{"lab": {"uuid": "eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb", "correspondence": [{"contact_email": "emh1YW5nQGNoZW1pc3RyeS5oYXJ2YXJkLmVkdQ==", "@id": "/users/acfc5a08-19ff-47ef-9261-75e6134dc0fe/", "display_title": "Xiaowei Zhuang"}], "display_title": "Xiaowei Zhuang, HARVARD", "status": "current", "@id": "/labs/xiaowei-zhuang-lab/", "@type": ["Lab", "Item"], "title": "Xiaowei Zhuang, HARVARD", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb"]}}, "name": "9a4086c5-ec74-4e84-b00a-7661505e1273", "award": {"project": "4DN", "@id": "/awards/1UM1HG011585-01/", "@type": ["Award", "Item"], "center_title": "CDIMV - Ren", "status": "current", "uuid": "ee89349a-1d43-4048-9142-bc750f0f3b32", "name": "1UM1HG011585-01", "display_title": "CENTER FOR INTEGRATED MULTI-MODAL AND MULTI-SCALE NUCLEOME RESEARCH", "description": "CDIMV: The transcriptional regulatory sequences communicate with each other dynamically in the 3D nuclear space to direct cell type specific gene expression. Currently, a major barrier to understanding the transcriptional regulatory programs is the lack of tools, models and maps to explore the chromatin architecture in diverse cell types and physiological contexts. We will address this pressing need by deploying transformative technologies to study the chromatin architecture in mammalian cells at an unprecedented resolution and scale. Specifically, we will generate navigable, cell-type-specific reference maps of chromatin architecture in the mouse, macaque and human brains by integrating high resolution and high throughput imaging and orthogonal single-cell-based genomic methods. We will also dissect the role of chromatin architecture in gene regulation through a set of controlled perturbation experiments in the mouse ES cells (ESC) and ESC-derived neural progenitor cells (NPC). We will develop structural models of chromatin organization with advanced polymer physics and statistical learning methods, and validate their predictive power in embryonic stem cells and in ex vivo brain slices. Finally, we will make the reference maps, analytical tools, visualization methods and structural models available to the broader community. The proposed research project will dramatically transform our ability to analyze the 4D Nucleome of complex tissues, and produce the much-needed maps, tools and models for understanding the gene regulatory programs encoded in the linear genome sequences.", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Harvard-Zhuang_lab_CT-STORM_Nikon_Eclipse_Ti-U_Liu-2023_Scope1", "status": "released", "microscope": {"ID": "126c3266-1d3c-4648-9874-973134eabd7d", "Name": "Harvard-Zhuang_lab_CT-STORM_Nikon_Eclipse_Ti-U_Liu-2023_Scope1", "Tier": 3, "Schema_ID": "Instrument.json", "AppVersion": "1.7.28-b1", "components": [{"ID": "dd0844db-fb5a-41e1-86ce-7509b306b0a7", "Name": "storm-control software", "Tier": 1, "Width": 196.72982, "Domain": "MicroscopeSpecifications", "Height": 172.67928999999998, "OffsetX": 1427.3280029296875, "OffsetY": 0, "Version": "v2019.06.28", "Category": "Software", "Language": "Phython", "Developer": "Hazen Babcock and Xiaowei Zhuang\u2019s laboratory", "Extension": "Basic", "PositionX": 1521.3412199999998, "PositionY": 518.2828549999999, "PositionZ": 0, "Schema_ID": "AcquisitionSoftware.json", "OpenSource": true, "WebsiteURL": "https://github.com/ZhuangLab/ storm-control", "Description": " This software provides an intuitive GUI control system and Python wrappers to integrate and control many widely used optical components, including various motorized stages, piezo stages, AOTFs, laser systems and cameras. The software also supports timing integration and communicates with the fluidics control software.", "ModelVersion": "2.01.1", "OccupiedSpot": "Software.AcquisitionSoftware_1", "SoftwareModule": ["na", "na", "na", "na"], "PrimaryPublicationID": "10.5281/zenodo.3264857"}, {"ID": "07edf1d9-145f-494e-a057-94be4b34cc7c", "DIC": true, "Iris": false, "Name": "Copy of 60x/1.4 Plan Apo ", "Tier": 1, "Model": "CFI Plan Apo Lambda 60x oil", "Width": 26.676789999999997, "Domain": "MicroscopeHardwareSpecifications", "Height": 58.123099999999994, "LensNA": 1.4, "OffsetX": 0, "OffsetY": 0, "Category": "Magnification", "Extension": "Core", "LightType": "Visible", "LotNumber": ":unav", "PositionX": 584.021165, "PositionY": 398.96327, "PositionZ": 0, "Schema_ID": "Objective.json", "Correction": "PlanApo", "Manufacturer": "Nikon", "ModelVersion": "2.01.1", "OccupiedSpot": "Magnification.Objective_0", "CatalogNumber": "MRD01605", "ImageDistance": -1, "ImmersionType": "Mineral Oil", "Magnification": 60, "WorkingDistance": 0.13, "CorrectionCollar": false, "ImageDistanceUnit": "mm", "InfinityCorrected": true, "ContrastModulation": "None", "ObjectiveViewField": 25, "BackFocalLengthUnit": "mm", "WorkingDistanceUnit": "mm", "FrontFocalLengthUnit": "mm", "ParfocalizingDistanceUnit": "mm"}, {"ID": "ff13a9f1-d303-460e-83e3-977eadb7cd45", "Name": "Copy of ORCA-Flash4.0 V3 Digital CMOS camera", "Tier": 1, "Type": "Scientific", "Color": "no-color", "Model": "ORCA-Flash4.0 V3", "Mount": "C-mount", "Width": 85.28099999999999, "Domain": "MicroscopeHardwareSpecifications", "Height": 85.45949999999999, "OffsetX": 0, "OffsetY": 0, "Category": "Detector.Camera", "Extension": "Basic ", "LotNumber": ":unav", "PositionX": 131.53616, "PositionY": 605.32677, "PositionZ": 0, "RelayLens": "na", "Schema_ID": "CMOS.json", "SpecsFile": "https://www.hamamatsu.com/eu/en/product/cameras/cmos-cameras/C13440-20CU.html", "ArrayWidth": 2048, "PixelWidth": 6.5, "ArrayHeight": 2048, "MaxBitDepth": "16bit", "PixelHeight": 6.5, "DynamicRange": 45.7, "Illumination": "Front", "Manufacturer": "Hamamatsu", "ModelVersion": "2.01.1", "OccupiedSpot": "Detector.Camera_1", "ReadOutNoise": 1.64, "CatalogNumber": "C13440-20CU", "ReadNoiseUnit": "e- rms", "PixelWidthUnit": "\u00b5m", "DarkCurrentRate": 0.06, "PixelHeightUnit": "\u00b5m", "DynamicRangeUnit": "decibel (dB)", "MaximumFrameRate": 100, "PixelWellCapacity": 30000, "QuantumEfficiency": 0.82, "DetectorNoiseModel": "Other", "MaximumReadoutRate": -1, "DarkCurrentRateUnit": "e-/Pixel/sec", "MaximumFrameRateUnit": "fps", "PixelWellCapacityUnit": "e-", "MaximumReadoutRateUnit": "MHz", "VerticalClockSpeedUnit": "\u00b5s", "ElectronicConversionFactor": 0.47, "AmbientOperatingTemperature": 25, "Max_Number_Of_WavelengthRange": -1, "Min_Number_Of_WavelengthRange": 0, "AmbientOperatingTemperatureUnit": "\u00b0C", "Current_Number_Of_WavelengthRange": 0}, {"ID": "6bb6e324-eab4-4926-9fc5-8e232b33899a", "Name": "Copy of Focus Lock: CMOS Monochrome Sensor ", "Tier": 1, "Type": "Scientific", "Color": "no-color", "Model": ":unav", "Mount": "Other", "Width": 60.13655965106278, "Domain": "MicroscopeHardwareSpecifications", "Height": 60.26243031273084, "OffsetX": 1795.9166259765625, "OffsetY": 54.421714782714844, "Category": "Detector.Camera", "Extension": "Basic ", "LotNumber": ":unav", "PositionX": 2133.5416381835935, "PositionY": 645.0252003479004, "PositionZ": 0, "RelayLens": "na", "Schema_ID": "CMOS.json", "ArrayWidth": -1, "PixelWidth": -1, "ArrayHeight": -1, "MaxBitDepth": "8bit", "PixelHeight": -3.55, "DynamicRange": 69, "Illumination": "Front", "Manufacturer": "Thorlabs Inc.", "ModelVersion": "2.01.1", "ReadOutNoise": -1, "CatalogNumber": "uc480", "ReadNoiseUnit": "e- rms", "PixelWidthUnit": "\u00b5m", "DarkCurrentRate": -1, "PixelHeightUnit": "\u00b5m", "WavelengthRange": [{"CutOn": -1, "CutOff": -1, "CutOnUnit": "nm", "CutOffUnit": "nm", "WavelengthProfile": "-1"}], "DynamicRangeUnit": "decibel (dB)", "MaximumFrameRate": -1, "PixelWellCapacity": -1, "QuantumEfficiency": -1, "DetectorNoiseModel": "Gaussian", "MaximumReadoutRate": -1, "DarkCurrentRateUnit": "e-/Pixel/sec", "MaximumFrameRateUnit": "fps", "PixelWellCapacityUnit": "e-", "MaximumReadoutRateUnit": "MHz", "VerticalClockSpeedUnit": "\u00b5s", "ElectronicConversionFactor": -1, "AmbientOperatingTemperature": 25, "Max_Number_Of_WavelengthRange": -1, "Min_Number_Of_WavelengthRange": 0, "AmbientOperatingTemperatureUnit": "\u00b0C", "Current_Number_Of_WavelengthRange": 1}, {"ID": "992ff2dc-84d8-4052-a1e7-4e1e50276b71", "Name": "Copy of Optical fiber", "Tier": 2, "Type": "Fiber optics", "Model": ":unav", "Width": 79.07199999999999, "Domain": "MicroscopeHardwareSpecifications", "Height": 30.15516, "OffsetX": 703.5386962890625, "OffsetY": 0, "Category": "LightSourceCoupling", "Diameter": 0.8, "Extension": "Basic", "LotNumber": ":unav", "PositionX": 887.9911599999999, "PositionY": 516.00621, "PositionZ": 0, "Schema_ID": "LightGuide.json", "SpecsFile": ":unav", "SingleMode": true, "Attenuation": -1, "CouplingLens": "na", "DiameterUnit": "\u00b5m", "Manufacturer": "Lumencor (OEM=:unav)", "ModelVersion": "2.01.1", "OccupiedSpot": "LightSourceCoupling.LightGuide_1", "CatalogNumber": ":unav", "Transmittance": -1, "NumericalAperture": -1, "AcceptanceAngleUnit": "deg", "Max_Number_Of_WavelengthRange": -1, "Min_Number_Of_WavelengthRange": 0, "Current_Number_Of_WavelengthRange": 0}, {"ID": "4ed8ce33-dd61-49c2-bc67-7eca7868b946", "Name": "Copy of Focus Lock: SM Fiber-Pigtail for Laser Diode", "Tier": 2, "Type": "Fiber optics", "Model": "Single Mode Fiber: 980 to 1650 nm", "Width": 79.07199999999999, "Domain": "MicroscopeHardwareSpecifications", "Height": 30.15516, "OffsetX": 1795.9166259765625, "OffsetY": 54.421714782714844, "Category": "LightSourceCoupling", "Diameter": 125, "Extension": "Basic", "PositionX": 1829.7416381835935, "PositionY": 675.1252003479003, "PositionZ": 0, "Schema_ID": "LightGuide.json", "SpecsFile": "https://www.thorlabs.com/newgrouppage9.cfm?objectgroup_id=949&pn=SM980-5.8-125#1370", "SingleMode": true, "Attenuation": 2, "CouplingLens": "na", "DiameterUnit": "mm", "Manufacturer": "Thorlabs Inc.", "ModelVersion": "2.01.1", "CatalogNumber": "SM980-5.8-125", "WavelengthRange": [{"CutOn": 980, "CutOff": 1550, "CutOnUnit": "nm", "CutOffUnit": "nm", "PeakWavelength": 980, "PeakWavelengthUnit": "nm"}], "NumericalAperture": 0.15, "AcceptanceAngleUnit": "deg", "Max_Number_Of_WavelengthRange": -1, "Min_Number_Of_WavelengthRange": 0, "Current_Number_Of_WavelengthRange": 1}, {"ID": "68332d8c-428a-452f-828b-5df9e87fedaf", "Name": "Copy of Vis Port Filter Cube", "Tier": 1, "Model": "Nikon Ti-2 Filter Cube", "Width": 49.31801, "Domain": "MicroscopeHardwareSpecifications", "Height": 48.93434, "OffsetX": 250.02439880371094, "OffsetY": 49.68939208984375, "Category": "FluorescenceLightPath", "Extension": "Core", "LotNumber": ":unav", "PositionX": 566.1473649999999, "PositionY": 523.79035, "PositionZ": 0, "Schema_ID": "FilterCube.json", "SpecsFile": ":unav", "Manufacturer": "Chroma", "ModelVersion": "2.01.1", "OccupiedSpot": "FluorescenceLightPath.FilterCube_2", "CatalogNumber": "91054", "EmissionFilter": "na", "ExcitationFilter": "na", "StandardDichroic": "na"}, {"ID": "3248dd91-d349-4202-9b0b-950f4c0d25e9", "Name": "Ludl Flat Top Stage for Nikon Ti2-U", "Tier": 1, "Type": "Linear", "Model": ":unav", "Width": 216.29999999999998, "Domain": "MicroscopeHardwareSpecifications", "Height": 17.5, "BuiltIn": false, "Encoded": "Linear", "OffsetX": 254.01600646972656, "OffsetY": 0, "Category": "SamplePositioning.Stage", "Extension": "Basic", "LotNumber": ":unav", "Motorized": true, "PositionX": 573.45113, "PositionY": 370.95052999999996, "PositionZ": 0, "Schema_ID": "MechanicalStage.json", "ZResolution": 0, "Manufacturer": "Ludl Electronic Products Ltd.", "ModelVersion": "2.01.1", "MovementAxes": "Z", "OccupiedSpot": "SamplePositioning.Stage.MechanicalStage_1", "XTravelRange": -4, "XYResolution": -1, "YTravelRange": -1, "ZMaxVelocity": 0, "ZTravelRange": 0, "CatalogNumber": ":unav", "XYMaxVelocity": -1, "ZRepeatability": 0, "XYRepeatability": -1, "ZResolutionUnit": "nm", "XTravelRangeUnit": "mm", "YTravelRangeUnit": "mm", "ZMaxVelocityUnit": "nm/s", "ZTravelRangeUnit": "\u00b5m", "RotationAngleUnit": "deg", "XYMaxVelocityUnit": "nm/s", "XYZResolutionUnit": "\u00b5m", "ZSettlingTimeUnit": "ms", "XYSettlingTimeUnit": "ms", "ZRepeatabilityUnit": "\u00b5m", "XYRepeatabilityUnit": "\u00b5m"}, {"ID": "910150cc-dfef-4061-96f5-a268b92229d4", "Name": "Copy of CELESTA Light Engine", "Tier": 2, "Laser": ["Fluorescence_LightSource_Laser/7fc302b2-b284-4619-8546-a0437ffd0f8e", "Fluorescence_LightSource_Laser/d768b84a-a51a-46dc-b6db-6a908ea38f38", "Fluorescence_LightSource_Laser/aea24f0a-cfa8-437a-954b-04415e6749eb", "Fluorescence_LightSource_Laser/02ace641-3e69-4baf-ab7c-0cafbf2330e4", "Fluorescence_LightSource_Laser/5c7c42ce-3433-4f96-bd47-af8ea23f2641"], "Model": "CELESTA Light Engine", "Width": 363.08943999999997, "Domain": "MicroscopeHardwareSpecifications", "Height": 73.5, "OffsetX": 703.5386962890625, "OffsetY": 0, "Category": "Fluorescence_LightSource", "Extension": "Advanced", "LotNumber": ":unav", "PositionX": 960.65725, "PositionY": 486.91504999999995, "PositionZ": 1, "Schema_ID": "Fluorescence_LightSource_MultiLaserEngine.json", "SpecsFile": "https://lumencor.com/products/celesta-light-engine", "SingleMode": true, "Manufacturer": "Lumencor", "ModelVersion": "2.01.1", "OccupiedSpot": "Fluorescence_LightSource.MultiLaserEngine_1", "PurchaseDate": "2020", "CatalogNumber": ":unav", "NumberOfLasers": 5, "OutputPortNumber": 1, "MultiportSwitchTime": 100, "MultiportSwitchTimeUnit": "\u00b5s", "IlluminationPowerReportingPosition": "Back of the Microscope Stand", "IlluminationPowerReportingStatistic": "Average"}, {"ID": "bf3ee059-0eb2-41ad-8aff-8c7b7d7648d4", "Name": "421/491/567/659/776 nm penta-edge dichroic beamsplitter ", "Tier": 1, "Type": "MultiPass", "Model": "421/491/567/659/776 nm BrightLine\u00ae penta-edge standard epi-fluorescence dichroic beamsplitter ", "Width": 25.941579999999995, "Domain": "MicroscopeHardwareSpecifications", "Height": 26.80678, "OffsetX": 0, "OffsetY": 54.421714782714844, "Category": "FluorescenceLightPath", "Extension": "Core", "PositionX": 578.52116, "PositionY": 535.61916, "PositionZ": 1, "Schema_ID": "StandardDichroic.json", "SpecsFile": "https://www.idex-hs.com/store/product-detail/ff421_491_567_659_776_di01_25x36/fl-410491", "MirrorType": "Planar", "Technology": "Thin-film interference-coating", "Manufacturer": "IDEX Health & Science", "ModelVersion": "2.01.1", "OccupiedSpot": "FilterCube_68332d8c-428a-452f-828b-5df9e87fedaf_FluorescenceLightPath.StandardDichroic_1", "CatalogNumber": "Semrock Part Number: FF421/491/567/659/776-Di01-25x36  IDEX Part Number: FL-410491", "CoatingMethod": "HardCoated", "AttenuationMethod": "Reflection", "LightPathLocation": "Infinity space", "TransmittanceRange": [{"Wavelength": 421, "FWHMBandwidth": -1, "Transmittance": 0.96, "WavelengthUnit": "nm"}, {"Wavelength": 491, "FWHMBandwidth": -1, "Transmittance": 0.97, "WavelengthUnit": "nm"}, {"Wavelength": 567, "FWHMBandwidth": -1, "Transmittance": 0.98, "WavelengthUnit": "nm"}, {"Wavelength": 659, "FWHMBandwidth": -1, "Transmittance": 0.98, "WavelengthUnit": "nm"}, {"Wavelength": 776, "FWHMBandwidth": -1, "Transmittance": 0.99, "WavelengthUnit": "nm"}], "AngleOfIncidenceUnit": "deg", "Max_Number_Of_ReflectanceRange": -1, "Min_Number_Of_ReflectanceRange": 0, "Max_Number_Of_TransmittanceRange": -1, "Min_Number_Of_TransmittanceRange": 1, "Current_Number_Of_ReflectanceRange": 0, "Current_Number_Of_TransmittanceRange": 5}, {"ID": "0d3d626d-36d3-494c-900e-5593b726de9b", "Name": "Copy of 405 Laser", "Pump": "na", "Tier": 1, "Type": "SolidState", "Model": ":unav", "Pulse": false, "Width": 45.50756, "Domain": "MicroscopeHardwareSpecifications", "Height": 48.53233, "IsPump": false, "OffsetX": 703.5386962890625, "OffsetY": 0, "Category": "Fluorescence_LightSource", "IsPumped": false, "Position": 1, "Tuneable": false, "Extension": "Core", "LotNumber": ":unav", "PositionX": 999.90128, "PositionY": 499.36661499999997, "PositionZ": 2, "Schema_ID": "Fluorescence_LightSource_Laser.json", "SpecsFile": "https://cms.lumencor.com/system/uploads/fae/file/asset/34/CELESTA_Light_Engine.pdf?_gl=1*1v0vlp2*_ga*MTI1OTQ3MjA0OC4xNjEwNzY2MjE5*_ga_364GJZVK77*MTY2NTAwNTc5MC4xLjEuMTY2NTAwNzI0My4yNi4wLjA.", "Manufacturer": "Lumencor (OEM=:unav)", "ModelVersion": "2.01.1", "OccupiedSpot": "MultiLaserEngine_910150cc-dfef-4061-96f5-a268b92229d4_Fluorescence_LightSource.Laser_0", "PurchaseDate": "2019", "CatalogNumber": ":unav", "PulseDurationUnit": "ms", "RepetitionRateUnit": "Hz", "ModulationMechanism": "Direct", "UsedAcoustoOpticalDevice": false, "IlluminationWavelengthRange": [{"CutOnUnit": "nm", "CutOffUnit": "nm", "PeakWavelength": 405, "IlluminationPower": 800, "PeakWavelengthUnit": "nm", "IlluminationPowerUnit": "mW"}], "IlluminationPowerReportingPosition": "Back of the Microscope Stand", "IlluminationPowerReportingStatistic": "Average", "Max_Number_Of_IlluminationWavelengthRange": -1, "Min_Number_Of_IlluminationWavelengthRange": 0, "Current_Number_Of_IlluminationWavelengthRange": 1}, {"ID": "4f6deb72-7427-4169-aeef-00dc67d5546d", "Name": "Copy of 477 Laser", "Pump": "na", "Tier": 1, "Type": "SolidState", "Model": ":unav", "Pulse": false, "Width": 45.50756, "Domain": "MicroscopeHardwareSpecifications", "Height": 48.53233, "IsPump": false, "OffsetX": 703.5386962890625, "OffsetY": 0, "Category": "Fluorescence_LightSource", "IsPumped": false, "Position": 1, "Tuneable": false, "Extension": "Core", "LotNumber": ":unav", "PositionX": 1053.45128, "PositionY": 499.36661499999997, "PositionZ": 2, "Schema_ID": "Fluorescence_LightSource_Laser.json", "SpecsFile": "https://cms.lumencor.com/system/uploads/fae/file/asset/34/CELESTA_Light_Engine.pdf?_gl=1*1v0vlp2*_ga*MTI1OTQ3MjA0OC4xNjEwNzY2MjE5*_ga_364GJZVK77*MTY2NTAwNTc5MC4xLjEuMTY2NTAwNzI0My4yNi4wLjA.", "Manufacturer": "Lumencor (OEM=:unav)", "ModelVersion": "2.01.1", "OccupiedSpot": "MultiLaserEngine_910150cc-dfef-4061-96f5-a268b92229d4_Fluorescence_LightSource.Laser_1", "PurchaseDate": "2019", "CatalogNumber": ":unav", "PulseDurationUnit": "ms", "RepetitionRateUnit": "Hz", "ModulationMechanism": "Direct", "UsedAcoustoOpticalDevice": false, "IlluminationWavelengthRange": [{"CutOnUnit": "nm", "CutOffUnit": "nm", "PeakWavelength": 477, "IlluminationPower": 800, "PeakWavelengthUnit": "nm", "IlluminationPowerUnit": "mW"}], "IlluminationPowerReportingPosition": "Back of the Microscope Stand", "IlluminationPowerReportingStatistic": "Average", "Max_Number_Of_IlluminationWavelengthRange": -1, "Min_Number_Of_IlluminationWavelengthRange": 0, "Current_Number_Of_IlluminationWavelengthRange": 1}, {"ID": "e27ffa27-42c0-44a1-bf90-c953f0aa00fa", "Name": "Copy of 546 Laser", "Pump": "na", "Tier": 1, "Type": "SolidState", "Model": ":unav", "Pulse": false, "Width": 45.50756, "Domain": "MicroscopeHardwareSpecifications", "Height": 48.53233, "IsPump": false, "OffsetX": 703.5386962890625, "OffsetY": 0, "Category": "Fluorescence_LightSource", "IsPumped": false, "Position": 1, "Tuneable": false, "Extension": "Core", "LotNumber": ":unav", "PositionX": 1107.00128, "PositionY": 499.36661499999997, "PositionZ": 2, "Schema_ID": "Fluorescence_LightSource_Laser.json", "SpecsFile": "https://cms.lumencor.com/system/uploads/fae/file/asset/34/CELESTA_Light_Engine.pdf?_gl=1*1v0vlp2*_ga*MTI1OTQ3MjA0OC4xNjEwNzY2MjE5*_ga_364GJZVK77*MTY2NTAwNTc5MC4xLjEuMTY2NTAwNzI0My4yNi4wLjA.", "Manufacturer": "Lumencor (OEM=:unav)", "ModelVersion": "2.01.1", "OccupiedSpot": "MultiLaserEngine_910150cc-dfef-4061-96f5-a268b92229d4_Fluorescence_LightSource.Laser_2", "PurchaseDate": "2019", "CatalogNumber": ":unav", "PulseDurationUnit": "ms", "RepetitionRateUnit": "Hz", "ModulationMechanism": "Direct", "UsedAcoustoOpticalDevice": false, "IlluminationWavelengthRange": [{"CutOnUnit": "nm", "CutOffUnit": "nm", "PeakWavelength": 546, "IlluminationPower": 800, "PeakWavelengthUnit": "nm", "IlluminationPowerUnit": "mW"}], "IlluminationPowerReportingPosition": "Back of the Microscope Stand", "IlluminationPowerReportingStatistic": "Average", "Max_Number_Of_IlluminationWavelengthRange": -1, "Min_Number_Of_IlluminationWavelengthRange": 0, "Current_Number_Of_IlluminationWavelengthRange": 1}, {"ID": "7ffdd0cc-98a5-41a2-8798-ffc9c1080c99", "Name": "Copy of 638 Laser", "Pump": "na", "Tier": 1, "Type": "SolidState", "Model": ":unav", "Pulse": false, "Width": 45.50756, "Domain": "MicroscopeHardwareSpecifications", "Height": 48.53233, "IsPump": false, "OffsetX": 703.5386962890625, "OffsetY": 0, "Category": "Fluorescence_LightSource", "IsPumped": false, "Position": 1, "Tuneable": false, "Extension": "Core", "LotNumber": ":unav", "PositionX": 1160.55128, "PositionY": 499.36661499999997, "PositionZ": 2, "Schema_ID": "Fluorescence_LightSource_Laser.json", "SpecsFile": "https://cms.lumencor.com/system/uploads/fae/file/asset/34/CELESTA_Light_Engine.pdf?_gl=1*1v0vlp2*_ga*MTI1OTQ3MjA0OC4xNjEwNzY2MjE5*_ga_364GJZVK77*MTY2NTAwNTc5MC4xLjEuMTY2NTAwNzI0My4yNi4wLjA.", "Manufacturer": "Lumencor (OEM=:unav)", "ModelVersion": "2.01.1", "OccupiedSpot": "MultiLaserEngine_910150cc-dfef-4061-96f5-a268b92229d4_Fluorescence_LightSource.Laser_3", "PurchaseDate": "2019", "CatalogNumber": ":unav", "PulseDurationUnit": "ms", "RepetitionRateUnit": "Hz", "ModulationMechanism": "Direct", "UsedAcoustoOpticalDevice": false, "IlluminationWavelengthRange": [{"CutOnUnit": "nm", "CutOffUnit": "nm", "PeakWavelength": 638, "IlluminationPower": 800, "PeakWavelengthUnit": "nm", "IlluminationPowerUnit": "mW"}], "IlluminationPowerReportingPosition": "Back of the Microscope Stand", "IlluminationPowerReportingStatistic": "Average", "Max_Number_Of_IlluminationWavelengthRange": -1, "Min_Number_Of_IlluminationWavelengthRange": 0, "Current_Number_Of_IlluminationWavelengthRange": 1}, {"ID": "e0b2d09c-ab6b-4d76-bdab-905777b7eceb", "Name": "Copy of 749 Laser", "Pump": "na", "Tier": 1, "Type": "SolidState", "Model": ":unav", "Pulse": false, "Width": 45.50756, "Domain": "MicroscopeHardwareSpecifications", "Height": 48.53233, "IsPump": false, "OffsetX": 703.5386962890625, "OffsetY": 0, "Category": "Fluorescence_LightSource", "IsPumped": false, "Position": 1, "Tuneable": false, "Extension": "Core", "LotNumber": ":unav", "PositionX": 1214.10128, "PositionY": 499.36661499999997, "PositionZ": 2, "Schema_ID": "Fluorescence_LightSource_Laser.json", "SpecsFile": "https://cms.lumencor.com/system/uploads/fae/file/asset/34/CELESTA_Light_Engine.pdf?_gl=1*1v0vlp2*_ga*MTI1OTQ3MjA0OC4xNjEwNzY2MjE5*_ga_364GJZVK77*MTY2NTAwNTc5MC4xLjEuMTY2NTAwNzI0My4yNi4wLjA.", "Manufacturer": "Lumencor (OEM=:unav)", "ModelVersion": "2.01.1", "OccupiedSpot": "MultiLaserEngine_910150cc-dfef-4061-96f5-a268b92229d4_Fluorescence_LightSource.Laser_4", "PurchaseDate": "2019", "CatalogNumber": ":unav", "PulseDurationUnit": "ms", "RepetitionRateUnit": "Hz", "ModulationMechanism": "Direct", "UsedAcoustoOpticalDevice": false, "IlluminationWavelengthRange": [{"CutOnUnit": "nm", "CutOffUnit": "nm", "PeakWavelength": 749, "IlluminationPower": 800, "PeakWavelengthUnit": "nm", "IlluminationPowerUnit": "mW"}], "IlluminationPowerReportingPosition": "Back of the Microscope Stand", "IlluminationPowerReportingStatistic": "Average", "Max_Number_Of_IlluminationWavelengthRange": -1, "Min_Number_Of_IlluminationWavelengthRange": 0, "Current_Number_Of_IlluminationWavelengthRange": 1}, {"ID": "c8d31dd2-5939-46f2-ac0f-135099e6fe46", "Name": "Copy of Focus Lock: Fiber-Pigtailed Laser Diode", "Pump": "na", "Tier": 1, "Type": "SemiconductorLaserDiode", "Model": "980 nm, 15 mW, E Pin Code, SM Fiber-Pigtailed Laser Diode, FC/PC ", "Pulse": false, "Width": 45.50756, "Domain": "MicroscopeHardwareSpecifications", "Height": 48.53233, "IsPump": false, "OffsetX": 1795.9166259765625, "OffsetY": 54.421714782714844, "Category": "Fluorescence_LightSource", "IsPumped": false, "Tuneable": false, "Extension": "Core", "LotNumber": ":unav", "PositionX": 1744.3416381835937, "PositionY": 661.8252003479004, "PositionZ": 0, "Schema_ID": "Fluorescence_LightSource_Laser.json", "SpecsFile": "https://www.thorlabs.com/thorproduct.cfm?partnumber=LP980-SF15", "Description": "\u00d85.6 mm SM Pigtail, FC/PC", "Manufacturer": "Thorlabs", "ModelVersion": "2.01.1", "PurchaseDate": "2017", "CatalogNumber": "LP980-SF15", "PulseDurationUnit": "ms", "RepetitionRateUnit": "Hz", "ModulationMechanism": "None", "UsedAcoustoOpticalDevice": false, "IlluminationWavelengthRange": [{"CutOff": -15, "CutOnUnit": "nm", "CutOffUnit": "nm", "PeakWavelength": 980, "IlluminationPower": 15, "PeakWavelengthUnit": "nm", "IlluminationPowerUnit": "mW"}], "IlluminationPowerReportingPosition": "Source", "IlluminationPowerReportingStatistic": "Maximum", "Max_Number_Of_IlluminationWavelengthRange": -1, "Min_Number_Of_IlluminationWavelengthRange": 0, "Current_Number_Of_IlluminationWavelengthRange": 1}, {"ID": "37c83861-af91-4af7-8b16-03c687f065a3", "Name": "441/511/593/684/817 penta-band bandpass filter", "Tier": 1, "Type": "MultiPass", "Model": "441/511/593/684/817 nm BrightLine\u00ae penta-band bandpass filter", "Width": 31.628939999999997, "Domain": "MicroscopeHardwareSpecifications", "Height": 17.5, "OffsetX": 0, "OffsetY": 54.421714782714844, "Category": "FluorescenceLightPath", "Extension": "Core", "PositionX": 575.21247, "PositionY": 563.0208, "PositionZ": 1, "Schema_ID": "EmissionFilter.json", "SpecsFile": "https://www.idex-hs.com/store/product-detail/ff01_441_511_593_684_817_25/fl-410484", "Technology": "Thin-film interference-coating", "Manufacturer": "IDEX Health & Science", "ModelVersion": "2.01.1", "OccupiedSpot": "FilterCube_68332d8c-428a-452f-828b-5df9e87fedaf_FluorescenceLightPath.EmissionFilter_1", "CatalogNumber": "Semrock Part Number: FF01-441/511/593/684/817-25; IDEX Part Number: FL-410484", "CoatingMethod": "HardCoated", "AttenuationMethod": "Reflection", "LightPathLocation": "Infinity space", "TransmittanceRange": [{"Wavelength": 44130, "FWHMBandwidth": 36.1, "Transmittance": 0.96, "WavelengthUnit": "nm"}, {"Wavelength": 511, "FWHMBandwidth": 34.3, "Transmittance": 0.96, "WavelengthUnit": "nm"}, {"Wavelength": 592.5, "FWHMBandwidth": 45.2, "Transmittance": 0.96, "WavelengthUnit": "nm"}, {"Wavelength": 684, "FWHMBandwidth": 44.4, "Transmittance": 0.96, "WavelengthUnit": "nm"}, {"Wavelength": 817, "FWHMBandwidth": 78.8, "Transmittance": 0.99, "WavelengthUnit": "nm"}], "Max_Number_Of_TransmittanceRange": -1, "Min_Number_Of_TransmittanceRange": 1, "Current_Number_Of_TransmittanceRange": 5}, {"ID": "48d397d2-4fad-4501-aa01-9a2614760897", "Name": "Focus Lock", "Tier": 1, "Model": "Focus Lock", "Width": 77.67823, "Domain": "MicroscopeHardwareSpecifications", "Height": 45.15014, "OffsetX": 743.0400390625, "OffsetY": 176.40000915527344, "TwoStep": false, "Category": "SamplePositioning.Focusing", "Algorithm": "A simple algorithm computes this separation and activates a piezo stage if the difference is greater or less than the value set by the lock", "Extension": "Basic", "LotNumber": ":unap", "Mechanism": "Hardware based", "PositionX": 1426.6913849999999, "PositionY": 642.56313, "PositionZ": 0, "Schema_ID": "FocusStabilizationDevice.json", "SpecsFile": "https://www.nature.com/articles/s41596-020-00478-x", "Wavelength": 980, "Description": "Custom build as described in https://www.nature.com/articles/s41596-020-00478-x", "Manufacturer": "Mateo and Boettiger", "ModelVersion": "2.01.1", "OccupiedSpot": "SamplePositioning.Focusing.FocusStabilizationDevice_1", "CatalogNumber": ":unap"}, {"ID": "b033d65a-a784-467f-94bb-b007e65a03dc", "Name": "Hal", "Tier": 1, "Width": 98.36491, "Domain": "MicroscopeSpecifications", "Height": 86.33964499999999, "OffsetX": 1427.3280029296875, "OffsetY": 0, "Version": "v2019.06.28", "Category": "Software", "Language": "Phython", "Developer": "Hazen Babcock and Xiaowei Zhuang\u2019s laboratory", "Extension": "Basic", "PositionX": 1518.5296020507812, "PositionY": 406.72999999999996, "PositionZ": 0, "Schema_ID": "SoftwareModule.json", "OpenSource": true, "WebsiteURL": "https://github.com/ZhuangLab/ storm-control", "Description": "Interactive control of the microscope, including moving the stage, setting the laser power, changing the image acquisition parameters, such as exposure time or z-scan depth, and recording images.", "ReleaseDate": "2019", "ModelVersion": "2.01.1", "PrimaryPublicationID": "10.5281/zenodo.3264857"}, {"ID": "17467f0d-5daf-460f-b7cd-08ae4ec9d869", "Name": "Steve", "Tier": 1, "Width": 98.36491, "Domain": "MicroscopeSpecifications", "Height": 86.33964499999999, "OffsetX": 1427.3280029296875, "OffsetY": 0, "Version": "v2019.06.28", "Category": "Software", "Language": "Phython", "Developer": "Hazen Babcock and Xiaowei Zhuang\u2019s laboratory", "Extension": "Basic", "PositionX": 1632.6296020507812, "PositionY": 409.53, "PositionZ": 0, "Schema_ID": "SoftwareModule.json", "OpenSource": true, "WebsiteURL": "https://github.com/ZhuangLab/ storm-control", "Description": "Directs Hal to record images in tiled mosaic, which is useful for reconstructing a larger field of view.", "ReleaseDate": "2019", "ModelVersion": "2.01.1", "PrimaryPublicationID": "10.5281/zenodo.3264857"}, {"ID": "605bfddb-5ed2-468a-86d4-b5118c85d160", "Name": "Kilroy", "Tier": 1, "Width": 98.36491, "Domain": "MicroscopeSpecifications", "Height": 86.33964499999999, "OffsetX": 1427.3280029296875, "OffsetY": 0, "Version": "v2019.06.28", "Category": "Software", "Language": "Phython", "Developer": "Hazen Babcock and Xiaowei Zhuang\u2019s laboratory", "Extension": "Basic", "PositionX": 1748.1296020507812, "PositionY": 406.72999999999996, "PositionZ": 0, "Schema_ID": "SoftwareModule.json", "OpenSource": true, "WebsiteURL": "https://github.com/ZhuangLab/ storm-control", "Description": "Controls the fluidics system, including choosing which well/buffer the needle goes to and when and at what speed the pump works.", "ReleaseDate": "2019", "ModelVersion": "2.01.1", "PrimaryPublicationID": "10.5281/zenodo.3264857"}, {"ID": "add20f8b-70be-4582-8d28-fa763b78303d", "Name": "Dave", "Tier": 1, "Width": 98.36491, "Domain": "MicroscopeSpecifications", "Height": 86.33964499999999, "OffsetX": 1427.3280029296875, "OffsetY": 0, "Version": "v2019.06.28", "Category": "Software", "Language": "Phython", "Developer": "Hazen Babcock and Xiaowei Zhuang\u2019s laboratory", "Extension": "Basic", "PositionX": 1867.8296020507812, "PositionY": 408.13, "PositionZ": 0, "Schema_ID": "SoftwareModule.json", "OpenSource": true, "WebsiteURL": "https://github.com/ZhuangLab/ storm-control", "Description": "Passes pre-written image acquisition protocols to Hal and prewritten fluidics control programs to Kilroy.", "ReleaseDate": "2019", "ModelVersion": "2.01.1", "PrimaryPublicationID": "10.5281/zenodo.3264857"}], "Description": "Custom-built microscope platform for super-resolution (STORM) ball-and-stick (bas) Chromatin Tracing. Described in: Liu et al., 2023 (https://doi.org/10.1101/2023.12.04.570024)", "ModelVersion": "2.01.1", "linkedFields": {"CMOS_1bba773c-9859-4103-ba01-46dae1778f53": {"RelayLens": {"value": "na", "schemaType": "CMOS"}}, "SoftwareModule_17467f0d-5daf-460f-b7cd-08ae4ec9d869": {"SoftwareModule": {"value": "Not assigned", "schemaType": "SoftwareModule"}}, "SoftwareModule_605bfddb-5ed2-468a-86d4-b5118c85d160": {"SoftwareModule": {"value": "Not assigned", "schemaType": "SoftwareModule"}}, "SoftwareModule_add20f8b-70be-4582-8d28-fa763b78303d": {"SoftwareModule": {"value": "Not assigned", "schemaType": "SoftwareModule"}}, "SoftwareModule_b033d65a-a784-467f-94bb-b007e65a03dc": {"SoftwareModule": {"value": "Not assigned", "schemaType": "SoftwareModule"}}, "AcquisitionSoftware_dd0844db-fb5a-41e1-86ce-7509b306b0a7": {"SoftwareModule": {"value": ["na", "na", "na", "na"], "schemaType": "AcquisitionSoftware"}}}, "ScalingFactor": 0.7, "ValidationTier": 3, "MicroscopeStand": {"ID": "2c8405fe-fb17-4e46-aa76-b60587dd83eb", "Name": "Nikon Eclipse Ti-U Microscope Stand", "Tier": 1, "Type": "Compound", "Model": "Eclipse Ti-U", "Domain": "MicroscopeHardwareSpecifications", "Origin": "Custom-built", "Category": "MicroscopeStand", "Extension": "Basic", "LotNumber": ":unav", "Schema_ID": "InvertedMicroscopeStand.json", "SpecsFile": "https://www.microscopy.uk.com/pdfs/Nikon_Eclipse_Ti_Brochure.pdf", "Description": "Inverted Microscope Eclipse Ti-U Main Body,with: left and rightside ports, intermediate magnification changer 1.5X, coaxial coarse/finefocus w/tension adjustment on coarse and focus stop on coarse, laser safety interlock signal output; Light-distribution: 100 Eyepiece, 100Left, 100 Right (*), and Auxiliary position (*) Note: (*) prism can beexchanged for optional prisms; Eye20/Left80, Eye20/Right80", "Manufacturer": "Nikon Instruments Inc.", "ModelVersion": "2.01.1", "CatalogNumber": "MEA53200"}}, "description": "Custom-built microscope platform for super-resolution (STORM) ball-and-stick (bas) Chromatin Tracing. Described in: Liu et al., 2023 (https://doi.org/10.1101/2023.12.04.570024)", "date_created": "2025-08-21T14:56:05.021355+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-08-21T16:37:03.487418+00:00"}, "schema_version": "1", "contributing_labs": [{"@id": "/labs/caterina-strambio-de-castillia-lab/", "uuid": "8bc160b9-bc86-4369-813b-533dd18cacb2", "display_title": "Caterina Strambio De Castillia, UMMS", "correspondence": [{"contact_email": "Y2F0ZXJpbmEuc3RyYW1iaW9AdW1hc3NtZWQuZWR1", "@id": "/users/77a9eb6a-a013-42ae-a921-cee85f0ae448/", "display_title": "Caterina Strambio De Castillia"}], "status": "current", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8bc160b9-bc86-4369-813b-533dd18cacb2"]}}], "@id": "/microscope-configurations/9a4086c5-ec74-4e84-b00a-7661505e1273/", "@type": ["MicroscopeConfiguration", "UserContent", "Item"], "uuid": "9a4086c5-ec74-4e84-b00a-7661505e1273", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Harvard-Zhuang_lab_CT-STORM_Nikon_Eclipse_Ti-U_Liu-2023_Scope1", "external_references": [], "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}