton R, Thomas J, Saez F, Kocer A, Tardivel M, Drevet J, Henry-Berger J. Three-dimensional imaging of vascular development in the mouse epididymis. ELife 2023, 12 PMID: 37310207, PMCID: PMC10264076, DOI: 10.7554/elife.82748.Peer-Reviewed Original ResearchConceptsProtection of spermatozoaComplex immune functionsAccessory tubulesVascular developmentMouse epididymisCellular levelSecretory roleImportant playersMale fertilityMale reproductive systemOrgan clearingMature adult miceReproductive systemTransgenic mouse modelFunctional maturationPeripheral toleranceBlood markersImmune responseLymphatic networkImmune functionKey determinantMouse modelSurvival of spermatozoaAdult miceImmune system
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