2012
Generating live cell data using total internal reflection fluorescence microscopy.
Toomre D. Generating live cell data using total internal reflection fluorescence microscopy. Cold Spring Harbor Protocols 2012, 2012: 439-46. PMID: 22474670, DOI: 10.1101/pdb.ip068676.Peer-Reviewed Original ResearchMeSH KeywordsCell Physiological PhenomenaCytological TechniquesCytoskeletonEndocytosisExocytosisImage Processing, Computer-AssistedMicroscopy, FluorescenceMicroscopy, VideoSpecimen HandlingConceptsTotal internal reflection fluorescence microscopyReflection fluorescence microscopyThinner optical planeDynamic cellular processesFluorescence microscopyLive-cell dataCell fluorescent microscopyRefractive indexHigh numerical aperture objective lensNumerical aperture objective lensMembrane traffickingCytoskeleton dynamicsCellular processesCytoskeleton remodelingCell cortexCell signalingTime-lapse moviesDifferent refractive indicesOrganelle levelTransient intermediate statesMolecular manipulationConventional epifluorescence microscopeDeep imagingEvanescent fieldObjective lens
2011
3-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 ResearchMeSH KeywordsAlgorithmsAnimalsBayes TheoremCalibrationCell LineComputer SimulationImage Processing, Computer-AssistedImaging, Three-DimensionalMicroscopy, FluorescenceMicrotubulesPhantoms, ImagingPotoroidaeReproducibility of ResultsConceptsEvanescent 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 curvatureAn 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 Research
2010
A New Wave of Cellular Imaging
Toomre D, Bewersdorf J. A New Wave of Cellular Imaging. Annual Review Of Cell And Developmental Biology 2010, 26: 285-314. PMID: 20929313, DOI: 10.1146/annurev-cellbio-100109-104048.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsImage Processing, Computer-AssistedMicroscopy, FluorescenceNanotechnologyOrganellesConceptsTransient intermediate statesDiffraction limitTotal internal reflection fluorescence microscopyNanoscopy techniquesEmission depletionStructured illuminationAxial resolutionOptical principlesNanometer resolutionUse of scanningIntermediate stateSingle moleculesCellular imagingReflection fluorescence microscopyBiological applications
2008
Analyzing Protein-Protein Spatial-Temporal Dependencies from Image Sequences Using Fuzzy Temporal Random Sets
Daz M, Ayala G, Len T, Zoncu R, Toomre D. Analyzing Protein-Protein Spatial-Temporal Dependencies from Image Sequences Using Fuzzy Temporal Random Sets. Journal Of Computational Biology 2008, 15: 1221-1236. PMID: 18973437, DOI: 10.1089/cmb.2008.0055.Peer-Reviewed Original ResearchMeSH KeywordsClathrinEndocytosisFuzzy LogicGreen Fluorescent ProteinsImage Processing, Computer-AssistedMicroscopy, FluorescenceModels, BiologicalMonte Carlo MethodProtein Interaction MappingProteinsConceptsTotal internal reflection fluorescence microscopyFluorescent-tagged proteinsReflection fluorescence microscopyEndocytic proteinsBiological questionsPlasma membraneDifferent proteinsFluorescence microscopyProteinSequenceK-functionArea of fluorescenceEndocytosisFree tuning parametersGFPBiologistsColocalizationHigh spatial-temporal resolutionMembraneSpatial-temporal resolutionPoisson cluster modelCellsFluorescence
2006
Two synaptojanin 1 isoforms are recruited to clathrin-coated pits at different stages
Perera RM, Zoncu R, Lucast L, De Camilli P, Toomre D. Two synaptojanin 1 isoforms are recruited to clathrin-coated pits at different stages. Proceedings Of The National Academy Of Sciences Of The United States Of America 2006, 103: 19332-19337. PMID: 17158794, PMCID: PMC1693868, DOI: 10.1073/pnas.0609795104.Peer-Reviewed Original ResearchMeSH KeywordsAcyltransferasesAnimalsChlorocebus aethiopsClathrin-Coated VesiclesCOS CellsImage Processing, Computer-AssistedMicroscopy, FluorescenceNerve Tissue ProteinsPhosphoric Monoester HydrolasesProtein IsoformsConceptsTotal internal reflection fluorescence microscopySynaptojanin 1CCP formationMulticolor total internal reflection fluorescence microscopyClathrin-coated pit dynamicsClathrin-coated pitsClathrin-dependent endocytosisEndocytic clathrin adaptorsSynaptic vesicle recyclingReflection fluorescence microscopyCell-free systemClathrin adaptorsPolyphosphoinositide phosphataseGenetic manipulationVesicle recyclingPit dynamicsIntact cellsSplice variantsFunctional studiesFluorescence microscopyEndophilinTemporal recruitmentDirect interactionIsoformsPredominant isoformAnalysis of spatial dependencies of endocytic proteins based on temporal random sets
Sebastian R, Diaz M, Ayala G, Zoncu R, Toomre D. Analysis of spatial dependencies of endocytic proteins based on temporal random sets. Annual International Conference Of The IEEE Engineering In Medicine And Biology Society (EMBC) 2006, 2006: 4175-4178. PMID: 17946228, DOI: 10.1109/iembs.2006.260479.Peer-Reviewed Original ResearchMeSH KeywordsCell Physiological PhenomenaClathrinEndocytosisImage Processing, Computer-AssistedMonte Carlo MethodProteins