[System] ;Specifies global configuration settings for the instrument. PollLaserMaintenanceLogs = True ;True if we run a background thread to poll laser status and log to maintenance logs InstrumentType = Proto2 ;Specifies the instrument type. LaserType = IxLaser ;Specifies the type of lasers used on the instrument. CameraType = Hamamatsu ;Specifies the camera used on the instrument. ScanEngineType = Embedded ;Specifies the type of scan engine to use on the system SbcRootFolder = C:\Illumina\NovaSeqTemp ;Root run folder on SBC. CeLinuxRootFolder = /ilmn/outputfolder ;Root run folder on CE as linux path. CeMountRootFolder = Z:\outputfolder ;Root run folder on CE as windows mount path. InitializeAllInSerial = False ;Indicates whether or not to initialize all devices in serial. Setting this to true will result in slower initialization performance but will help diagnose device initialization issues. ReportDeviceSections = True ;Indicates something. MaintenanceLogsFolder = C:\Illumina Maintenance Logs ;MaintenanceLogsFolder SecondaryMaintenanceLogsFolder = ;Secondary Maintenance Logs Folder (e.g. Network location) to copy results to ILMNOnlyRecipeFolder = C:\ILMNOnlyRecipeFolder\ ; SimulationImagesPath = ;Folder containing simulation images UseMinimumSimulationImages = False ;Use only camera 1, lane 1, swath 1, tile 1, top surface image (but multiple Z positions for focus) FPGAFlashDefaultFolder = C:\ ;Directory for FPGA flash / firmware files. TempDirectoryDeletionAgeDays = 7 ;Age allowed for temporary run folders. Run folders in the Temporary Folder older than this age will be deleted. ScanCounterFile = C:\ScanCounter.txt ;The folder and file name for keeping track of the number of runs started. Delete this file and the counts starts over. InstrumentName = A00104 ;Indicates the name of the instrument DefaultFlowcell = NovaSeq ;Default flow cell LogEstimatedCompletionTimeMetrics = True ;Specifies whether to log metrics related to Estimated Completion times. This could add a small amount of overhead when executing operations and should therefore not be enabled in a "production" setting. DefaultTimeoutMs = 60000 ;System wide timeout for devices SystemType = NovaSeqProto2 ;Indicates the type of system or instrument. TraceIfNotSimulated = False ;Indicates whether or not to trace devices if not simulated. FastSimulation = True ;Indicates whether or not to use fast simulation when simulating the instrument. LogAllComms = False ;Log all device communications system wide. [XyStageTesting] ;Configuration items for XY stage testing parameters. CanReachYFrontLimitSensor = True ;Proto1 and Proto1.5 cannot reach the limit sensor for the eject position XLeftLimitSensorPositionMm = 70 ;X positive limit sensor position (without X offset) XRightLimitSensorPositionMm = -70.8 ;X negative limit sensor position (without X offset) YRearLimitSensorPositionMm = 5 ;Y positive limit sensor position (without Y offset) YFrontLimitSensorPositionMm = -261 ;Y negative limit sensor position (without Y offset) [DriftCorrection] ;Drift correction config settings MaxCumulativeXCorrectionInPixels = 2900 ;Maximum total drift correction in X MaxCumulativeYCorrectionInPixels = 2900 ;Maximum total drift correction in Y MaxPerCycleDriftCorrectionInXInPixels = 255 ;Maximum per cycle drift correction in X MaxPerCycleDriftCorrectionInYInPixels = 255 ;Maximum per cycle drift correction in X TileChoiceMethod = Average ;The tile choice method to use if the center tile is unavailable DriftCorrect = True ;Turns on drift correction BlockingTimeForDriftCorrectionInMilliseconds = 500 ;The amount of time to wait for drift values from RTA VerboseDriftCorrectionLogging = False ;Logs more info during drift correction [CHM] ;CHMConfigSection IpAddress = ;The IP Address of the IX device. Port = 5555 ;The port of the IX device. BroadcastPort = 5555 ;The port to broadcast to for the IX device. HostName = novaseq_chm ;The host name of the IX device. FirmwareUpdatePackageFileName = novaseq_chm.pkg ;The name of the firmware update package file DefaultResponseTimeoutMs = 60000 ;Timeout for reading a response from the IX device. SendTimeoutMs = 60000 ;Timeout for sending a response to the IX device. BoardId = ;The board ID used to identify which board to connect to. TraceAll = False ;If true, will have the effect of tracing all IX communication Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [CIB] ;CIBConfigSection IpAddress = ;The IP Address of the IX device. Port = 5555 ;The port of the IX device. BroadcastPort = 5555 ;The port to broadcast to for the IX device. HostName = novaseq_cib ;The host name of the IX device. FirmwareUpdatePackageFileName = novaseq_cib_2.pkg ;The name of the firmware update package file DefaultResponseTimeoutMs = 60000 ;Timeout for reading a response from the IX device. SendTimeoutMs = 60000 ;Timeout for sending a response to the IX device. BoardId = ;The board ID used to identify which board to connect to. TraceAll = False ;If true, will have the effect of tracing all IX communication Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FIB] ;FIBConfigSection IpAddress = ;The IP Address of the IX device. Port = 5555 ;The port of the IX device. BroadcastPort = 5555 ;The port to broadcast to for the IX device. HostName = novaseq_fib ;The host name of the IX device. FirmwareUpdatePackageFileName = novaseq_fib_2.pkg ;The name of the firmware update package file DefaultResponseTimeoutMs = 60000 ;Timeout for reading a response from the IX device. SendTimeoutMs = 60000 ;Timeout for sending a response to the IX device. BoardId = ;The board ID used to identify which board to connect to. TraceAll = False ;If true, will have the effect of tracing all IX communication Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FLU] ;FLUConfigSection IpAddress = ;The IP Address of the IX device. Port = 5555 ;The port of the IX device. BroadcastPort = 5555 ;The port to broadcast to for the IX device. HostName = novaseq_flu ;The host name of the IX device. FirmwareUpdatePackageFileName = novaseq_flu.pkg ;The name of the firmware update package file DefaultResponseTimeoutMs = 60000 ;Timeout for reading a response from the IX device. SendTimeoutMs = 60000 ;Timeout for sending a response to the IX device. BoardId = ;The board ID used to identify which board to connect to. TraceAll = False ;If true, will have the effect of tracing all IX communication Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FCH] ;FCHConfigSection IpAddress = ;The IP Address of the IX device. Port = 5555 ;The port of the IX device. BroadcastPort = 5555 ;The port to broadcast to for the IX device. HostName = novaseq_fch ;The host name of the IX device. FirmwareUpdatePackageFileName = novaseq_fch_2.pkg ;The name of the firmware update package file DefaultResponseTimeoutMs = 60000 ;Timeout for reading a response from the IX device. SendTimeoutMs = 60000 ;Timeout for sending a response to the IX device. BoardId = ;The board ID used to identify which board to connect to. TraceAll = False ;If true, will have the effect of tracing all IX communication Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [RCA] ;RCAConfigSection IpAddress = ;The IP Address of the IX device. Port = 5555 ;The port of the IX device. BroadcastPort = 5555 ;The port to broadcast to for the IX device. HostName = novaseq_rca ;The host name of the IX device. FirmwareUpdatePackageFileName = novaseq_rca.pkg ;The name of the firmware update package file DefaultResponseTimeoutMs = 60000 ;Timeout for reading a response from the IX device. SendTimeoutMs = 60000 ;Timeout for sending a response to the IX device. BoardId = ;The board ID used to identify which board to connect to. TraceAll = False ;If true, will have the effect of tracing all IX communication Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [RCALeft] ;RCALeftConfigSection IpAddress = ;The IP Address of the IX device. Port = 5555 ;The port of the IX device. BroadcastPort = 5555 ;The port to broadcast to for the IX device. HostName = novaseq_rca ;The host name of the IX device. FirmwareUpdatePackageFileName = novaseq_rca.pkg ;The name of the firmware update package file DefaultResponseTimeoutMs = 60000 ;Timeout for reading a response from the IX device. SendTimeoutMs = 60000 ;Timeout for sending a response to the IX device. BoardId = left_RCA ;The board ID used to identify which board to connect to. TraceAll = False ;If true, will have the effect of tracing all IX communication Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [RCARight] ;RCARightConfigSection IpAddress = ;The IP Address of the IX device. Port = 5555 ;The port of the IX device. BroadcastPort = 5555 ;The port to broadcast to for the IX device. HostName = novaseq_rca ;The host name of the IX device. FirmwareUpdatePackageFileName = novaseq_rca.pkg ;The name of the firmware update package file DefaultResponseTimeoutMs = 60000 ;Timeout for reading a response from the IX device. SendTimeoutMs = 60000 ;Timeout for sending a response to the IX device. BoardId = right_RCA ;The board ID used to identify which board to connect to. TraceAll = False ;If true, will have the effect of tracing all IX communication Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [SYST] ;SYSTConfigSection IpAddress = ;The IP Address of the IX device. Port = 5555 ;The port of the IX device. BroadcastPort = 5555 ;The port to broadcast to for the IX device. HostName = novaseq_syst ;The host name of the IX device. FirmwareUpdatePackageFileName = novaseq_syst.pkg ;The name of the firmware update package file DefaultResponseTimeoutMs = 60000 ;Timeout for reading a response from the IX device. SendTimeoutMs = 60000 ;Timeout for sending a response to the IX device. BoardId = ;The board ID used to identify which board to connect to. TraceAll = False ;If true, will have the effect of tracing all IX communication Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [BIMLeft] ;BIMLeftConfigSection IpAddress = ;The IP Address of the IX device. Port = 5555 ;The port of the IX device. BroadcastPort = 5555 ;The port to broadcast to for the IX device. HostName = novaseq_bim ;The host name of the IX device. FirmwareUpdatePackageFileName = novaseq_bim.pkg ;The name of the firmware update package file DefaultResponseTimeoutMs = 60000 ;Timeout for reading a response from the IX device. SendTimeoutMs = 60000 ;Timeout for sending a response to the IX device. BoardId = left_BIM ;The board ID used to identify which board to connect to. TraceAll = False ;If true, will have the effect of tracing all IX communication Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [BIMRight] ;BIMRightConfigSection IpAddress = ;The IP Address of the IX device. Port = 5555 ;The port of the IX device. BroadcastPort = 5555 ;The port to broadcast to for the IX device. HostName = novaseq_bim ;The host name of the IX device. FirmwareUpdatePackageFileName = novaseq_bim.pkg ;The name of the firmware update package file DefaultResponseTimeoutMs = 60000 ;Timeout for reading a response from the IX device. SendTimeoutMs = 60000 ;Timeout for sending a response to the IX device. BoardId = right_BIM ;The board ID used to identify which board to connect to. TraceAll = False ;If true, will have the effect of tracing all IX communication Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [AutoCenter] ;Auto Center Config settings ZDistanceBetweenPeaks = 0.001 ;The expected Z distance between peaks in mm. ZoomLensPosition = Top ;Use compensator or not. RedLaserPower = 750 ;Red Laser power to use in mW. ScanVelocity = 5 ;TDI Scan velocity in mm/s TDIScanLength = 2 ;TDI scan length for AutoCenter in mm. UbertargetDistanceBetweenSlicesUm = 7 ;The Z distance, in µm, between each subsequent image slice when surface finding for ubertarget. UbertargetSlicesAboveCenter = 4 ;The number of image slices to capture above the center of the stack when surface finding for ubertarget. NumberOfDebugPixels = 12 ;The number of debug pixels in the image MaxCornersToTry = 50, 100 ;Max number of corners for GoodFeaturesToTrackDetector. If the first parameter did not return enough corners, we try second and third, if needed StdDevsToTry = 3 ;Max number of standard deviations for GoodFeaturesToTrackDetector. If the first parameter did not return enough corners, we try second and third, if needed CloseError = 2 ;Error used to call two corners 'friends' WidthError = 3 ;Max error to call two corners 'width friends' LengthError = 3 ;Max error to call two corners 'length friends' NumCrossCorners = 12 ;Number of corners in RevB cross MinNumGoodCornersFoundOnImage = 8 ;Minimum corners to use on a good image MinNumCornersInGoodCross = 6 ;Minimum number of corners to detect a cross MedianFilterSize = 25 ;Median filter size for OpenCV corner refining ArmLengthDownScaledX = 36 ;Horizontal cross arm length on down scaled image ArmLengthDownScaledY = 36 ;Vertical cross arm length on down scaled image ArmWidthDownScaledX = 18 ;Horizontal width of cross center square on down scaled image ArmWidthDownScaledY = 18 ;Vertical height of cross center square on down scaled image MaxCornersOffsetOnDownScaledImage = 5 ;Max accumulated offset of a corner from all other corners of the cross on down scaled image MaxCornersOffsetOnFullSizeImage = 50 ;Max accumulated offset of a corner from all other corners of the cross on full size image MinNumberCornerFriends = 5 ;Minimum number of friends for a corner to have to be a candidate for the given cross corner number MinNumberCrossDiagonals = 3 ;Cross validation MaxNumberOfCrosses = 100 ;Max number of crosses for a reliable call MinNumberCrossDiagonalIntersections = 3 ;Cross diagonal intersections for center calculation StdDevCenterPosition = 1 ;Standard deviation for cross center calculation MinCrossForegroundBackgroundRatio = 1.5 ;Background threshold BackgroundIntensityShift = 50 ;Background intensity shift BackgroundIntensityWidth = 300 ;Background intensity width BackgroundIntensityLength = 600 ;Background intensity length BackgroundIntensityMinPixels = 1000 ;Background intensity minimum pixels CurrentDrawImagePathIn = ;Image draw path in CurrentDrawImagePathOut = ;Image draw path out DebugEnabled = False ;Enables autocenter debugging DebugImagePath = ;Image path for saving debug images DebugLogFilePath = ;Log path for debugging NumberOfPlusAndMinusRetriesInX = 4 ;The number of retries for autocenter around X in the positive and negative directions RetryStepSizeInMillimeters = 0.5538462 ;The step size to use in autocenter retry BypassFailure = True ;Allow sequencing to proceed if autocenter fails [Focus] ;Focus config settings. Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FocusTracker] ;Focus config settings. LaserPowerToControlScale = 1 ;The scale of laser power mW to DAC control voltage. MinLaserPowerMw = 0 ;Minimum allowable laser power in mW. MaxLaserPowerMw = 2.5 ;Maximum allowable laser power in mW. Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [SystemPower] ;System Power config settings. Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [SystemThermal] ;System Thermal config settings. BypassSystemThermalPowerUp = False ;Bypass all SystemThermal powerup. BypassSystemThermalPowerUpOptical = False ;Bypass SystemThermal Optical powerup. BypassSystemThermalPowerUpFch = False ;Bypass SystemThermal FCH powerup. BypassSystemThermalPowerUpRca = False ;Bypass SystemThermal RCA powerup. BypassSystemThermalPowerUpOptEnclosure = True ;Bypass SystemThermal Optical enclosure powerup. BypassSystemThermalPowerUpEboxEnclosure = False ;Bypass SystemThermal Ebox enclosure powerup. BypassSystemThermalPowerUpFluidicsEnclosure = False ;Bypass SystemThermal Fluidics enclosure powerup. BypassSystemThermalPowerUpSma = False ;Bypass SystemThermal SMA powerup. ReadLogSmaRtdValues = False ;Determines if we will read and log RCA SMA RTD values to its own log file. CompressorSetPoint = 24000 ;Optical loop compressor servo set point. PumpOptServoDetltaSetPoint = 1000 ;Optical loop pump delta set point CompressorSetPointThreshold = 500 ;Optical loop compressor set point allowable range. CompressorPreRunCheckThreshold = 3000 ;Optical loop compressor set point allowable range during pre-run checks in control software PumpOptConstantSetPointMilliVolts = 3200 ;Optical loop pump constant set point in milivolts. PumpFchServoDetltaSetPoint = 4000 ;FCH loop pump delta set point FanFchSetPointHigh = 35000 ;FCH loop temperature high point FanFchSetPointLow = 25000 ;FCH loop temperature low point FanFchPercentHigh = 40 ;FCH loop fan high pwm FanFchPercentLow = 20 ;FCH loop fan low pwm PumpFchConstantSetPointMillivolts = 2800 ;FCH loop pump constant set point in millivolts. PumpRcaServoDetltaSetPoint = 4000 ;RCA loop pump delta set point FanRcaSetPointHigh = 35000 ;RCA loop temperature high point FanRcaSetPointLow = 25000 ;RCA loop temperature low point FanRcaPercentHigh = 40 ;RCA loop fan high pwm FanRcaPercentLow = 20 ;RCA loop fan low pwm PumpRcaConstantSetPointMilliVolts = 2500 ;RCA loop pump constant set point in millivolts. FaneeSetPointHigh = 35000 ;Ebox enclosure loop temperature high point FaneeSetPointLow = 20000 ;x enclosure loop temperature low point FaneePercentHigh = 60 ;Ebox enclosure loop fan high pwm FaneePercentLow = 20 ;Ebox enclosure loop fan low pwm FanfeSetPointHigh = 35000 ;Fluidics enclosure loop temperature high point FanfeSetPointLow = 20000 ;Fluidics enclosure loop temperature low point FanfePercentHigh = 50 ;Fluidics enclosure loop fan high pwm FanfePercentLow = 20 ;Fluidics enclosure loop fan low pwm FanOptSetPointHigh = 30000 ;Optics enclosure loop temperature high point FanOptSetPointLow = 20000 ;Optics enclosure loop temperature low point FanOptPercentHigh = 60 ;Optics enclosure loop temperature high point FanOptPercentLow = 60 ;Optics enclosure loop temperature low point Fan1OptConstantSetPointPercent = 60 ;Optics enclosure loop fan 1 PWM set point in percent. Fan2OptConstantSetPointPercent = 60 ;Optics enclosure loop fan 2 PWM set point in percent CalibratedTemperatureSensorValues = True ;Sets whether to retrieve calibrated temperature sensor values. SensorPollingPeriodInSeconds = 1 ;Polling frequency in seconds SmaSensorPollingPeriodInSeconds = 60 ;Polling frequency in minutes FanSmaLowPwmPercent = 0 ;Low PWM set point for RCA SMA fans FanSmaMediumPwmPercent = 25 ;Medium PWM set point for RCA SMA fans FanSmaHighPwmPercent = 50 ;High PWM set point for RCA SMA fans Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FluidicsBoard] ;Fluidics board config settings. Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FlowCellDoor] ;Flow Cell Door config settings. Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FlowCellClamp1] ;Flow cell clamp board config settings. Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FluidicsSensors] ;Fluidics Sensor Config Section PressureSlopePsiPerVolt = 12.58 ;Slope used for pressure sensor value calculation, in PSI/volt PressureOffsetPsi = -20.7 ;Offset used for pressure sensor value calculation, in PSI FlowrateAdjustmentScale = 100 ;Correction factor used for flowrate sensor value calculation ZeroOffsetMaxAdjustmentPsi = 3.5 ;Max value allowed when zeroing the sensor. May change depending on atmospheric pressure from altitude. Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [BufferInterfaceModule1] ;BufferInterfaceModuleConfigSection Id = left_BIM ; StrawMotorPositionPollingIntervalMs = 1000 ;Straw motor position polling interval (milliseconds) StrawStatePollingIntervalMs = 1000 ;Straw state polling interval (milliseconds) Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [ReagentChiller] ;Reagent chiller config settings. DefaultMixUpHeightMm = 50 ;Default mix up height position in mm. DefaultMixDownHeightMm = 0 ;Default mix up height position in mm. DefaultTargetTemperatureCelcius = 7 ;Default target temperature in celcius. Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FlowCellSelectorValves1] ;Selector valve(s) for one flow cell Type = SelectorValve ;Configuration item type Exists = True ;Whether or not the device exists in this instrument configuration. Length = 3 ;Number of device instances in the array. [FlowCellSelectorValves] ;Selector valve(s) for one flow cell Type = SelectorValve ;Configuration item type Exists = True ;Whether or not the device exists in this instrument configuration. Length = 2 ;Number of device instances in the array. [FlowCellFluidicsSystem1.IxSelectorValve1] ;Settings for a Ix Valve selector Valve. ValveId = clsv ;The Id of the valve ValveType = CommonLine ;The type/function of this valve AirPosition = 13 ;The position connect to the air line. AvoidPosition = 11 ;The position to avoid during long moves. InitialPosition = 1 ;The initial position to set the valve to. NumberOfPorts = 24 ;The number of position ports on the valve. NumberOfRetries = 4 ;The number of attempts to recover from a failure. NumberOfRetriesInSequencing = 3 ;Gets the number of total retries duing a single sequencing run. PlugPosition = 0 ;The position that contains the plug. ValveMap = Configuration\NovaSeqProto1_CommonLineValveMapA.xml ;Reagent valve map. Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = FC1 IxSelectorValve1 ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FlowCellFluidicsSystem1.IxSelectorValve2] ;Settings for a Ix Valve selector Valve. ValveId = reagent ;The Id of the valve ValveType = Reagent ;The type/function of this valve AirPosition = 0 ;The position connect to the air line. AvoidPosition = 16 ;The position to avoid during long moves. InitialPosition = 6 ;The initial position to set the valve to. NumberOfPorts = 24 ;The number of position ports on the valve. NumberOfRetries = 4 ;The number of attempts to recover from a failure. NumberOfRetriesInSequencing = 3 ;Gets the number of total retries duing a single sequencing run. PlugPosition = 6 ;The position that contains the plug. ValveMap = Configuration\NovaSeqProto1_ReagentMapA.xml ;Reagent valve map. Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = FC1 IxSelectorValve2 ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FlowCellFluidicsSystem1.IxSelectorValve3] ;Settings for a Ix Valve selector Valve. ValveId = wsv_side_a ;The Id of the valve ValveType = Waste ;The type/function of this valve AirPosition = 2 ;The position connect to the air line. AvoidPosition = 0 ;The position to avoid during long moves. InitialPosition = 1 ;The initial position to set the valve to. NumberOfPorts = 2 ;The number of position ports on the valve. NumberOfRetries = 4 ;The number of attempts to recover from a failure. NumberOfRetriesInSequencing = 3 ;Gets the number of total retries duing a single sequencing run. PlugPosition = 2 ;The position that contains the plug. ValveMap = Configuration\NovaSeqProto2_WasteValveMapA.xml ;Reagent valve map. Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = FC1 IxSelectorValve3 ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FlowCellSyringePumps1] ;Syringe pump(s) for one flow cell Type = SyringePump ;Configuration item type Exists = True ;Whether or not the device exists in this instrument configuration. Length = 2 ;Number of device instances in the array. [FlowCellSyringePumps] ;Syringe pump(s) for one flow cell Type = SyringePump ;Configuration item type Exists = True ;Whether or not the device exists in this instrument configuration. Length = 2 ;Number of device instances in the array. [FlowCellClamp2] ;Flow cell clamp board config settings. Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [BufferInterfaceModule2] ;BufferInterfaceModuleConfigSection Id = right_BIM ; StrawMotorPositionPollingIntervalMs = 1000 ;Straw motor position polling interval (milliseconds) StrawStatePollingIntervalMs = 1000 ;Straw state polling interval (milliseconds) Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FlowCellSelectorValves2] ;Selector valve(s) for one flow cell Type = SelectorValve ;Configuration item type Exists = True ;Whether or not the device exists in this instrument configuration. Length = 3 ;Number of device instances in the array. [FlowCellFluidicsSystem2.IxSelectorValve1] ;Settings for a Ix Valve selector Valve. ValveId = clsv ;The Id of the valve ValveType = CommonLine ;The type/function of this valve AirPosition = 13 ;The position connect to the air line. AvoidPosition = 11 ;The position to avoid during long moves. InitialPosition = 1 ;The initial position to set the valve to. NumberOfPorts = 24 ;The number of position ports on the valve. NumberOfRetries = 4 ;The number of attempts to recover from a failure. NumberOfRetriesInSequencing = 3 ;Gets the number of total retries duing a single sequencing run. PlugPosition = 0 ;The position that contains the plug. ValveMap = Configuration\NovaSeqProto1_CommonLineValveMapB.xml ;Reagent valve map. Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = FC2 IxSelectorValve1 ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FlowCellFluidicsSystem2.IxSelectorValve2] ;Settings for a Ix Valve selector Valve. ValveId = reagent ;The Id of the valve ValveType = Reagent ;The type/function of this valve AirPosition = 0 ;The position connect to the air line. AvoidPosition = 16 ;The position to avoid during long moves. InitialPosition = 6 ;The initial position to set the valve to. NumberOfPorts = 24 ;The number of position ports on the valve. NumberOfRetries = 4 ;The number of attempts to recover from a failure. NumberOfRetriesInSequencing = 3 ;Gets the number of total retries duing a single sequencing run. PlugPosition = 6 ;The position that contains the plug. ValveMap = Configuration\NovaSeqProto1_ReagentMapB.xml ;Reagent valve map. Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = FC2 IxSelectorValve2 ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FlowCellFluidicsSystem2.IxSelectorValve3] ;Settings for a Ix Valve selector Valve. ValveId = wsv_side_b ;The Id of the valve ValveType = Waste ;The type/function of this valve AirPosition = 2 ;The position connect to the air line. AvoidPosition = 0 ;The position to avoid during long moves. InitialPosition = 1 ;The initial position to set the valve to. NumberOfPorts = 2 ;The number of position ports on the valve. NumberOfRetries = 4 ;The number of attempts to recover from a failure. NumberOfRetriesInSequencing = 3 ;Gets the number of total retries duing a single sequencing run. PlugPosition = 2 ;The position that contains the plug. ValveMap = Configuration\NovaSeqProto2_WasteValveMapB.xml ;Reagent valve map. Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = FC2 IxSelectorValve3 ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FlowCellSyringePumps2] ;Syringe pump(s) for one flow cell Type = SyringePump ;Configuration item type Exists = True ;Whether or not the device exists in this instrument configuration. Length = 2 ;Number of device instances in the array. [Camera] ;Settings for the CiB. Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [IxLaser1] ;Base settings for LED, Laser and Autofocus laser -- Edit the settings under AutoFocusLaser instead of these. Color = Green ;Color emitted by this LED LaserNumber = 1 ;Laser number (one-based) DefaultPower = 50 ;Default laser power in mW WarmupPower = 4300 ;Initial power when warming up the laser, mW IdlePower = 50 ;Idle powerto use after warming up laser and after sequencing, mW MaxPower = 5000 ;Maximum laser power in mW MinPower = 50 ;Minimum laser power in mW MoveToAlignmentOnInit = True ;Move to alignment position on initialization PowerBlockingPercentMargin = 5 ;Percentage Margin criterion for use with IX SetPowerBlocking PowerBlockingDeltaMarginMw = 50 ;MilliWatt Power Delta criterion for use with IX SetPowerBlocking PowerBlockingTimeoutSeconds = 180 ;Seconds timeout for use with IX SetPowerBlocking PowerBlockingPollingIntervalMs = 200 ;The interval, in ms, at which to poll the laser power. PowerBlockingSuccessfulSamples = 3 ;The number of consecutive samples at the specified power level it takes for success. WarmupPowerBlockingPercentMargin = 5 ;Warmup Percentage Margin criterion for use with IX SetPowerBlocking WarmupPowerBlockingDeltaMarginMw = 0 ;Warmup MilliWatt Power Delta criterion for use with IX SetPowerBlocking WarmupPowerBlockingTimeoutSeconds = 1200 ;Warmup Seconds timeout for use with IX SetPowerBlocking WarmupPowerBlockingPollingIntervalMs = 200 ;The interval, in ms, at which to poll the laser power during warmup. WarmupPowerBlockingSuccessfulSamples = 3 ;The number of consecutive samples at the specified power level it takes for success during warmup. PollingIntervalMs = 3000 ;Polling interval in milliseconds MaxLogSize = 10 ;Maximum size (in MB) for laser monitoring CSV log file. MaxNumBackups = 10 ;Maximum number of old laser monitoring CSV log files to keep. LaserMonitorUpdateRateSeconds = 300 ;How often laser monitor background thread updates laser status and writes it to maintenance logs. LogPollingCommandsAndResponses = False ;True if we want to log laser-polling commands and responses (they are normally not logged) ZbeRangeMax = 3000 ;Maximum value for ZBE position ZbeRangeMin = -3000 ;Minimum value for ZBE position XMirrorRangeMax = 7600 ;Max value for X Mirror position XMirrorRangeMin = -7600 ;Min value for X Mirror position YMirrorRangeMax = 7600 ;Max value for Y Mirror position YMirrorRangeMin = -7600 ;Min value for Y Mirror position LaserTemperaturePollingPeriodSeconds = 0 ;The number of seconds to wait between laser temperature checks Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = Green5WLaser ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [IxLaser2] ;Base settings for LED, Laser and Autofocus laser -- Edit the settings under AutoFocusLaser instead of these. Color = Red ;Color emitted by this LED LaserNumber = 2 ;Laser number (one-based) DefaultPower = 50 ;Default laser power in mW WarmupPower = 4300 ;Initial power when warming up the laser, mW IdlePower = 50 ;Idle powerto use after warming up laser and after sequencing, mW MaxPower = 5000 ;Maximum laser power in mW MinPower = 50 ;Minimum laser power in mW MoveToAlignmentOnInit = True ;Move to alignment position on initialization PowerBlockingPercentMargin = 5 ;Percentage Margin criterion for use with IX SetPowerBlocking PowerBlockingDeltaMarginMw = 50 ;MilliWatt Power Delta criterion for use with IX SetPowerBlocking PowerBlockingTimeoutSeconds = 180 ;Seconds timeout for use with IX SetPowerBlocking PowerBlockingPollingIntervalMs = 200 ;The interval, in ms, at which to poll the laser power. PowerBlockingSuccessfulSamples = 3 ;The number of consecutive samples at the specified power level it takes for success. WarmupPowerBlockingPercentMargin = 5 ;Warmup Percentage Margin criterion for use with IX SetPowerBlocking WarmupPowerBlockingDeltaMarginMw = 0 ;Warmup MilliWatt Power Delta criterion for use with IX SetPowerBlocking WarmupPowerBlockingTimeoutSeconds = 1200 ;Warmup Seconds timeout for use with IX SetPowerBlocking WarmupPowerBlockingPollingIntervalMs = 200 ;The interval, in ms, at which to poll the laser power during warmup. WarmupPowerBlockingSuccessfulSamples = 3 ;The number of consecutive samples at the specified power level it takes for success during warmup. PollingIntervalMs = 3000 ;Polling interval in milliseconds MaxLogSize = 10 ;Maximum size (in MB) for laser monitoring CSV log file. MaxNumBackups = 10 ;Maximum number of old laser monitoring CSV log files to keep. LaserMonitorUpdateRateSeconds = 300 ;How often laser monitor background thread updates laser status and writes it to maintenance logs. LogPollingCommandsAndResponses = False ;True if we want to log laser-polling commands and responses (they are normally not logged) ZbeRangeMax = 3000 ;Maximum value for ZBE position ZbeRangeMin = -3000 ;Minimum value for ZBE position XMirrorRangeMax = 7600 ;Max value for X Mirror position XMirrorRangeMin = -7600 ;Min value for X Mirror position YMirrorRangeMax = 7600 ;Max value for Y Mirror position YMirrorRangeMin = -7600 ;Min value for Y Mirror position LaserTemperaturePollingPeriodSeconds = 0 ;The number of seconds to wait between laser temperature checks Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = Red5WLaser ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FchMibLink] ;FCH-MIB Link Config Settings Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [ObjectiveAirShield] ;Objective Air Shield Configuration Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [AnalyticsStorage] ;Parameters for instrument analytics long term storage. IsEnabled = True ;Indicates whether long-term data storage is enabled. LongTermStorageFolder = D:\Illumina\InstrumentAnalytics ;Long-term analytics data storage folder. MinFreeStorageSpaceGB = 8 ;The minimum required free space for the long-term analytics data storage. StorageCleanupIntervalHrs = 24 ;The interval at which automatic cleanup should be performed on the long-term analytics data storage. [Instrument] ;Specifies instrument specific settings Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [StageSafety] ;Configuration items for stage safety parameters. MaxTiltHeightSafeForHomingZMm = 3 ; AllowUnsafeStageMoves = False ; UndockedXMm = 141 ; UndockedXToleranceMm = 0.1 ; UndockedYMm = -75 ; UndockedYToleranceMm = 0.1 ; [Alignment] ;Alignment Config settings AutoTiltExpectedFocusUm = 400 ;Z position, in µm, where we expected focus to be. TiltMotor1XLocationMm = 257.375 ;Tilt Motor 1 physical X position, in mm. TiltMotor1YLocationMm = 198 ;Tilt Motor 1 physical Y position, in mm. TiltMotor2XLocationMm = 257.375 ;Tilt Motor 2 physical X position, in mm. TiltMotor2YLocationMm = 38 ;Tilt Motor 2 physical Y position, in mm. TiltMotor3XLocationMm = 17.125 ;Tilt Motor 3 physical X position, in mm. TiltMotor3YLocationMm = 118 ;Tilt Motor 3 physical Y position, in mm. TiltMotor3ToFlowCellACenterXDistanceMm = 77 ;Tilt Motor 3 to flow cell left center X distance in mm. TiltMotor1And2ToFlowCellACenterXDistanceMm = 163.25 ;Tilt Motor 1 and 2 to flow cell left center X distance in mm. FlowCellATiltOffsetXUmPerMm = 0.8263212227332 ;Tilt offset in X for flow cell A to align flow cell to camera plane. Positive value is rising from tilt 3 to tilts 1 & 2. TiltMotor3ToFlowCellBCenterXDistanceMm = 174.5 ;Tilt Motor 3 to flow cell right center X distance in mm. TiltMotor1And2ToFlowCellBCenterXDistanceMm = 65.75 ;Tilt Motor 1 and 2 to flow cell right center X distance in mm. FlowCellBTiltOffsetXUmPerMm = 1.15786638663802 ;Tilt offset in X for flow cell B to align flow cell to camera plane. Positive value is rising from tilt 3 to tilts 1 & 2. TiltMotor3ToFlowCellBIRDCenterXDistanceMm = 127.49 ;Tilt Motor 3 to flow cell BIRD center X distance in mm. TiltMotor1And2ToFlowCellBIRDCenterXDistanceMm = 112.76 ;Tilt Motor 1 and 2 to flow cell BIRD center X distance in mm. FlowCellBIRDTiltOffsetXUmPerMm = 0 ;Tilt offset in X for flow cell BIRD to align flow cell to camera plane. Positive value is rising from tilt 3 to tilts 1 & 2. FlowCellLeftTiltMotor1StartPositionMm = 5.49875 ;Left Flow Cell Tilt Motor 1 initial position, in mm, for AutoTilt. FlowCellLeftTiltMotor2StartPositionMm = 5.615 ;Left Flow Cell Tilt Motor 2 initial position, in mm, for AutoTilt. FlowCellLeftTiltMotor3StartPositionMm = 5.44375 ;Left Flow Cell Tilt Motor 3 initial position, in mm, for AutoTilt. FlowCellRightTiltMotor1StartPositionMm = 5.47125 ;Right Flow Cell Tilt Motor 1 initial position, in mm, for AutoTilt. FlowCellRightTiltMotor2StartPositionMm = 5.59 ;Right Flow Cell Tilt Motor 2 initial position, in mm, for AutoTilt. FlowCellRightTiltMotor3StartPositionMm = 5.4625 ;Right Flow Cell Tilt Motor 3 initial position, in mm, for AutoTilt. FlowCellBIRDTiltMotor1StartPositionMm = 5.775 ;BIRD Flow Cell Tilt Motor 1 initial position, in mm, for AutoTilt. FlowCellBIRDTiltMotor2StartPositionMm = 5.938 ;BIRD Flow Cell Tilt Motor 2 initial position, in mm, for AutoTilt. FlowCellBIRDTiltMotor3StartPositionMm = 5.903 ;BIRD Flow Cell Tilt Motor 3 initial position, in mm, for AutoTilt. VerifyAutoTilt = True ;Whether or not to verify AutoTilt correction. TiltTolerance = 0.0015 ;Tilt tolerance expressed as the ratio of Z difference over distance between the two worst sample points (mm per mm). TiltPositionDuringXyMovesMm = 3 ;Move the tilt motors to this position during XY LowerTiltMotorsDuringXyMoves = True ;Lower the tilt motors during XY moves to reduce chance of collision SurfaceFindingTopZUm = 800 ;Starting point for Z when searching for the surface SurfaceFindingBottomZUm = 200 ;Ending point for Z when searching for the surface SurfaceFindingStepSizeUm = 5 ;Step size to use when searching for the surfade SurfaceFindingWindowsizeUm = 31 ;Window size to use when evaluating Z positions SurfaceFindingThresholdUm = 6 ;Maximum distance between calculated Z positions for the same surface SurfaceFindingMinNumberOfGoodDataPoints = 5 ;Must have at least this many good data points to determine surface position SurfaceFindingSpotMoveRatioMinPercent = 75 ;Make sure the left and right FTM laser spots move about the same distance UbertargetUsePwm = True ;For ubertarget, use PWM instead of having focus laser on continuously FtmPwmLaserPowerAdjustWaitPeriodMs = 1000 ;After changing the FTM power or pulse, wait this long before using PWM FocusModelTopNominalBestFocusDeltaX = 1477.31811523438 ;Top surface nominal focus spot delta X when in best focus for top surface FocusModelTopNominalGainPixUm = -17.1923828125 ;Top surface nominal focus model gain FocusModelTopNominalServoGain = -50 ;Top surface servo gain to pass to FW. FocusModelBottomNominalBestFocusDeltaX = 876 ;Bottom surface nominal focus spot delta X when in best focus for top surface FocusModelBottomNominalGainPixUm = -17.1923828125 ;Bottom surface nominal focus model gain FocusModelBottomNominalServoGain = -50 ;Bottom surface servo gain to pass to FW. FocusModelBirdBottomNominalBestFocusDeltaX = 0 ;BIRD Bottom surface nominal focus spot delta X when in best focus for top surface DistanceBetweenFlowCellS1AndS2Um = 185 ;Distance between the top of the flow cell glass and the lane top. 300um (physical distance) / 1.55 (refractive index for glass) DistanceBetweenFlowCellS2AndS3WetUm = 71.65 ;Distance between lane top and lane bottom. 100um (physical distance) / 1.33 (refractive index for liquid). This is for FTM laser or red/green without zoom lens. 71.65 is the median from a number of actual runs. DistanceBetweenFlowCellS2AndS3DryUm = 105 ;Distance between lane top and lane bottom. 100um (physical distance). This is for FTM laser or red/green without zoom lens. DistanceBetweenFlowCellS2AndS3WithZoomLensUm = 32.6 ;Distance between lane top and lane bottom for red/green when using zoom lens. 32.6 is the median from a number of actual runs. DistanceBetweenFlowCellSurfaceThreshold = 20 ;Distance the actual surface can be from the expected location +/- DistanceBetweenBIRDS1AndS3Um = 245 ;Thickness of the top glass on a BIRD ubertarget. 395um (physical distance) / 1.55 (refractive index for glass) YDistanceBetweenFtmFovEomFovUm = 96 ;Y distance between middle of FTM field of view and middle of EOM field of view (um) MaxZMoveDistancePerTriggerNm = 200 ;Max movement per trigger allowed during scanning (nm) DelayAfterZMoveMs = 500 ;When finding the surface, delay after the first big Z move to let the Z motor stabilize DoNotMoveTiltsOnThroughFocusStackScans = True ;When taking a through focus stack, do not move the tilts during TDI scans [FocusModel] ;FocusModelConfigSection MaxZMoveAttempts = 3 ;Max number of attempts per z move ScanVelocityMmPerSec = 12 ;Scan velocity in mm per sec ScanVelocityUbertargetMmPerSec = 4 ;Scan velocity in mm per sec for 1 um pinholes at 3um pitch in sequencing lane ThroughFocusStackStepSizeUm = 0.2 ;Step size for through focus stack ThroughFocusStackNumImagesAboveAndBelow = 35 ;Number of images to take above and below the starting Z position ScanLengthMm = 0.25 ;Scan length in mm Gain = 0 ;Camera gain Lane = 1 ;Lane to use Swath = 3 ;Swath to use YOffsetMm = 0.5 ;How far into the lane to take the images RedLaserPowerMw = 500 ;Red laser power mW RedLaserPowerUbertargetMw = 75 ;Red laser power mW for 1 um pinholes at 3um pitch in sequencing lane GreenLaserPowerMw = 600 ;Green laser power mW GreenLaserPowerUbertargetMw = 50 ;Green laser power mW for 1 um pinholes at 3um pitch in sequencing lane DepthOfFocusUm = 2.5 ;The depth of focus for focus model generation StandardDeviationThreshold = 1 ;The standard deviation threshold used in focus model generation FocusModelChromatismThresholdInNanometers = 1000 ;The max value allowed for chromatism during focus model generation UseBrennerTiling = True ;Use subregions of the image to calculate brenner values BrennerTilingColumns = 3 ;The numbr of columns to use in generating brenner subregions BrennerTilingRows = 1 ;The number of rows to use in generating brenner subregions FocusModelRetries = 3 ;The number of retries for generating the focus model FocusModelRetryStepSizeInMillimeters = 2 ;How far to move in Y during focus model retries ServoGain = -100 ;The focus model servo gain used by FW. ServoGainBoostMultiplier = 2 ;The focus model servo gain boost multiplier used by FW. BoostSampleCount = 4 ;The boost sample count used by FW. MaxDifferenceBetweenSlopeAndInterpolatedSpotSeparation = 3 ;Max difference allowed between slope and interpolated best spot separation calculation (pixels) MaxSlopeResidualErrorStepSizeMultiplier = 2 ;Max error for any single point used in the slope calculation as a multiple of the avg step size MiniFocusModelStackStepSizeUm = 0.3 ;Step size for through focus stack MiniFocusModelStackNumImagesAboveAndBelow = 8 ;Number of images to take above and below the starting Z position MaxFocusModelAdjustPixels = 1 ;When adjusting the focus model, this is the max adjustment (in pixels) per cycle MiniFocusModelMaxFailuresToSave = 5 ;Save this many failed mini-focus models MiniFocusModelMaxSlopeDifference = 0.01 ;If the difference in slope is greater than this amount, discard the mini-focus model MiniFocusModelSaveExtraDataOnError = False ;Save the FW Z stage log when the mini focus model fails MiniFocusModelTotalNumberOfTries = 3 ;Try this many times to make a mini focus model SpotMoveRatioMinPercent = 75 ;Make sure the left and right FTM laser spots move about the same distance EtfScanLengthMm = 1.666 ;Length of scan for ETF in mm EtfZDeltaNm = 52 ;How far to move Z after each FTM capture in nm EtfYUpdateFrequency = 2132 ;The number of Y triggers between each FTM capture [ImageAcquisition] ;ImageAcquisitionConfigSection CameraResolutionMicronsPerPixel = 0.346153846153846 ;The um/pixel resolution of the camera CameraFieldOfViewYDimensionPixels = 82 ;The y dimension field of view of the camera CameraFieldOfViewXDimensionPixels = 3200 ;The x dimension field of view of the camera StartLaserSafetyPositionMm = 15 ;The lower Y position safe to use lasers without hitting gasket EndLaserSafetyPositionMm = 155 ;The upper Y position safe to use lasers without hitting gasket [FindBestZSurfaces] ;FindBestZSurfacesConfigSection ZDistanceMmBetweenSlices = 0.01 ;Z distance in mm between slices RedLaserPower = 500 ;Red laser power for finding best Z surfaces GreenLaserPower = 500 ;Green laser power for finding best Z surfaces ScanVelocity = 12 ;Scan velocity for finding surfaces [FocusLaser] ;FocusLaserConfigSection EncoderTrigger = 2133 ;Encoder trigger Threshold = 25 ;Focus spot intensity threshold FrameRate = 5 ;Frame rate ExposureUs = 250 ;Camera exposure μs LaserPulseDurationUs = 250 ;Laser pulse duration for a wet flow cell μs LaserPulseDurationUbertargetUs = 21 ;Laser pulse duration for the ubertarget μs LaserPulseDurationDryFlowCellUs = 250 ;Laser pulse duration for a dry flow cell μs LaserPowerMw = 0.5 ;Laser power mW for a wet flow cell LaserPowerUbertargetMw = 0.1 ;Laser power mW for the ubertarget LaserPowerDryFlowCellMw = 0.1 ;Laser power mW for a dry flow cell (7.8 times brighter than wet) Gain = 1 ;Gain [FocusLaserRoi] ;FocusLaserROIConfigSection Top = 480 ;Top Y pixel position Height = 100 ;ROI height Region1Left = 40 ;Region 1 left pixel Region1Width = 500 ;Region 1 width Region2Left = 370 ;Region 2 left pixel Region2Width = 500 ;Region 2 width Region3Left = 1180 ;Region 3 left pixel Region3Width = 500 ;Region 3 width Region4Left = 1520 ;Region 4 left pixel Region4Width = 500 ;Region 4 width [FocusStackAnalysis1] ;Through focus stack config settings MaxCorrelationShift = 4 ;Max correlation shift value allowed when calculating FWHM FiducialDetectionThreshold = 5 ;Min pixel value for fiducial SkipFiducialDetection = True ;Whether or not to skip fiducial detection MaxFwhmAllowed = 10 ;Maximum allowed FWHM observed UDOFFwhmLimitRed = 2.05 ;Usable depth of field limit for red channel. Filters out poor fwhm values for poly fit. UDOFFwhmLimitGreen = 2.05 ;Usable depth of field limit for green channel. Filters out poor fwhm values for poly fit. RangeFwhmLow = 1.2 ;Lower bound for valid FWHM RangeFwhmHigh = 2.5 ;Upper bound for valid FWHM for 0.5um pinholes FiducialInnerRadius = 58 ;Inner radius of fiducial FiducialOuterRadius = 115 ;Out radius of fiducial BestZThresholdDistanceForParabola = 2.3 ;Per side distance to look for best observed Z NumParabolaFitPointsPerSide = 3 ;Number of parabola fit points per side for polyfit. UdofSmoothMethod = Average ;Method for uDOF smoothing. Valid values are 'Average', 'Median', or 'None'. UdofSmoothWindowSize = 5 ;Window size for uDOF smoothing. UdofRoiRedX0 = 0 ;X0 for red uDOF ROI. UdofRoiRedY0 = 1350 ;Y0 for red uDOF ROI UdofRoiGreenX0 = 0 ;X0 for green uDOF ROI UdofRoiGreenY0 = 1350 ;Y0 for green uDOF ROI UdofRoiWidth = 3200 ;Width for uDOF region of interest. If 0, max possible is applied UdofRoiHeight = 300 ;Height for uDOF region of interest. If 0, max possible is applied ChromatismRoiRedX0 = 1350 ;X0 for red Chromatism ROI. ChromatismRoiRedY0 = 1350 ;Y0 for red Chromatism ROI ChromatismRoiGreenX0 = 1350 ;X0 for green Chromatism ROI ChromatismRoiGreenY0 = 1350 ;Y0 for green Chromatism ROI ChromatismRoiWidth = 500 ;Width for Chromatism region of interest. If 0, max possible is applied ChromatismRoiHeight = 500 ;Height for Chromatism region of interest. If 0, max possible is applied PixelSaturationThreshold = 4095 ;Threshold for considering a pixel saturated MinBufferAroundBestBrenner = 3 ;Required num datapoints around best brenner image FieldOfViewPixelWidth = 2240 ;Field of view width (in pixels) MaxThreads = 16 ;Max number of threads to use at any time MaxImagesInMemory = 4 ;Max number of images to hold in memory at any given point IntensitySignalThreshold = 500 ;Threshold for intensity signal check FwhmRoiRedX0 = 0 ;X0 for red FWHM ROI. FwhmRoiRedY0 = 0 ;Y0 for red FWHM ROI FwhmRoiGreenX0 = 0 ;X0 for green FWHM ROI FwhmRoiGreenY0 = 0 ;Y0 for green FWHM ROI FwhmRoiWidth = 0 ;Width for FWHM region of interest. If 0, max possible is applied FwhmRoiHeight = 0 ;Height for FWHM region of interest. If 0, max possible is applied [FocusStackAnalysis2] ;Through focus stack config settings MaxCorrelationShift = 4 ;Max correlation shift value allowed when calculating FWHM FiducialDetectionThreshold = 5 ;Min pixel value for fiducial SkipFiducialDetection = True ;Whether or not to skip fiducial detection MaxFwhmAllowed = 10 ;Maximum allowed FWHM observed UDOFFwhmLimitRed = 2.95 ;Usable depth of field limit for red channel. Filters out poor fwhm values for poly fit. UDOFFwhmLimitGreen = 2.95 ;Usable depth of field limit for green channel. Filters out poor fwhm values for poly fit. RangeFwhmLow = 1.2 ;Lower bound for valid FWHM RangeFwhmHigh = 3.3 ;Upper bound for valid FWHM for 0.5um pinholes FiducialInnerRadius = 58 ;Inner radius of fiducial FiducialOuterRadius = 115 ;Out radius of fiducial BestZThresholdDistanceForParabola = 2.3 ;Per side distance to look for best observed Z NumParabolaFitPointsPerSide = 3 ;Number of parabola fit points per side for polyfit. UdofSmoothMethod = Average ;Method for uDOF smoothing. Valid values are 'Average', 'Median', or 'None'. UdofSmoothWindowSize = 5 ;Window size for uDOF smoothing. UdofRoiRedX0 = 0 ;X0 for red uDOF ROI. UdofRoiRedY0 = 1350 ;Y0 for red uDOF ROI UdofRoiGreenX0 = 0 ;X0 for green uDOF ROI UdofRoiGreenY0 = 1350 ;Y0 for green uDOF ROI UdofRoiWidth = 3200 ;Width for uDOF region of interest. If 0, max possible is applied UdofRoiHeight = 300 ;Height for uDOF region of interest. If 0, max possible is applied ChromatismRoiRedX0 = 1350 ;X0 for red Chromatism ROI. ChromatismRoiRedY0 = 1350 ;Y0 for red Chromatism ROI ChromatismRoiGreenX0 = 1350 ;X0 for green Chromatism ROI ChromatismRoiGreenY0 = 1350 ;Y0 for green Chromatism ROI ChromatismRoiWidth = 500 ;Width for Chromatism region of interest. If 0, max possible is applied ChromatismRoiHeight = 500 ;Height for Chromatism region of interest. If 0, max possible is applied PixelSaturationThreshold = 4095 ;Threshold for considering a pixel saturated MinBufferAroundBestBrenner = 3 ;Required num datapoints around best brenner image FieldOfViewPixelWidth = 2240 ;Field of view width (in pixels) MaxThreads = 16 ;Max number of threads to use at any time MaxImagesInMemory = 4 ;Max number of images to hold in memory at any given point IntensitySignalThreshold = 500 ;Threshold for intensity signal check FwhmRoiRedX0 = 0 ;X0 for red FWHM ROI. FwhmRoiRedY0 = 0 ;Y0 for red FWHM ROI FwhmRoiGreenX0 = 0 ;X0 for green FWHM ROI FwhmRoiGreenY0 = 0 ;Y0 for green FWHM ROI FwhmRoiWidth = 0 ;Width for FWHM region of interest. If 0, max possible is applied FwhmRoiHeight = 0 ;Height for FWHM region of interest. If 0, max possible is applied [FocusStackAnalysis3] ;Through focus stack config settings MaxCorrelationShift = 4 ;Max correlation shift value allowed when calculating FWHM FiducialDetectionThreshold = 5 ;Min pixel value for fiducial SkipFiducialDetection = True ;Whether or not to skip fiducial detection MaxFwhmAllowed = 10 ;Maximum allowed FWHM observed UDOFFwhmLimitRed = 2.05 ;Usable depth of field limit for red channel. Filters out poor fwhm values for poly fit. UDOFFwhmLimitGreen = 2.05 ;Usable depth of field limit for green channel. Filters out poor fwhm values for poly fit. RangeFwhmLow = 1.2 ;Lower bound for valid FWHM RangeFwhmHigh = 2.5 ;Upper bound for valid FWHM for 0.5um pinholes FiducialInnerRadius = 58 ;Inner radius of fiducial FiducialOuterRadius = 115 ;Out radius of fiducial BestZThresholdDistanceForParabola = 2.3 ;Per side distance to look for best observed Z NumParabolaFitPointsPerSide = 3 ;Number of parabola fit points per side for polyfit. UdofSmoothMethod = Average ;Method for uDOF smoothing. Valid values are 'Average', 'Median', or 'None'. UdofSmoothWindowSize = 5 ;Window size for uDOF smoothing. UdofRoiRedX0 = 0 ;X0 for red uDOF ROI. UdofRoiRedY0 = 1350 ;Y0 for red uDOF ROI UdofRoiGreenX0 = 0 ;X0 for green uDOF ROI UdofRoiGreenY0 = 1350 ;Y0 for green uDOF ROI UdofRoiWidth = 3200 ;Width for uDOF region of interest. If 0, max possible is applied UdofRoiHeight = 300 ;Height for uDOF region of interest. If 0, max possible is applied ChromatismRoiRedX0 = 1854 ;X0 for red Chromatism ROI. ChromatismRoiRedY0 = 1386 ;Y0 for red Chromatism ROI ChromatismRoiGreenX0 = 1854 ;X0 for green Chromatism ROI ChromatismRoiGreenY0 = 986 ;Y0 for green Chromatism ROI ChromatismRoiWidth = 300 ;Width for Chromatism region of interest. If 0, max possible is applied ChromatismRoiHeight = 300 ;Height for Chromatism region of interest. If 0, max possible is applied PixelSaturationThreshold = 4095 ;Threshold for considering a pixel saturated MinBufferAroundBestBrenner = 3 ;Required num datapoints around best brenner image FieldOfViewPixelWidth = 2240 ;Field of view width (in pixels) MaxThreads = 16 ;Max number of threads to use at any time MaxImagesInMemory = 4 ;Max number of images to hold in memory at any given point IntensitySignalThreshold = 500 ;Threshold for intensity signal check FwhmRoiRedX0 = 0 ;X0 for red FWHM ROI. FwhmRoiRedY0 = 0 ;Y0 for red FWHM ROI FwhmRoiGreenX0 = 0 ;X0 for green FWHM ROI FwhmRoiGreenY0 = 0 ;Y0 for green FWHM ROI FwhmRoiWidth = 0 ;Width for FWHM region of interest. If 0, max possible is applied FwhmRoiHeight = 0 ;Height for FWHM region of interest. If 0, max possible is applied [FocusStackAnalysis4] ;Through focus stack config settings MaxCorrelationShift = 4 ;Max correlation shift value allowed when calculating FWHM FiducialDetectionThreshold = 5 ;Min pixel value for fiducial SkipFiducialDetection = True ;Whether or not to skip fiducial detection MaxFwhmAllowed = 10 ;Maximum allowed FWHM observed UDOFFwhmLimitRed = 2.95 ;Usable depth of field limit for red channel. Filters out poor fwhm values for poly fit. UDOFFwhmLimitGreen = 2.95 ;Usable depth of field limit for green channel. Filters out poor fwhm values for poly fit. RangeFwhmLow = 1.2 ;Lower bound for valid FWHM RangeFwhmHigh = 3.3 ;Upper bound for valid FWHM for 0.5um pinholes FiducialInnerRadius = 58 ;Inner radius of fiducial FiducialOuterRadius = 115 ;Out radius of fiducial BestZThresholdDistanceForParabola = 2.3 ;Per side distance to look for best observed Z NumParabolaFitPointsPerSide = 3 ;Number of parabola fit points per side for polyfit. UdofSmoothMethod = Average ;Method for uDOF smoothing. Valid values are 'Average', 'Median', or 'None'. UdofSmoothWindowSize = 5 ;Window size for uDOF smoothing. UdofRoiRedX0 = 0 ;X0 for red uDOF ROI. UdofRoiRedY0 = 1350 ;Y0 for red uDOF ROI UdofRoiGreenX0 = 0 ;X0 for green uDOF ROI UdofRoiGreenY0 = 1350 ;Y0 for green uDOF ROI UdofRoiWidth = 3200 ;Width for uDOF region of interest. If 0, max possible is applied UdofRoiHeight = 300 ;Height for uDOF region of interest. If 0, max possible is applied ChromatismRoiRedX0 = 1854 ;X0 for red Chromatism ROI. ChromatismRoiRedY0 = 1386 ;Y0 for red Chromatism ROI ChromatismRoiGreenX0 = 1854 ;X0 for green Chromatism ROI ChromatismRoiGreenY0 = 986 ;Y0 for green Chromatism ROI ChromatismRoiWidth = 300 ;Width for Chromatism region of interest. If 0, max possible is applied ChromatismRoiHeight = 300 ;Height for Chromatism region of interest. If 0, max possible is applied PixelSaturationThreshold = 4095 ;Threshold for considering a pixel saturated MinBufferAroundBestBrenner = 3 ;Required num datapoints around best brenner image FieldOfViewPixelWidth = 2240 ;Field of view width (in pixels) MaxThreads = 16 ;Max number of threads to use at any time MaxImagesInMemory = 4 ;Max number of images to hold in memory at any given point IntensitySignalThreshold = 500 ;Threshold for intensity signal check FwhmRoiRedX0 = 0 ;X0 for red FWHM ROI. FwhmRoiRedY0 = 0 ;Y0 for red FWHM ROI FwhmRoiGreenX0 = 0 ;X0 for green FWHM ROI FwhmRoiGreenY0 = 0 ;Y0 for green FWHM ROI FwhmRoiWidth = 0 ;Width for FWHM region of interest. If 0, max possible is applied FwhmRoiHeight = 0 ;Height for FWHM region of interest. If 0, max possible is applied [DistortionAnalysis] ;Distortion analysis config settings Magnification = 26 ;Magnification SearchWindow = 3 ;Search window RoiUpperLeftX = 0 ;X coordinate of starting position of ROI RoiUpperLeftY = 635 ;Y coordinate of starting position of ROI RoiWidth = 3200 ;ROI width RoiHeight = 80 ;ROI height PhaseThreshold = 200 ;Phase threshold SmoothWindowSize = 10 ;Window size to use when smoothing TemplateGenerationType = PatternedHexagon ;Template generation type UpperLeftFiducialXInPixels = 1102 ;Upper left fiducial X coordinate UpperLeftFiducialYInPixels = 431 ;Upper left fiducial Y coordinate RegistratorType = Fiducial ;Registration method HexagonalPatternOrientation = Horizontal ;Hexagon pattern orientation RigidRegistrationNumberOfColumns = 119 ;Number of columns to use in rigid registration RigidRegistrationNumberOfRows = 121 ;Number of rows to use in rigid registration RigidRegistrationPitchInPixels = 8.666 ;Pitch to use in rigid registration HighPassFilterSubregions = False ;Whether or not to perform high pass filtering on sub regions SubRegionSize = 512 ;Sub region size WriteDebugImages = False ;Whether or not to output debug images FiducialDarkRing1RadiiInPixels = 58.2 ;1st dark ring fiducial radii FiducialDarkRing2RadiiInPixels = 116.4 ;2nd dark ring fiducial radii FiducialDarkRing1ThicknessInPixels = 14 ;1st dark ring fiducial radii thickness FiducialDarkRing2ThicknessInPixels = 14 ;2nd dark ring fiducial radii thickness FiducialBrightRing1RadiiInPixels = 58.2 ;1st dark ring fiducial radii FiducialBrightRing2RadiiInPixels = 116.4 ;2nd dark ring fiducial radii FiducialBrightRing1ThicknessInPixels = 2 ;1st dark ring fiducial radii thickness FiducialBrightRing2ThicknessInPixels = 2 ;2nd dark ring fiducial radii thickness [LightBar] ;LightBars Color Settings Blue = 0, 0, 84 ;R, G, B - RGB Values for Blue. Orange = 110, 85, 0 ;R, G, B - RGB Values for Orange. White = 255, 255, 255 ;R, G, B - RGB Values for White. Green = 0, 66, 0 ;R, G, B - RGB Values for Green. Red = 255, 0, 0 ;R, G, B - RGB Values for Red. [Rta] ;RTA config settings IpAddress = 169.254.0.1 ;The IP Address of the IX device. Port = 9030 ;The port to communicate with RTA over. UserName = sbsuser ;Username used to update RTA with Password = 8L0<3D.oU7! ;Password used to update RTA with SshPort = 22 ; The port used to update RTA with StagingDirectory = /home/sbsuser/IlluminaTemp ; Remote staging directory for RTA RemoteDirectory = /home/sbsuser/ ; Remote app directory for RTA SymLinkName = Illumina ;Symlink name for RTA [Sequencing] ;Sequencing Config settings MaxCyclesToFindSurface = 5 ;Max cycle to find surface before scanning swath FindSurfaceBeforeScan = FirstSwathPerLaneUpToMaxCycle ;When to find surface before scanning FirstSurfaceInCycle = Bottom ;Specifying which surface is scanned first at the start of a cycle. FocusLeadNm = 1250000 ;Focus lead length (nm) for embedded scan only. AdjustFocusModelEachCycle = True ;Adjust the focus model each cycle AdjustFocusModelSurface = AlternateTopBottomByCycle ;Adjust the focus model using these surfaces AdjustFocusModelUsingEtf = True ;If true, use ETF. If false, use mini focus model UseEndingZPositionForNextSwath = True ;When not surface finding, use the ending Z position from the last swath as the starting Z for the current swath MaximumNumberOfPreRunFolders = 10 ;The maximum number of pre run folders to retain in the pre run folder WriteComputerName = False ;Write the computer name to the run folder (only for in-house use) PowerScalingMode = None ;Mode to use for laser power scaling ('none', 'absolute', 'dynamic'). Default is 'none' PercentPowerScalingFactor = 1 ;Decimal percentage by which to scale. Only applicable when power scaling mode is 'absolute'. Must be number greater than 0 and less than 1, otherwise no scaling is applied TargetAutocenterIntensity = 2000 ;Target autocenter intensity. Provides baseline for scaling. Only applicable when power scaling mode is 'dynamic' AutocenterSquareAreaPixel = 150 ;Width and height of square area, centered on autocenter cross to measure intensity. Only applicable when power scaling mode is 'dynamic' RedStartingPowerUpperLimitMilliwatt = 1000 ;Upper limit of red laser power at cycle 1 (milliwatts). Only applicable when power scaling RedStartingPowerLowerLimitMilliwatt = 700 ;Lower limit of red laser power at cycle 1 (milliwatts). Only applicable when power scaling GreenStartingPowerUpperLimitMilliwatt = 1500 ;Upper limit of green laser power at cycle 1 (milliwatts). Only applicable when power scaling mode GreenStartingPowerLowerLimitMilliwatt = 1050 ;Lower limit of green laser power at cycle 1 (milliwatts). Only applicable when power scaling mode [IxXMotor] ;IX X Motor Configs CoordinateSystemOffsetMm = -143.521801061626 ;Coordinate system offset in mm. AccelerationMmPerSec2 = 300 ;Acceleration for normal motion in mm/s^2. DecelerationMmPerSec2 = 300 ;Deceleration for normal motion in mm/s^2. VelocityMmPerSec = 15 ;Velocity for normal motion in mm/s. LowerLimitMm = 74 ;Lower limit in mm, when soft limits are enabled. UpperLimitMm = 214 ;Upper limit in mm, when soft limits are enabled. AbsoluteLowerLimitMm = 71 ;Absolute lower limit in mm, when soft limits are "disabled". AbsoluteUpperLimitMm = 221 ;Absolute upper limit in mm, when soft limits are "disabled". HomeAccelerationMmPerSec2 = 300 ;Home acceleration in mm/s^2. HomeDecelerationMmPerSec2 = 300 ;Home deceleration in mm/s^2. HomeFastVelocityMmPerSec = 20 ;Home fast velocity in mm/s. HomeCreepVelocityMmPerSec = 10 ;Home creep velocity in mm/s. PositionPollingIntervalMs = 250 ;Polling interval time in ms AllowHoming = True ;If false, disables motor homing Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [IxYMotor] ;IX Y Motor Configs CoordinateSystemOffsetMm = -184.028363548792 ;Coordinate system offset in mm. AccelerationMmPerSec2 = 360 ;Acceleration for normal motion in mm/s^2. DecelerationMmPerSec2 = 360 ;Deceleration for normal motion in mm/s^2. VelocityMmPerSec = 48 ;Velocity for normal motion in mm/s. LowerLimitMm = 50 ;Lower limit in mm, when soft limits are enabled. UpperLimitMm = 187 ;Upper limit in mm, when soft limits are enabled. AbsoluteLowerLimitMm = -75 ;Absolute lower limit in mm, when soft limits are "disabled". AbsoluteUpperLimitMm = 191 ;Absolute upper limit in mm, when soft limits are "disabled". HomeAccelerationMmPerSec2 = 360 ;Home acceleration in mm/s^2. HomeDecelerationMmPerSec2 = 360 ;Home deceleration in mm/s^2. HomeFastVelocityMmPerSec = 20 ;Home fast velocity in mm/s. HomeCreepVelocityMmPerSec = 10 ;Home creep velocity in mm/s. PositionPollingIntervalMs = 250 ;Polling interval time in ms AllowHoming = True ;If false, disables motor homing Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [IxZMotor] ;IX Z Motor Configs CoordinateSystemOffsetMm = -0.4 ;Coordinate system offset in mm. AccelerationMmPerSec2 = 10 ;Acceleration for normal motion in mm/s^2. DecelerationMmPerSec2 = 10 ;Deceleration for normal motion in mm/s^2. VelocityMmPerSec = 10 ;Velocity for normal motion in mm/s. LowerLimitMm = 0 ;Lower limit in mm, when soft limits are enabled. UpperLimitMm = 0.8 ;Upper limit in mm, when soft limits are enabled. AbsoluteLowerLimitMm = 0 ;Absolute lower limit in mm, when soft limits are "disabled". AbsoluteUpperLimitMm = 0.8 ;Absolute upper limit in mm, when soft limits are "disabled". HomeAccelerationMmPerSec2 = 5 ;Home acceleration in mm/s^2. HomeDecelerationMmPerSec2 = 5 ;Home deceleration in mm/s^2. HomeFastVelocityMmPerSec = 10 ;Home fast velocity in mm/s. HomeCreepVelocityMmPerSec = 5 ;Home creep velocity in mm/s. PositionPollingIntervalMs = 250 ;Polling interval time in ms AllowHoming = True ;If false, disables motor homing Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [LaserShutter] ;Static config items for an laser shutter ShutterDelayMs = 100 ;Shutter delay in milliseconds Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FlowCellFluidicsSystem1] ;FlowCellFluidicsSystemConfigSection CommonVolumeBCalbrationuL = 0 ;Volume in uL from RSV to flowcell inlet for 2 lane flowcells CommonVolumeABCalbrationuL = 0 ;Volume in uL from RSV to flowcell inlet for 4 lane flowcells VolumeTemplateCalbrationuL = 0 ;Volume in uL from TMP sipper to RSV for priming Label = A ; Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FlowCellFluidicsSystem1.IxSyringePump1] ;Settings for a Ix Valve selector Valve. DeviceID = pump_side_a_1 ;Device ID Prefix /1. NumberOfSyringes = 2 ;Number of syringes in a Pump. SyringeVolumeUl = 1000 ;Number of uL for one full syringe. MaxVelocityUlPerMinute = 15000 ;Maximum Pump Speed in uL / min DelayMsBetweenReagentValveAndAspirate = 100 ;Delay between moving the pump to aspirate and moving the valve to the dispense position. MultiAspirate = True ;Allows aspirating multiple times before dispensing. UseAspirateAutorecovery = False ;When true software will attempt recovery and resynch of pumps on a syringe overload. UseDispenseAutorecovery = False ;When true software will attempt recovery and resynch of pumps on a syringe overload. EnablePolling = False ;Sampling rate for pump position updates PressureChangePerPumpStep = 0.002667 ;Initial guess for pressure feedback slope (PSI / step). SamplingRate = 1000 ;Sampling rate in ms. Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FlowCellFluidicsSystem1.IxSyringePump2] ;Settings for a Ix Valve selector Valve. DeviceID = pump_side_a_2 ;Device ID Prefix /1. NumberOfSyringes = 2 ;Number of syringes in a Pump. SyringeVolumeUl = 1000 ;Number of uL for one full syringe. MaxVelocityUlPerMinute = 15000 ;Maximum Pump Speed in uL / min DelayMsBetweenReagentValveAndAspirate = 100 ;Delay between moving the pump to aspirate and moving the valve to the dispense position. MultiAspirate = True ;Allows aspirating multiple times before dispensing. UseAspirateAutorecovery = False ;When true software will attempt recovery and resynch of pumps on a syringe overload. UseDispenseAutorecovery = False ;When true software will attempt recovery and resynch of pumps on a syringe overload. EnablePolling = False ;Sampling rate for pump position updates PressureChangePerPumpStep = 0.002667 ;Initial guess for pressure feedback slope (PSI / step). SamplingRate = 1000 ;Sampling rate in ms. Simulated = True ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FlowCellFluidicsSystem2] ;FlowCellFluidicsSystemConfigSection CommonVolumeBCalbrationuL = 0 ;Volume in uL from RSV to flowcell inlet for 2 lane flowcells CommonVolumeABCalbrationuL = 0 ;Volume in uL from RSV to flowcell inlet for 4 lane flowcells VolumeTemplateCalbrationuL = 0 ;Volume in uL from TMP sipper to RSV for priming Label = B ; Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FlowCellFluidicsSystem2.IxSyringePump1] ;Settings for a Ix Valve selector Valve. DeviceID = pump_side_b_1 ;Device ID Prefix /1. NumberOfSyringes = 2 ;Number of syringes in a Pump. SyringeVolumeUl = 1000 ;Number of uL for one full syringe. MaxVelocityUlPerMinute = 15000 ;Maximum Pump Speed in uL / min DelayMsBetweenReagentValveAndAspirate = 100 ;Delay between moving the pump to aspirate and moving the valve to the dispense position. MultiAspirate = True ;Allows aspirating multiple times before dispensing. UseAspirateAutorecovery = False ;When true software will attempt recovery and resynch of pumps on a syringe overload. UseDispenseAutorecovery = False ;When true software will attempt recovery and resynch of pumps on a syringe overload. EnablePolling = False ;Sampling rate for pump position updates PressureChangePerPumpStep = 0.002667 ;Initial guess for pressure feedback slope (PSI / step). SamplingRate = 1000 ;Sampling rate in ms. Simulated = True ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [FlowCellFluidicsSystem2.IxSyringePump2] ;Settings for a Ix Valve selector Valve. DeviceID = pump_side_b_2 ;Device ID Prefix /1. NumberOfSyringes = 2 ;Number of syringes in a Pump. SyringeVolumeUl = 1000 ;Number of uL for one full syringe. MaxVelocityUlPerMinute = 15000 ;Maximum Pump Speed in uL / min DelayMsBetweenReagentValveAndAspirate = 100 ;Delay between moving the pump to aspirate and moving the valve to the dispense position. MultiAspirate = True ;Allows aspirating multiple times before dispensing. UseAspirateAutorecovery = False ;When true software will attempt recovery and resynch of pumps on a syringe overload. UseDispenseAutorecovery = False ;When true software will attempt recovery and resynch of pumps on a syringe overload. EnablePolling = False ;Sampling rate for pump position updates PressureChangePerPumpStep = 0.002667 ;Initial guess for pressure feedback slope (PSI / step). SamplingRate = 1000 ;Sampling rate in ms. Simulated = True ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [Degasser] ;DegasserConfigSection Id = degasser ; DegasserCanInitialize = True ;Prevents degasser initialization if false DefaultServoPointMmhg = 50 ;Default set point for whenever servo is turned on (mmHg) DefaultMotorRpm = 120 ;Default motor speed for whenever servo is turned off (rpm) Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [IxTiltMotor1] ;Ix Tilt Motor Configs CoordinateSystemOffsetMm = 0 ;Coordinate system offset in mm. AccelerationMmPerSec2 = 10 ;Acceleration for normal motion in mm/s^2. DecelerationMmPerSec2 = 10 ;Deceleration for normal motion in mm/s^2. VelocityMmPerSec = 10 ;Velocity for normal motion in mm/s. LowerLimitMm = 0 ;Lower limit in mm, when soft limits are enabled. UpperLimitMm = 6.1 ;Upper limit in mm, when soft limits are enabled. AbsoluteLowerLimitMm = 0 ;Absolute lower limit in mm, when soft limits are "disabled". AbsoluteUpperLimitMm = 6.1 ;Absolute upper limit in mm, when soft limits are "disabled". HomeAccelerationMmPerSec2 = 5 ;Home acceleration in mm/s^2. HomeDecelerationMmPerSec2 = 5 ;Home deceleration in mm/s^2. HomeFastVelocityMmPerSec = 10 ;Home fast velocity in mm/s. HomeCreepVelocityMmPerSec = 5 ;Home creep velocity in mm/s. PositionPollingIntervalMs = 250 ;Polling interval time in ms AllowHoming = True ;If false, disables motor homing Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [IxTiltMotor2] ;Ix Tilt Motor Configs CoordinateSystemOffsetMm = 0 ;Coordinate system offset in mm. AccelerationMmPerSec2 = 10 ;Acceleration for normal motion in mm/s^2. DecelerationMmPerSec2 = 10 ;Deceleration for normal motion in mm/s^2. VelocityMmPerSec = 10 ;Velocity for normal motion in mm/s. LowerLimitMm = 0 ;Lower limit in mm, when soft limits are enabled. UpperLimitMm = 6.1 ;Upper limit in mm, when soft limits are enabled. AbsoluteLowerLimitMm = 0 ;Absolute lower limit in mm, when soft limits are "disabled". AbsoluteUpperLimitMm = 6.1 ;Absolute upper limit in mm, when soft limits are "disabled". HomeAccelerationMmPerSec2 = 5 ;Home acceleration in mm/s^2. HomeDecelerationMmPerSec2 = 5 ;Home deceleration in mm/s^2. HomeFastVelocityMmPerSec = 10 ;Home fast velocity in mm/s. HomeCreepVelocityMmPerSec = 5 ;Home creep velocity in mm/s. PositionPollingIntervalMs = 250 ;Polling interval time in ms AllowHoming = True ;If false, disables motor homing Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [IxTiltMotor3] ;Ix Tilt Motor Configs CoordinateSystemOffsetMm = 0 ;Coordinate system offset in mm. AccelerationMmPerSec2 = 10 ;Acceleration for normal motion in mm/s^2. DecelerationMmPerSec2 = 10 ;Deceleration for normal motion in mm/s^2. VelocityMmPerSec = 10 ;Velocity for normal motion in mm/s. LowerLimitMm = 0 ;Lower limit in mm, when soft limits are enabled. UpperLimitMm = 6.1 ;Upper limit in mm, when soft limits are enabled. AbsoluteLowerLimitMm = 0 ;Absolute lower limit in mm, when soft limits are "disabled". AbsoluteUpperLimitMm = 6.1 ;Absolute upper limit in mm, when soft limits are "disabled". HomeAccelerationMmPerSec2 = 5 ;Home acceleration in mm/s^2. HomeDecelerationMmPerSec2 = 5 ;Home deceleration in mm/s^2. HomeFastVelocityMmPerSec = 10 ;Home fast velocity in mm/s. HomeCreepVelocityMmPerSec = 5 ;Home creep velocity in mm/s. PositionPollingIntervalMs = 250 ;Polling interval time in ms AllowHoming = True ;If false, disables motor homing Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [UcsService] ;UcsServiceConfigSection MappedDriveKeepAliveCmdLineString = cmd /k mount \\fddc:65e5:66fa::1\ilmn z: ;Cmd line to keep alive for mapped drive. UcsServiceHostAddressString = localhost ;Universal Copy Service http host. UcsServiceHttpPort = 29644 ;Http port on which the Universal Copy Service is listening. ExecutableFilePath = C:\Program Files\Illumina\UniversalCopyService\ucs.exe ;The full file path for the Universal Copy Service executable. UploadContractTemplatePath = ;The full file path for an optional upload contract template. BeforeRetryConnectWaitSeconds = 30 ;Number of seconds to wait before a connect to UCS retry. RunProgressMonitoringIntervalSeconds = 300 ;Interval in seconds between run progress updates RemapCeTimeoutMinutes = 10 ;The length of time to wait to remap the CE. CopyThumbnailImages = True ;Whether or not thumbnails will be copied out to file channel [UcsChannelMonitor] ;UcsChannelMonitorConfigSection PollingIntervalSeconds = 30 ;Length of polling interval in seconds NumberOfFailedPollsAllowed = 1 ;Number of polls failed per channel to allow before notifying customer [FlowCellRfid] ;Parameters for reading flow cell RFID tags. LeftRfidXPositionMm = 114 ;The X position, in mm, for reading the left flow cell's RFID tag. LeftRfidYPositionMm = 82.5 ;The Y position, in mm, for reading the left flow cell's RFID tag. RightRfidXPositionMm = 209.5 ;The X position, in mm, for reading the right flow cell's RFID tag. RightRfidYPositionMm = 82.5 ;The Y position, in mm, for reading the right flow cell's RFID tag. RfidTildHeightMm = 4 ;The tilt motor height, in mm, for reading flow cell RFID tags. [AnalyticsLogging] ;Parameters for instrument analytics logging. NonRunLogLongIntervalHrs = 24 ;The interval for short term non-run logging which spec says should be done once per hour, in hours. NonRunLogShortIntervalMins = 60 ;The interval for short term non-run logging which spec says should be done once per hour, in minutes. RunLogIntervalSecs = 60 ;The interval for short term run logging which spec says should be done once per minute, in seconds. EnableLogging = True ;Enables all writing of analytics structured logs, and whether or not the associated information is gathered. EnableLoggingFluidicsPressureCsv = True ;Enables writing CSV report file per run for Fluidics Pressure. [FcBirdAnalysis] ;Fc BIRD Analysis config settings MicronOffsetFromBestFocusZ = 100 ;During TDI capture, offset in microns from surface find BestZ TdiScanSpeedMillimetersPerSecond = 48 ;TDI capture speed in millimeters per second TdiScanNumLines = 4046 ;Number of lines to capture during TDI scan TdiRedLaserPowerMilliwatts = 500 ;Red laser power in milliwatts during TDI capture TdiRedLaserPowerDeltaFromTargetMilliwatts = 5 ;Delta from target power for Red laser in milliwatts TdiGreenLaserPowerMilliwatts = 500 ;Green laser power in milliwatts during TDI capture TdiGreenLaserPowerDeltaFromTargetMilliwatts = 5 ;Delta from target power for Green laser in milliwatts TdiLaserStabilityPollingIntervalSec = 10 ;Length of interval in seconds to check for laser power stability. TdiRequiredSuccessfulSamplesForLaserStability = 4 ;Number of consecutive successful samples for laser power stability. FullFrameExposureMilliSeconds = 3 ;Exposure time in milliseconds during full frame capture FullFrameRedLaserPowerMilliwatts = 50 ;Red laser power in milliwatts during TDI capture FullFrameRedLaserPowerDeltaFromTargetMilliwatts = 5 ;Delta from target power for Green laser in milliwatts FullFrameGreenLaserPowerMilliwatts = 50 ;Green laser power in milliwatts during TDI capture FullFrameGreenLaserPowerDeltaFromTargetMilliwatts = 5 ;Delta from target power for Green laser in milliwatts FullFrameLaserStabilityPollingIntervalSec = 10 ;Length of interval in seconds to check for laser power stability. FullFrameRequiredSuccessfulSamplesForLaserStability = 4 ;Number of consecutive successful samples for laser power stability. MinimumPostAnalysisRedLaserPowerMilliwatts = 50 ;Minimum red laser power post analysis MinimumPostAnalysisGreenLaserPowerMilliwatts = 50 ;Minimum green laser power post analysis MaxLaserPowerStabilityWaitSeconds = 600 ;Maximum duration in seconds to wait for laser power stability. LogFolder = D:\Illumina\BIRD_Measurement ;Folder to save BIRD measurement logs MaxLogFiles = 10 ;Max log files to save MaxLinesPerLogFile = 1000 ;Max lines for each log file MaxIntensityDropFromBaselinePercent = 10 ;Display a warning message in VCS if the intensity has dropped by this much from the baseline NominalAvgIntensityRed = 1207.5 ;Baseline average intensity on BIRD for Red channel NominalAvgIntensityGreen = 2372.1 ;Baseline average intensity on BIRD for Green channel RunBirdAtStartOfSequencing = True ;Run Bird when sequencing starts RunBirdAtEndOfSequencing = True ;Run Bird when sequencing ends [RecipeValidator] ;Recipe Validation config settings PerformRecipeValidation = True ;Whether or not to perform recipe validation IPortTwoLaneMinFlowRate = 50 ;Min flow rate in uL per minute for I port on two lane flowcell. IPortTwoLaneMaxFlowRate = 7000 ;Max flow rate in uL per minute for I port on two lane flowcell. BPortTwoLaneMinFlowRate = 50 ;Min flow rate in uL per minute for B port on two lane flowcell. BPortTwoLaneMaxFlowRate = 7000 ;Max flow rate in uL per minute for B port on two lane flowcell. OPortTwoLaneMinFlowRate = 50 ;Min flow rate in uL per minute for O port on two lane flowcell. OPortTwoLaneMaxFlowRate = 15000 ;Max flow rate in uL per minute for O port on two lane flowcell. IPortFourLaneMinFlowRate = 50 ;Min flow rate in uL per minute for I port on four lane flowcell. IPortFourLaneMaxFlowRate = 7000 ;Max flow rate in uL per minute for I port on four lane flowcell. BPortFourLaneMinFlowRate = 50 ;Min flow rate in uL per minute for B port on four lane flowcell. BPortFourLaneMaxFlowRate = 7000 ;Max flow rate in uL per minute for B port on four lane flowcell. OPortFourLaneMinFlowRate = 50 ;Min flow rate in uL per minute for O port on four lane flowcell. OPortFourLaneMaxFlowRate = 15000 ;Max flow rate in uL per minute for O port on four lane flowcell. SyringeVolumeUl = 1000 ;Max syringe volume in ul. [ExternalFlowCellThermalProbe] ;Settings for the external FC thermal probe. LogInfo = False ;Outputs informational logs when set to true. AutoDetectRepeatCount = 1 ;Number of times to perform auto-detect, for checking consistency using given timeouts. AutoDetectTimeoutMs = 100 ;Timeout in ms only for auto-detect Serial communication. OpenCloseDelayMs = 100 ;Delay in ms between open and close SerialPort to prevent hanging. TimeoutMs = 5000 ;Timeout in ms for general Serial communication. TecRtdLsl = 0 ;Lsl in degrees celsius below which FCH external probe readings are considered invalid TecRtdUsl = 100 ;Usl in degrees celsius above which FCH external probe readings are considered invalid FlushAndWarn = False ;Flush device on Errors AutoDetect = True ;If true software will try to scan COM ports and find device (all devices may not support this) UsbPortApi = FTDI ;DotNetApi (only for 32-bit Win) / FTDI (x64) OkIfNoUsbSerialPorts = False ;Okay if no USB serial devices are found FTDIReadTimeoutMs = 5000 ;FTDI read timeout: was 10, CyVera had to use 5000 FTDIWriteTimeoutMs = 0 ;FTDI write timeout: was 500, CyVera had to use 0 because of an FTDI device driver bug which caused blue screens FTDISetUSBParameters = True ;If true, call FTDISetUSBParameters() using CyVera's buffer sizes FTDIRegisteringTimeoutSecs = 60 ;FTDI registering timeout in seconds FTDIResetPipeRetryCount = 1000 ;Max # of times driver tries to reset pipe if error. Default = 50. Increase for noisy environments with many USB errors. ComPortName = COM4 ;Windows COMx port name, e.g. COM1 Handshake = None ;The control protocol used in establishing a serial port communication. BaudRate = 115200 ;Baud rate in bits per second. Up to 115200 ComPortOffset = 9 ;The com position to start at. 0 = start at COM1, 9 = start at COM10, etc PositionPollingInterval = 200 ;PositionPollingInterval Simulated = Auto ;Whether or not the device is simulated in this instrument configuration. If set to Auto, the device defaults to the [Instrument]'s simulated tag. The Auto option for the [Instrument] is equivalent to NotSimulated. CosmeticName = ;Name to be used for this device for logging, display, etc. If blank, automatically generates dotted name. TraceLevel = 1 ;Controls how much information about this device gets logged. Higher numbers cause more logging: 0 = only log initialization information such as device name, port, simulated or not, etc. 1 = log generally useful information, such as all communications (except polling) and moves. 2 or higher = log more detailed information if available [CameraTapTest] ;Camera Tap test configuration. PerformInitializationTests = True ;Determines if the camera will perform init tests. IntensityTolerance = 80 ;Allowable percent difference in image intensity values. ConsecutiveTapsToTest = 4 ;The number of consecutive bad taps in a row to look for. TapWidth = 100 ;The width in pixels of each tap. InitAttempts = 3 ;Total number of initialization attempts. TestAttempts = 2 ;Total number of test attempts before power cycling TapScanLength = 82 ;The TDI scan length during init Tap Testing in pixels YOrigin = 62 ;The tap test scan start Y position in mm XOrigin = 90 ;The tap test scan start X position in mm SaveImages = True ;Save the last failed set of images. [FlowCellFlatness] ;Config for flowcell flatness test PerformFcFlatnessTest = True ;Perform flowcell flatness test SamplingRate = 500 ;Sampling rate to set the y encoder counts FcFlatnessIndex = 100000 ;Flow cell flatness index. 100000 is the max allowable index. ScanSpeed = 48 ;Speed of flowcell flatness scan, in mm/s [PressureDecay] ;Pressure Decay Test Config settings HighOutputPressureDecayRecipe = Line Pressure Test 4 Lane.xml ;Recipe for high output flow cell RapidRunPressureDecayRecipeLanePairA = Line Pressure Test 2 Lane Pair A.xml ;Recipe for rapid run flow cell lane pair A RapidRunPressureDecayRecipeLanePairB = Line Pressure Test 2 Lane Pair B.xml ;Recipe for rapid run flow cell lane pair B BypassPressureDecayRecipe = Line Pressure Test Bypass.xml ;Recipe for bypass test DeprimeDefinitionName = Deprime ;Name of the Deprime ChemistryDefinition PerformPressureDecayPreRunCheck = False ;Perform Pressure Decay as part of PreRunChecks