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POLARITY[0]": "NEGATIVE", + "COM5-DelayBetweenCharsMs": "0.0000", + "XYStage-Description": "ASI XY stage driver adapter", + "HamamatsuHam_sCMOS2-CCDTemperature": "-10.0000", + "Hamamatsu_sCMOS-Module Version": "21.7.4322.6307", + "COM4-Handshaking": "Off", + "HamamatsuHam_sCMOS2-OUTPUT TRIGGER PERIOD[0]": "0.0000", + "Hamamatsu_sCMOS-INTERNAL LINE INTERVAL": "0.0097", + "ZeissDefiniteFocus-Name": "Definite Focus", + "PixelType": "GRAY16", + "HamamatsuHam_sCMOS2-Camera Version": "4.04.B", + "COM1-DelayBetweenCharsMs": "0.0000", + "ZeissDefiniteFocus-Period": "0", + "ZeissSidePort-Name": "ZeissSidePort", + "HamamatsuHam_sCMOS2-OUTPUT TRIGGER SOURCE[2]": "READOUT END", + "COM4-AnswerTimeout": "500.0000", + "ZeissBasePort-Name": "ZeissBasePort", + "HamamatsuHam_sCMOS2-CONVERSION FACTOR OFFSET": "100.0000", + "HamamatsuHam_sCMOS2-Trigger": "NORMAL", + "YPositionUm": 786.2, + "COM1-BaudRate": "57600", + "Multi Camera-TransposeMirrorY": "0", + "Spectra-White_Level": "100", + "Multi Camera-TransposeMirrorX": "0", + "ZStage-Acceleration-AC(ms)": "0", + "Hamamatsu_sCMOS-ScanMode": "2", + "HamamatsuHam_sCMOS2-OUTPUT TRIGGER PERIOD[1]": "0.0000", + "Hamamatsu_sCMOS-TRIGGER GLOBAL EXPOSURE": "DELAYED", + "Hamamatsu_sCMOS-ReadoutTime": "0.0250", + "ZeissObjectiveTurret-Name": "ZeissObjectiveTurret", + "ZeissDefiniteFocus-DF Working Position": "576.6290", + "XYStage-JoyStick Reverse": "Off", + "XYStage-OnlySendSerialCommandOnChange": "Yes", + "ZeissDefiniteFocus-Description": "Zeiss Definite Focus adapter", + "COM1-Name": "COM1", + "Hamamatsu_sCMOS-OUTPUT TRIGGER POLARITY[2]": "NEGATIVE", + "HamamatsuHam_sCMOS2-TRIGGER GLOBAL EXPOSURE": "DELAYED", + "Hamamatsu_sCMOS-OUTPUT TRIGGER KIND[0]": "LOW", + "XYStage-FinishError-PCROS(nm)": "24.0000" +}, +"FrameKey-0-0-8": { + "Hamamatsu_sCMOS-Exposure": "150.00", + "Core-Initialize": "1", + "Multi Camera-Description": "Combines multiple cameras into a single camera", + "ZStage-Wait_Cycles": "9", + "Hamamatsu_sCMOS-OUTPUT TRIGGER PRE HSYNC COUNT": "0", + "XYStage-BuildName": "ADEPT_XYPZ", + "COM1-Description": "Serial port driver (boost:asio)", + "HamamatsuHam_sCMOS2-INTERNAL LINE INTERVAL UNITS": "MILLISECONDS", + "ZeissReflectedLightShutter-Description": "Zeiss Reflected Light Shutter", + "ZStage-Error-E(nm)": "0.0000", + "XYStage-Speed-S": "5.7459", + "ROI": "0-0-1024-1024", + "ZStage-MotorOnOff": "On", + "HamamatsuHam_sCMOS2-INTERNAL LINE INTERVAL": "0.0097", + "COM5-AnswerTimeout": "500.0000", + "COM1-AnswerTimeout": "500.0000", + "COM5-StopBits": "1", + "XYStage-Error-E(nm)": "400.0000", + "XYStage-StepSizeX_um": "0.0100", + "HamamatsuHam_sCMOS2-INTERNAL LINE SPEED UNITS": "METERS PER SECOND", + "ZStage-Port": "COM5", + "SlicePosition": 2, + "Exposure-ms": 500, + "HamamatsuHam_sCMOS2-EXPOSURE TIME UNITS": "MILLISECONDS", + "ZeissBasePort-Label": "Eyepiece", + "ZStage-Axis": "Z", + "ZeissSidePort-Description": "Side Port", + "ZeissScope-Description": "Zeiss microscope CAN bus adapter", + 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"XYStage-CompileDate": "May 03 2019:11:44:26", + "ZeissReflectedLightShutter-State": "1", + "Spectra-Port": "COM4", + "Summary": { + "Slices": 9, + "InitialPositionList": null, + "Interval_ms": 0, + "UUID": "0a6cd6b4-0a54-4bfa-a4b6-af582985baab", + "UserName": "in.brouwer", + "Depth": 2, + "PixelType": "GRAY16", + "Time": "2023-01-31 12:36:56 +0100", + "Date": "2023-01-31", + "z-step_um": 0.5, + "MetadataVersion": 10, + "PositionIndex": 0, + "SlicesFirst": true, + "ChContrastMin": [0], + "Width": 1024, + "PixelAspect": 1, + "MicroManagerVersion": "1.4.22", + "ROI": [ + 0, + 0, + 1024, + 1024 + ], + "ChNames": ["mScarlet_GFP-mSc-filter"], + "IJType": 1, + "GridRow": 0, + "Comment": "5-GFP-mScarlet/GFP/OD2.0/100x/1x/2x2binning/15s_interval/{-2,2,0/5zstack}/autofocus/mScarlet_GFP-mSc-filter/500ms/100% OR: GFP 20%/exp150ms", + "Height": 1024, + "GridColumn": 0, + "Prefix": "YTL1841B2-2-1_1hr_DMSO_galinduction_1", + "PixelSize_um": 0, + "Frames": 1, + "BitDepth": 16, + "KeepShutterOpenChannels": false, + "Source": "Micro-Manager", + "Channels": 1, + "ComputerName": "WS0203", + "CustomIntervals_ms": [], + "KeepShutterOpenSlices": false, + "ChColors": [-1], + "TimeFirst": false, + "ChContrastMax": [65536], + "Positions": 1, + "Directory": "D:\\Ineke2\\20230131" + }, + "Source": "HamamatsuHam_sCMOS2", + "XYStage-OverShoot(um)": "0.0000", + "XYStage-Wait_Cycles": "0", + "HamamatsuHam_sCMOS2-OUTPUT TRIGGER DELAY[0]": "0.0000", + "Hamamatsu_sCMOS-DEFECT CORRECT MODE": "ON", + "COM4-StopBits": "1", + "Hamamatsu_sCMOS-OUTPUT TRIGGER PERIOD[0]": "0.0000", + "ZeissDefiniteFocusOffset-Description": "Definite Focus offset treated as a ZStage", + "HamamatsuHam_sCMOS2-OUTPUT TRIGGER KIND[0]": "LOW", + "ZStage-Speed-S": "4.9580", + "ZStage-RingBufferSize": "50", + "Hamamatsu_sCMOS-OUTPUT TRIGGER BASE SENSOR[0]": "ALL VIEWS", + "HamamatsuHam_sCMOS2-OUTPUT TRIGGER BASE SENSOR[1]": "ALL VIEWS", + "HamamatsuHam_sCMOS2-CameraName": "C13440-20CU", + "Hamamatsu_sCMOS-TransposeCorrection": "0", + "COM4-DataBits": "8", + "ZeissSidePort-Label": "2-100%L", + "XYStage-MotorOnOff": "On", + "HamamatsuHam_sCMOS2-SENSOR MODE": "AREA", + "COM5-DataBits": "8", + "Hamamatsu_sCMOS-OUTPUT TRIGGER DELAY UNITS": "SECONDS", + "Binning": "2x2", + "ZeissHalogenLamp-Volt": "0.0000", + "HamamatsuHam_sCMOS2-Driver Version": "1.2.6.6307", + "Hamamatsu_sCMOS-CCDTemperature": "-10.0000", + "Spectra-Cyan_Enable": "0", + "Hamamatsu_sCMOS-INTERNAL LINE SPEED": "0.6671", + "COM4-DelayBetweenCharsMs": "0.0000", + "COM5-Parity": "None", + "HamamatsuHam_sCMOS2-OUTPUT TRIGGER POLARITY[1]": "NEGATIVE", + "ZeissDefiniteFocusOffset-AutoFocus Device": "ZeissDefiniteFocus", + "COM5-Description": "Serial port driver (boost:asio)", + "ZeissBasePort-Description": "Base Port", + "HamamatsuHam_sCMOS2-OUTPUT TRIGGER DELAY UNITS": "SECONDS", + "COM4-Description": "Serial port driver (boost:asio)", + "HamamatsuHam_sCMOS2-Name": "HamamatsuHam_DCAM", + "Multi Camera-Physical Camera 1": "Hamamatsu_sCMOS", + "XYStage-TransposeMirrorY": "0", + "Multi Camera-Physical Camera 2": "HamamatsuHam_sCMOS2", + "XPositionUm": -8466.5, + "XYStage-TransposeMirrorX": "0", + "ZeissFocusAxis-Velocity-Acceleration": "Default", + "Hamamatsu_sCMOS-TriggerPolarity": "NEGATIVE", + "ZeissReflectorTurret-Label": "5-GFP/mSc", + "ZeissScope-DefiniteFocusVersion": "2", + "HamamatsuHam_sCMOS2-PixelType": "16bit", + "FileName": "img_000000000_mScarlet_GFP-mSc-filter_008.tif", + "HamamatsuHam_sCMOS2-OUTPUT TRIGGER POLARITY[0]": "NEGATIVE", + "Core-Galvo": "", + "Position": "Default", + "Hamamatsu_sCMOS-CONVERSION FACTOR COEFF": "0.5000", + "CameraChannelIndex": 0, + "Hamamatsu_sCMOS-OUTPUT TRIGGER PERIOD[2]": "0.0000", + "SliceIndex": 8, + "ZPositionUm": 2, + "Core-Focus": "ZStage", + "Channel": "mScarlet_GFP-mSc-filter", + "ZeissSidePort-State": "1", + "COM1-Verbose": "1", + "Spectra-Violet_Enable": "0", + "XYStage-SerialResponse": "", + "Spectra-SetLE_Type": "Spectra", + "COM5-Name": "COM5", + "Spectra-Blue_Enable": "0", + "FrameIndex": 0, + "ZeissOptovar-Description": "Tube Lens (optoavar)", + "ZeissBasePort-State": "1", + "XYStage-Version": "Version: USB-9.2m ", + "ZStage-Use Sequence": "No", + "ZStage-Use Fast Sequence": "No", + "Spectra-Teal_Level": "100", + "ZeissDefiniteFocusOffset-Name": "ZeissDefiniteFocusOffset", + "HamamatsuHam_sCMOS2-Camera Bus": "USB3", + "Spectra-Red_Enable": "0", + "HamamatsuHam_sCMOS2-OUTPUT TRIGGER SOURCE[0]": "READOUT END", + "XYStage-Backlash-B": "0.0400", + "ZStage-Maximum Speed (Do Not Change)": "7.4000", + "Hamamatsu_sCMOS-OUTPUT TRIGGER DELAY[0]": "0.0000", + "ZStage-Name": "ZStage", + "Hamamatsu_sCMOS-CameraName": "C13440-20CU", + "ZeissOptovar-Label": "1x", + "Hamamatsu_sCMOS-SENSOR MODE": "AREA", + "Hamamatsu_sCMOS-TRIGGER DELAY": "0.0000", + "Camera": "", + "ZeissOptovar-Name": "ZeissTubeLens", + "COM4-Parity": "None", + "Core-ImageProcessor": "", + "HamamatsuHam_sCMOS2-TransposeCorrection": "0", + "HamamatsuHam_sCMOS2-TRIGGER DELAY": "0.0000", + "HamamatsuHam_sCMOS2-ScanMode": "2", + "Spectra-Description": "Lumencor Spectra Light Engine", + "Spectra-Green_Enable": "1", + "Spectra-Teal_Enable": "0", + "Spectra-White_Enable": "0", + "XYStage-StepSizeY_um": "0.0100", + "HamamatsuHam_sCMOS2-OUTPUT TRIGGER SOURCE[1]": "READOUT END", + "COM1-DataBits": "8", + "ZeissObjectiveTurret-Label": "4-alpha Plan-Apochromat 100x/1.46 Oil DIC (UV) M27", + "ZeissFocusAxis-Position": "0.0010", + "Core-AutoShutter": "1", + "Hamamatsu_sCMOS-TransposeXY": "0", + "HamamatsuHam_sCMOS2-OUTPUT TRIGGER BASE SENSOR[0]": "ALL VIEWS", + "Hamamatsu_sCMOS-PixelType": "16bit", + "NextFrame": null, + "Core-XYStage": "XYStage", + "HamamatsuHam_sCMOS2-TriggerPolarity": "NEGATIVE", + "Time": "2023-01-31 12:37:03 +0100", + "ZeissHalogenLamp-Description": "Halogen Lamp intensity", + "Hamamatsu_sCMOS-TransposeMirrorY": "0", + "Hamamatsu_sCMOS-TransposeMirrorX": "0", + "COM4-Name": "COM4", + "ZeissScope-AnswerTimeOut": "250.0000", + "COM4-BaudRate": "9600", + "Hamamatsu_sCMOS-OUTPUT TRIGGER BASE SENSOR[1]": "ALL VIEWS", + "Core-AutoFocus": "ZeissDefiniteFocus", + "ZeissDefiniteFocus-Focus Method": "Last Position", + "Spectra-Violet_Level": "100", + "Hamamatsu_sCMOS-OUTPUT TRIGGER SOURCE[0]": "READOUT END", + "Hamamatsu_sCMOS-EXPOSURE FULL RANGE": "DISABLE", + "Hamamatsu_sCMOS-Driver Version": "1.2.6.6307", + "HamamatsuHam_sCMOS2-EXPOSURE FULL RANGE": "DISABLE", + "BitDepth": 16, + "Slice": 8, + "XYStage-JoyStick Slow Speed": "5", + "Spectra-Red_Level": "100", + "COM4-Verbose": "1", + "Hamamatsu_sCMOS-Camera Version": "4.04.B", + "ZeissScope-Microscope Version": "Application version: ", + "Hamamatsu_sCMOS-OUTPUT TRIGGER BASE SENSOR[2]": "ALL VIEWS", + "ChannelIndex": 0, + "Hamamatsu_sCMOS-OUTPUT TRIGGER SOURCE[1]": "READOUT END", + "Core-Shutter": "Spectra", + "Multi Camera-TransposeCorrection": "0", + "HamamatsuHam_sCMOS2-ReadoutTime": "0.0250", + "Hamamatsu_sCMOS-INTERNAL LINE SPEED UNITS": "METERS PER SECOND", + "ZeissReflectorTurret-Name": "ZeissReflectorTurret", + "Hamamatsu_sCMOS-Name": "HamamatsuHam_DCAM", + "Core-TimeoutMs": "5000", + "XYStage-JoyStick Fast Speed": "60", + "HamamatsuHam_sCMOS2-Description": "Hamamatsu device adapter 1.8.12.52", + "XYStage-Maximum Speed (Do Not Change)": "8.5760", + "ElapsedTime-ms": 8072, + "ZeissObjectiveTurret-Description": "Objective Turret", + "Multi Camera-Name": "Multi Camera", + "Hamamatsu_sCMOS-Trigger": "NORMAL", + "Hamamatsu_sCMOS-OUTPUT TRIGGER KIND[1]": "LOW", + "Frame": 0, + "HamamatsuHam_sCMOS2-OUTPUT TRIGGER PRE HSYNC COUNT": "0", + "Width": 1024, + "HamamatsuHam_sCMOS2-TransposeMirrorX": "0", + "Multi Camera-Binning": "0", + "HamamatsuHam_sCMOS2-TransposeMirrorY": "0", + "COM5-Handshaking": "Off", + "Hamamatsu_sCMOS-OUTPUT TRIGGER POLARITY[1]": "NEGATIVE", + "Hamamatsu_sCMOS-Bits per Channel": "16", + "HamamatsuHam_sCMOS2-OUTPUT TRIGGER PERIOD UNITS": "SECONDS", + "PositionName": null, + "ZStage-OverShoot(um)": "0.0000", + "Spectra-Cyan_Level": "20", + "Hamamatsu_sCMOS-OUTPUT TRIGGER SOURCE[2]": "READOUT END", + "ZeissReflectorTurret-State": "4", + "Hamamatsu_sCMOS-EXPOSURE TIME UNITS": "MILLISECONDS", + "ZeissHalogenLamp-Name": "ZeissHalogenLamp", + "Height": 1024, + "HamamatsuHam_sCMOS2-Binning": "2x2", + "ZeissOptovar-State": "0", + "HamamatsuHam_sCMOS2-Module Version": "21.7.4322.6307", + "HamamatsuHam_sCMOS2-INTERNAL LINE SPEED": "0.6671", + "Hamamatsu_sCMOS-OUTPUT TRIGGER KIND[2]": "LOW", + "Hamamatsu_sCMOS-OUTPUT TRIGGER POLARITY[0]": "NEGATIVE", + "COM5-DelayBetweenCharsMs": "0.0000", + "XYStage-Description": "ASI XY stage driver adapter", + "HamamatsuHam_sCMOS2-CCDTemperature": "-10.0000", + "Hamamatsu_sCMOS-Module Version": "21.7.4322.6307", + "COM4-Handshaking": "Off", + "HamamatsuHam_sCMOS2-OUTPUT TRIGGER PERIOD[0]": "0.0000", + "Hamamatsu_sCMOS-INTERNAL LINE INTERVAL": "0.0097", + "ZeissDefiniteFocus-Name": "Definite Focus", + "PixelType": "GRAY16", + "HamamatsuHam_sCMOS2-Camera Version": "4.04.B", + "COM1-DelayBetweenCharsMs": "0.0000", + "ZeissDefiniteFocus-Period": "0", + "ZeissSidePort-Name": "ZeissSidePort", + "HamamatsuHam_sCMOS2-OUTPUT TRIGGER SOURCE[2]": "READOUT END", + "COM4-AnswerTimeout": "500.0000", + "ZeissBasePort-Name": "ZeissBasePort", + "HamamatsuHam_sCMOS2-CONVERSION FACTOR OFFSET": "100.0000", + "HamamatsuHam_sCMOS2-Trigger": "NORMAL", + "YPositionUm": 786.2, + "COM1-BaudRate": "57600", + "Multi Camera-TransposeMirrorY": "0", + "Spectra-White_Level": "100", + "Multi Camera-TransposeMirrorX": "0", + "ZStage-Acceleration-AC(ms)": "0", + "Hamamatsu_sCMOS-ScanMode": "2", + "HamamatsuHam_sCMOS2-OUTPUT TRIGGER PERIOD[1]": "0.0000", + "Hamamatsu_sCMOS-TRIGGER GLOBAL EXPOSURE": "DELAYED", + "Hamamatsu_sCMOS-ReadoutTime": "0.0250", + "ZeissObjectiveTurret-Name": "ZeissObjectiveTurret", + "ZeissDefiniteFocus-DF Working Position": "576.6290", + "XYStage-JoyStick Reverse": "Off", + "XYStage-OnlySendSerialCommandOnChange": "Yes", + "ZeissDefiniteFocus-Description": "Zeiss Definite Focus adapter", + "COM1-Name": "COM1", + "Hamamatsu_sCMOS-OUTPUT TRIGGER POLARITY[2]": "NEGATIVE", + "HamamatsuHam_sCMOS2-TRIGGER GLOBAL EXPOSURE": "DELAYED", + "Hamamatsu_sCMOS-OUTPUT TRIGGER KIND[0]": "LOW", + "XYStage-FinishError-PCROS(nm)": "24.0000" +} +} diff --git a/ndbioimage/tests/files/tiffseq/YTL1841B2-2-1_1hr_DMSO_galinduction_1/display_and_comments.txt b/ndbioimage/tests/files/tiffseq/YTL1841B2-2-1_1hr_DMSO_galinduction_1/display_and_comments.txt new file mode 100755 index 0000000..d811fe6 --- /dev/null +++ b/ndbioimage/tests/files/tiffseq/YTL1841B2-2-1_1hr_DMSO_galinduction_1/display_and_comments.txt @@ -0,0 +1,12 @@ +{ + "Channels": [{ + "Name": "mScarlet_GFP-mSc-filter", + "DisplayMode": 1, + "HistogramMax": -1, + "Max": 523, + "Gamma": 1, + "Min": 352, + "Color": -1 + }], + "Comments": {"Summary": "5-GFP-mScarlet/GFP/OD2.0/100x/1x/2x2binning/15s_interval/{-2,2,0/5zstack}/autofocus/mScarlet_GFP-mSc-filter/500ms/100% OR: GFP 20%/exp150ms"} +} \ No newline at end of file