Microscope Settings Documentation
Microscope Control Software version 2.2.0.2
Settings folder structure
Microscope: All microscope configurations, one folder each, including settings for the microscope and its components.
Objective: All objective configurations, one folder each, including settings for the objective.
Drivers: All drivers configurations, one folder each, including settings for the drivers.
User: All user configurations, one folder each, including the settings for the user.
| Field | Type/Value | Description | Required | Default |
|---|---|---|---|---|
| Microscope control | ||||
| ApplicationSettings | Settings of the Microscope Control Software application. | |||
| DefaultMicroscope | string | The default folder for microscope settings. | Yes | |
| DefaultObjective | string | The default folder for objective settings. | Yes | |
| DefaultDrivers | string | The default folder for driver settings. | Yes | |
| DefaultUser | string | The default folder for user settings. | Yes | |
| Version | string | The version of the settings. | Yes | |
| MicroscopeSettings | Microscope-specific settings, define the list of components to be utilized by the application. | |||
| Components | list of string | The list of components to load. | Yes | |
| Common for all components | ||||
| ComponentSettings | Component | Represent the configuration settings of an application component. | ||
| ComponentLabel | string | The user readable name of the component. | Yes | |
| ComponentType | string | The type of the component to load. | Yes | |
| DriverSettings | Driver | Specify the hardware driver to be used for a device and how to configure it. | ||
| DriverType | string | Name of the driver to use and configure. | Yes | |
| UserSettings | User | Represent settings that can be edited by the user while the application is running. Can be exported and imported. | ||
| Version | string | The version of the settings. | Yes | |
| IlluminationModule | ||||
| <name>_Component | Component | Settings of an illumination module component. | ||
| Scanner1Offsets | list of double | Voltage offsets applied on scanner 1 at branches 1, 2, 3, etc. | No | |
| Scanner2Offsets | list of double | Voltage offsets applied on scanner 2 at branches 1, 2, 3, etc. | No | |
| OffsetsBase | list of dict | Keys of dict listed below. | No | |
| Branch | int | Unique number of illumination branch (value 1, 2 or 3). | Yes | |
| Scanner1Offset | double | Voltage on scanner 1. | Yes | |
| Scanner2Offset | double | Voltage on scanner 2. | Yes | |
| Scanner3Offset | double | Voltage on scanner 3. | Yes | |
| Scanner4Offset | double | Voltage on scanner 4. | Yes | |
| StageXYZName | string | The name of the stage XYZ component. | Yes | |
| SetMode | enum | Define when the device should be configured during time-lapse. Possible values listed below. | Yes | |
| BeforePosition | string | For the whole experiment, set before every position. | - | |
| BeforeSettings | string | For every settings profile, set before every settings profile. | - | |
| BeforeStack | string | For every channel, set before every stack acquisition. | - | |
| None | string | Not set. | - | |
| SetLabel | string | The label of the illumination module editor. | No | |
| SetLinkedDevice | string | The name of the device that will be linked to the illumination module. Same settings will be applied to the linked device. | No | |
| ShowTranslationY | bool | Whether to show the translation Y editor. | Yes | |
| PanelLocation | enum | The location of the illumination module panel. Possible values listed below. | Yes | |
| Illumination1 | string | Illumination 1 location. | - | |
| Illumination2 | string | Illumination 2 location. | - | |
| <name>_Objective | Objective | Objective-specific settings of an illumination module device. | ||
| TranslationX | double | Translation X in micrometers to compensate for objective block misalignment measured at production. | Yes | |
| RotationX | double | Rotation X in degrees to compensate for objective block misalignment measured at production. | Yes | |
| TranslationZ | double | Translation Z in micrometers to compensate for objective block misalignment measured at production. | Yes | |
| RotationZ | double | Rotation Z in degrees to compensate for objective block misalignment measured at production. | Yes | |
| ResidualTranslationX | double | Additional translation X in micrometers to compensate for residual objective block misalignment of undetermined origin. | No | 0 |
| ResidualRotationX | double | Additional rotation X in degrees to compensate for residual objective block misalignment of undetermined origin. | No | 0 |
| ResidualTranslationZ | double | Additional translation Z in micrometers to compensate for residual objective block misalignment of undetermined origin. | No | 0 |
| ResidualRotationZ | double | Additional rotation Z in degrees to compensate for residual objective block misalignment of undetermined origin. | No | 0 |
| <name>_Driver: LS1LiveIlluminationModule | Driver | Settings of a LS1 Live illumination module driver. | ||
| BranchCount | int | Number of illumination branches (3 for LS1 Live). | Yes | |
| IPAddress | string | TCP/IP address of illumination module positioning controller. | Yes | |
| Port | int | TCP/IP port of illumination module positioning controller | Yes | |
| Controller | string | Type of MCS controller ('MCS' or 'MCS2'). | Yes | |
| ReverseRefDirection | list of bool | List of three values defining if for each postioning axis to reverse referencing direction. | Yes | |
| Axis0Offsets | list of int | List of offset for each branch to apply on positioning axis 0. | Yes | |
| Axis1Offsets | list of int | List of offset for each branch to apply on positioning axis 1. | Yes | |
| Axis2Offsets | list of int | List of offset for each branch to apply on positioning axis 2. | Yes | |
| <name>_Driver: SoftwareIlluminationModule | Driver | Settings of a software illumination module driver. | ||
| BranchCount | int | Number of emulated branches. | Yes | |
| Delay | int | Delay in ms to simulate switching time between branches. | Yes | |
| <name>_DeviceSettings | User | User settings of an illumination module device. | ||
| IlluminationSettings | string | The default illumination settings to apply on the device. | Yes | |
| <name>_IlluminationSettings | User (list) | The illumination settings. | ||
| Branch | int | Selected illumination branch. | Yes | |
| TranslationX | double | Translation X in um to apply. | Yes | |
| RotationX | double | Rotation X in degrees to apply. | Yes | |
| TranslationY | double | Translation Y in um to apply. | Yes | |
| TranslationZ | double | Translation Z in um to apply. | Yes | |
| RotationZ | double | Rotation Z in degrees to apply. | Yes | |
| Name | string | The name of the settings. | Yes | |
| <name>_PositionAlignmentSettings | User (list) | |||
| TranslationZ | double | Translation Z in um to apply on this position. | Yes | |
| Enable | bool | Enable position specific alignment for this position. | Yes | |
| Name | string | The name of the settings. | Yes | |
| Photomanipulation | ||||
| <name>_Component | Component | Settings of a photomanipulation component. | ||
| OffsetsBaseInternal | dict | Offsets to apply on scanners to switch internal lasers to photomanipulation path. Keys of dict listed below. | Yes | |
| Scanner1Offset | double | Voltage on scanner 1 (closest to scan lens). | Yes | |
| Scanner2Offset | double | Voltage on scanner 2. | Yes | |
| Scanner3Offset | double | Voltage on scanner 3. | Yes | |
| Scanner4Offset | double | Voltage on scanner 4 (furthest from scan lens). | Yes | |
| OffsetsBaseExternal | dict | Offsets to apply on scanners to switch external laser to photomanipulation path. Keys of dict listed below. | Yes | |
| Scanner1Offset | double | Voltage on scanner 1 (closest to scan lens). | Yes | |
| Scanner2Offset | double | Voltage on scanner 2. | Yes | |
| Scanner3Offset | double | Voltage on scanner 3. | Yes | |
| Scanner4Offset | double | Voltage on scanner 4 (furthest from scan lens). | Yes | |
| StageXYZName | string | The name of the stage XYZ component. | Yes | |
| ExternalLaser | bool | Whether an external photomanipulation laser is connected to the microscope. | No | false |
| InternalOffsetX | double | Offset X in um of internal lasers to center photomanipulation beam in X. | No | |
| InternalOffsetY | double | Offset Y in um of internal lasers to center photomanipulation beam in Y. | No | |
| ExternalOffsetX | double | Offset X in um of external laser to center photomanipulation beam in X. | No | |
| ExternalOffsetY | double | Offset Y in um of external laser to center photomanipulation beam in Y. | No | |
| <name>_RegionSettings | User (list) | The region settings. | ||
| Type | enum | The region type. Possible values listed below. | Yes | |
| Point | string | Point region. | - | |
| Line | string | Line region. | - | |
| Width | double | The width of the region in micrometers. | No | 10 |
| Height | double | The height of the region in micrometers. | No | 0 |
| Rotation | double | The rotation of the region in degrees. | No | 0 |
| ExposureTime | int | The exposure time. | No | 20 |
| Repetitions | int | The number of time to apply this region. | No | 10 |
| Name | string | The name of the settings. | Yes | |
| <name>_PositionCoordinatesSettings | User (list) | The position coordinates settings. | ||
| OffsetX | double | The offset from position along X axis in micrometers. | Yes | |
| OffsetY | double | The offset from position along Y axis in micrometers. | Yes | |
| OffsetZ | double | The offset from position along Z axis in micrometers. | Yes | |
| Region | string | The name of the region settings to apply. | Yes | |
| Name | string | The name of the settings. | Yes | |
| FilterWheel | ||||
| <name>_Component | Component | Settings of a filter wheel component. | ||
| SetMode | enum | Define when the device should be configured during time-lapse. Possible values listed below. | Yes | |
| BeforePosition | string | For the whole experiment, set before every position. | - | |
| BeforeSettings | string | For every settings profile, set before every settings profile. | - | |
| BeforeStack | string | For every channel, set before every stack acquisition. | - | |
| None | string | Not set. | - | |
| SetLabel | string | The label of the filter wheel editor. | No | |
| SetLinkedDevice | string | The name of the device that will be linked to the filter wheel. Same settings will be applied to the linked device. | No | |
| PanelLocation | enum | The location of the filter wheel panel. Possible values listed below. | Yes | |
| Illumination | string | Illumination filter wheel location. | - | |
| Emission1 | string | Emission filter wheel 1 location. | - | |
| Emission2 | string | Emission filter wheel 2 location. | - | |
| <name>_Driver: SerialFilterWheel | Driver | Settings of serial filter wheel driver. | ||
| VIDs | list of string | List of USB device VID values to identify filter wheel port. | Yes | |
| PIDs | list of string | List of USB device PID values to identify filter wheel port. | Yes | |
| SNs | list of string | List of USB device serial numbers to identify filter wheel port. | Yes | |
| COM | string | If not null override COM port automatic detection and use specified COM port. | No | |
| BaudRate | int | COM port bound rate. | Yes | |
| ReadTimeout | int | Read time out for serial port. | Yes | |
| MoveCommandPrefix | string | Prefix of move to filter position command. | Yes | |
| MoveCommandSuffix | string | Suffix of move to filter position command. | Yes | |
| MoveCommandResponse | string | Response of move command indicating move completed. | Yes | |
| GetPositionCommand | string | Command to get current filter wheel position. | Yes | |
| Echo | bool | Indicates if sent bytes are being sent back (echo on COM port). | Yes | |
| <name>_Driver: MAC6000FilterWheel | Driver | Settings of a MAC6000 filter wheel driver. | ||
| IPAddress | string | TCP/IP address of MAC6000 controller. | Yes | |
| FilterWheel | int | Index of filter wheel (one or two). | Yes | |
| <name>_Driver: SoftwareFilterWheel | Driver | Settings of a software filter wheel driver. | ||
| FilterCount | int | Number of filter positions. | Yes | |
| Delay | int | Delay to simulate filter wheel turn. | Yes | |
| CommandErrorPosition | int | Trigger simulated command error when moved to this position. | Yes | |
| DeviceErrorPosition | int | Trigger simulated device error when moved to this position. | Yes | |
| <name>_DeviceSettings | User | User settings of a filter wheel device. | ||
| FilterSettings | string | The default filter settings applied on the device. | Yes | |
| <name>_FilterSettings | User (list) | The filter settings. | ||
| Position | int | The position in the filter wheel. | Yes | |
| Name | string | The name of the settings. | Yes | |
| AcquisitionController | ||||
| <name>_Component | Component | Settings of an acquisition controller component. | ||
| MicroscopeModel | string | Yes | ||
| IlluminNames | list of string | List of unique identifiers of illumination sources. | Yes | |
| IlluminLabels | dict (string => string) | The labels associated to each illumination source. | Yes | |
| IlluminAOChannels | dict (string => int) | The analog modulation AO channels associated to each illumination source. | Yes | |
| IlluminAOMaxVoltage | int | Analog output voltage corresponding to maximum power. | No | 5 |
| IlluminDOChannels | dict (string => int) | The digital modulation DO channels associated to each illumination source. | Yes | |
| Camera1DOChannel | int | DO channel for camera 1. | Yes | |
| Camera2DOChannel | int | DO channel for camera 2. | Yes | |
| CameraReadoutTime | int | Readout time of camera full chip in ms. | Yes | |
| FrameDOChannel | int | DO for oscilloscope trigger signal. | Yes | |
| IlluminModule1Name | string | Name of the illumination module component 1. | No | |
| IlluminModule2Name | string | Name of the illumination module component 2. | No | |
| Illumin1Scanner1AOChannel | int | AO channel connected to scanner 1 for illumination module device 1. | Yes | |
| Illumin1Scanner2AOChannel | int | AO channel connected to scanner 2 for illumination module device 1. | Yes | |
| Illumin2Scanner1AOChannel | int | AO channel connected to scanner 1 of illumination module device 2. | Yes | |
| Illumin2Scanner2AOChannel | int | AO channel connected to scanner 2 of illumination module device 2. | Yes | |
| Illumin1Scanner1Offset | double | Voltage offset applied to scanner 1 of illumination module device 1. | Yes | |
| Illumin1Scanner1Factor | double | Factor to convert translation in micrometer to voltage for scanner 1 of illumination module device 1. | Yes | |
| Illumin1Scanner1Disabled | double | Voltage applied to scanner 1 of illumination module device 1 when disabled. | Yes | |
| Illumin1Scanner2Offset | double | Voltage offset applied to scanner 2 of illumination module device 1. | Yes | |
| Illumin1Scanner2Factor | double | Factor to convert translation in micrometer to voltage for scanner 2 of illumination module device 1. | Yes | |
| Illumin1ScannerRelation | int | Relation factor of scanner 1 to scanner 2 to generate only beam rotation for illumination module device 1. | Yes | |
| Illumin2Scanner1Offset | double | Voltage offset applied to scanner 1 of illumination module device 2. | Yes | |
| Illumin2Scanner1Factor | double | Factor to convert translation in micrometer to voltage for scanner 1 of illumination module device 2. | Yes | |
| Illumin2Scanner1Disabled | double | Voltage applied to scanner 1 of illumination module device 2 when disabled. | Yes | |
| Illumin2Scanner2Offset | double | Voltage offset applied to scanner 2 of illumination module device 2. | Yes | |
| Illumin2Scanner2Factor | double | Factor to convert translation in micrometer to voltage for scanner 2 of illumination module device 2. | Yes | |
| Illumin2ScannerRelation | int | Relation factor of scanner 1 to scanner 2 to generate only beam rotation for illumination module device 2. | Yes | |
| Scanner1AO | int | Analog output channel for Viventis Deep scanner 1 (closest to scan lens). | No | |
| Scanner2AO | int | Analog output channel for Viventis Deep scanner 2. | No | |
| Scanner3AO | int | Analog output channel for Viventis Deep scanner 3. | No | |
| Scanner4AO | int | Analog output channel for Viventis Deep scanner 4 (furthest from scan lens). | No | |
| Scanner1Factor | double | Factor to convert micrometer of translation XY to scanner 1 voltage. | No | |
| Scanner2Factor | double | Factor to convert micrometer of translation XY to scanner 2 voltage. | No | |
| Scanner3Factor | double | Factor to convert degrees of rotation Z to scanner 3 voltage. | No | |
| Scanner4Factor | double | Factor to convert degrees of rotation Z to scanner 4 voltage. | No | |
| Scanner2To3Factor | double | Relation factor of scanner 2 rotation to scanner 3 rotation to generate pure beam translation. | No | 0 |
| PhotomanName | string | Name of the photomanipulation component. | No | |
| PhotomanShutterDO | int | Digital output channel for internal laser photomanipulation switch. | No | |
| PhotomanExternalDO | int | Digital output channel for external photomanipulation laser shutter. | No | |
| PhotomanExternalAO | int | Analog output channel for external photomanipulation laser analog modulation. | No | |
| PhotomanExternalPercentage | list of double | List of modulation percentages for external photomanipulation laser for which corresponding analog modulation voltages are provided. | No | |
| PhotomanExternalVoltage | list of double | List of analog modulation voltages for external photomanipulation laser for which corresponding modulation percentages are provided. | No | |
| PhotomanScannerFactor | double | Factor to convert micrometer of translation XY to scanner 1 and 2 voltage for photomanipulation light path. | No | |
| AblationLaserUVDOChannel | int | Digital output to trigger pulsed UV laser. Only for R&D use. | No | |
| <name>_Objective | Objective | Objective-specific settings of an acquisition controller device. | ||
| Illumin1TiltFactor | double | Factor of scanner 1 to tilt the scan plane for illumination 1. | No | 0 |
| Illumin2TiltFactor | double | Factor of scanner 1 to tilt the scan plane for illumination 2. | No | 0 |
| <name>_Driver: RTC1AcquisitionController | Driver | Settings of a RTC1 acquisition controller driver. | ||
| IPAddress | string | TCP/IP address. | Yes | |
| Port | int | TCP/IP port. | Yes | |
| AOCount | int | Number of analog output channels. | Yes | |
| AOVoltages | list of string | Analog output voltage range for each channel ("0to5V", "0to10V", "-5to5V", "-10to10V"). | Yes | |
| AOOffsetEncoding | list of bool | Analog output sent in two's complement or offset encoding (according to Analog Devices AD5754 documentation). | Yes | |
| DOCount | int | Number of digital output channels. | Yes | |
| <name>_Driver: SoftwareAcquisitionController | Driver | Settings of a software acquisition controller driver. | ||
| Delay | int | Time of filter movement. | Yes | |
| <name>_IlluminationSettings | User (list) | |||
| IlluminIntensities | dict (string => double) | The intensity (as a percentage of the maximum) for each illumination. | Yes | |
| Name | string | The name of the settings. | Yes | |
| <name>_ExposureSettings | User (list) | |||
| ExposureTime | int | Exposure time in ms. | Yes | |
| Scans | int | Number of scans, not implemented, value will be ignored. | Yes | |
| Range | int | Range of scanning to generate light sheet in um. | Yes | |
| Illumination1 | bool | Enable or disable illumination one. | Yes | |
| Illumination2 | bool | Enable or disable illumination two. | Yes | |
| Offset1 | int | Translation X to apply on illumination one. | Yes | |
| Offset2 | int | Translation X to apply on illumination two. | Yes | |
| MLS | bool | Multi-directional light sheet, not implemented. | Yes | |
| Name | string | The name of the settings. | Yes | |
| StageXYZ | ||||
| <name>_Component | Component | Settings of a stage XYZ component. | ||
| ImagingPositionX | double | Imaging position X coordinate in micrometer. | Yes | |
| ImagingPositionY | double | Imaging position Y coordinate in micrometer. | Yes | |
| ImagingPositionZ | double | Imaging position Z coordinate in micrometer. | Yes | |
| ImagingPositionMoveOrder | string | Order in which axis move to the imaging position ('XYZ', 'XZY' etc.). | Yes | |
| LoadPositionX | double | Load position X coordinate in micrometer. | Yes | |
| LoadPositionY | double | Load position Y coordinate in micrometer. | Yes | |
| LoadPositionZ | double | Load position Z coordinate in micrometer. | Yes | |
| LoadPositionMoveOrder | string | Order in which axis move to the load position ('XYZ', 'XZY' etc.). | Yes | |
| PositionXLimit | list of double | Limit of stage movement in X (min, max) during acquisition. | Yes | |
| PositionYLimit | list of double | Limit of stage movement in Y (min, max) during acquisition. | Yes | |
| PositionZLimit | list of double | Limit of stage movement in Z (min, max) during acquisition. | Yes | |
| StackDirection | int | Direction of stage movement in Z stack (1 or -1). | Yes | |
| <name>_Driver: SmarActMCSStageXYZ | Driver | Settings of SmarAct MCS stage XYZ driver. | ||
| IPAddress | string | IP address of the MCS controller. | Yes | |
| Port | int | TCP port of the MCS controller. | Yes | |
| Controller | string | Type of MCS controller. | Yes | |
| ReverseRefDirection | list of bool | List of three values defining if for each positioning axis to reverse referencing direction. | Yes | |
| ReferenceOrder | string | Order in which axis move to the reference position after cold start ('XYZ', 'XZY', etc.). | Yes | |
| HoldTimes | list of int | Hold times in ms programmed to each positioning axis. | No | |
| <name>_Driver: SoftwareStageXYZ | Driver | Settings of software stage XYZ driver. | ||
| Delay | int | Latency of communication in ms. | Yes | |
| <name>_PositionSettings | User (list) | |||
| PositionX | double | The position along stage X axis. | Yes | |
| PositionY | double | The position along stage Y axis. | Yes | |
| PositionZ | double | The position along stage Z axis. | Yes | |
| RangeZ | double? | The range along the Z axis. May be null if not defined. | No | null |
| MinRangeZMarker | list of double | The X and Y relative coordinates of the range Z marker with minimum Z value. | No | null |
| MaxRangeZMarker | list of double | The X and Y relative coordinates of the range Z marker with maximum Z value. | No | null |
| SkipPosition | bool | Whether the acquisition of the position should be skipped. | Yes | |
| Name | string | The name of the settings. | Yes | |
| <name>_ZStackSettings | User (list) | |||
| Step | double | The step size in micrometer between each plane. | Yes | |
| Planes | int | The number of planes of the stack. | Yes | |
| Name | string | The name of the settings. | Yes | |
| ImageViewer | ||||
| <name>_Component | Component | Settings for the image viewer component. | ||
| StageXYZName | string | The name of the stage XYZ component. | Yes | |
| PhotomanName | string | The name of the photomanipulation component. | No | null |
| Illumination1Angle | double | The angle of the illumination 1 in degrees from the horizontal axis. | Yes | |
| Illumination2Angle | double | The angle of the illumination 2 in degrees from the horizontal axis. | Yes | |
| Camera | ||||
| <name>_Component | Component | Settings of a camera component. | ||
| BufferLength | int | Number of images in buffer, maximum number of images per channel. | Yes | |
| Channels | int | Number of channels in buffer, maximum number of channels. | Yes | |
| MagFactors | list of double | List of magnification factors, it can be list multiple values if magnification switch is installed. | Yes | |
| Views | int | Number of views. | No | |
| Cameras | int | Number of cameras on view one (single or dual camera system). | No | |
| JetrawEnable | bool | Enable jetraw compression integration. | No | |
| JetrawLiceseKey | string | Jetraw license key. | No | |
| JetrawDevice | string | Jetraw device to use calibration data. | No | |
| StageXYZName | string | The name of the stage XYZ component. | Yes | |
| ImageViewerName | string | The name of the image viewer component. | No | |
| <name>_Objective | Objective | Objective-specific settings of a camera device. | ||
| OffsetX | int | Offset between view 1 and view 2 along X in pixels. | No | |
| OffsetY | int | Offset between view 1 and view 2 along Y in pixels. | No | |
| Objective | string | Name of used objective. | Yes | |
| Magnification | double | Magnification of used objective. | Yes | |
| NumericalAperture | double | Numerical aperture of used objective. | Yes | |
| <name>_Driver: HamamatsuCamera | Driver | Settings of a Hamamatsu camera driver. | ||
| View1Camera1 | string | Serial number of camera installed on view one. | Yes | |
| View1Camera1FlipVertically | bool | Flip image of view one vertically. | No | |
| View2Camera1 | string | Serial number of camera installed on view two. | No | |
| View2Camera1FlipVertically | bool | Flip image of view two vertically. | No | |
| BufferLength | int | Length of the buffer (in full frames) sent to the camera driver. | Yes | |
| SensorWidth | int | Width of camera sensor in px. | Yes | |
| SensorHeight | int | Height of camera sensor in px. | Yes | |
| Cooling | bool | Enable camera cooling. | No | |
| Temperature | string | Requested cooling temperature, not implemented. | No | |
| <name>_Driver: AndorCamera | Driver | Settings of an Andor camera driver. | ||
| BufferLength | int | Length of the buffer (in full frames) sent to the camera driver. | Yes | |
| SensorWidth | int | Width of camera sensor in px. | Yes | |
| SensorHeight | int | Height of camera sensor in px. | Yes | |
| Cooling | bool | Enable camera cooling. | No | |
| Temperature | string | Requested cooling temperature. | No | |
| <name>_Driver: SoftwareCamera | Driver | Settings of a software camera driver. | ||
| Width | int | Camera AOI width in px. | Yes | |
| Height | int | Camera AOI height in px. | Yes | |
| Exposure | int | Exposure time in ms used to simulate stream of images. | Yes | |
| SensorWidth | int | Width of camera sensor in px. | Yes | |
| SensorHeight | int | Height of camera sensor in px. | Yes | |
| <name>_DeviceSettings | User | User settings of a camera device. | ||
| CameraSettings | string | The default camera settings to apply on the device. | Yes | |
| StorageSettings | string | The default storage settings to apply on the device. | Yes | |
| <name>_CameraSettings | User (list) | |||
| AOIWidth | int | The width of the area of interest in pixels. | Yes | |
| AOIHeight | int | The height of the area of interest in pixels. | Yes | |
| MagFactor | double | The magnification factor. | Yes | |
| Name | string | The name of the settings. | Yes | |
| <name>_StorageSettings | User (list) | |||
| Path | string | The path of the folder where to store the images. | Yes | |
| Directory | string | The directory naming format. | Yes | |
| File | string | The image file naming format. | Yes | |
| Format | string | The file format of the images. | Yes | |
| Compression | string | The compression method. | Yes | |
| Project | bool | Whether to compute the maximum projection images. | No | false |
| Autosave | bool | Whether to save the images. | Yes | |
| Name | string | The name of the settings. | Yes | |
| TimeLapseController | ||||
| <name>_Component | Component | Settings of a time lapse controller component. | ||
| VerifyCameraImageReceived | bool | Whether to wait for image to be received by camera driver after each camera trigger. | No | false |
| StageXYZName | string | The name of the stage XYZ component. | Yes | |
| CameraName | string | The name of the camera component. | Yes | |
| AcquisitionControllerName | string | The name of the acquisition controller component. | Yes | |
| SettableDevices | list of string | The names of the settable devices. | No | null |
| PhotomanName | string | Name of the photomanipulation component. | No | null |
| IlluminationFilterWheelName | string | Name of the illumination filter wheel component. Required if photomanipulation is set. | No | null |
| EmissionFilterWheelsName | list of string | Name of emission filter wheel components. Required if photomanipulation is set (at least one). | No | null |
| PhotomanipulationEmissionFilter | string | Name of the settings to use on emission filter wheels for photomanipulation. Required if photomanipulation is set. | No | null |
| <name>_AcquisitionSettings | User | Settings of an acquisition. | ||
| TimeInterval | double | The time interval in seconds between two time points. | Yes | |
| Repetitions | int | The number of time points to acquire. | Yes | |
| ExperimentName | string | The name of the experiment. | Yes | |
| DeviceSettings | list of dict | Acquisition-related settings for some devices. Keys of dict listed below. | No | |
| Name | string | The name of the device to set. | Yes | |
| Settings | string | The name of the settings to apply. | No | |
| SettingsProfiles | list of dict | The list of settings profiles. Keys of dict listed below. | Yes | |
| Name | string | The name of the settings profile. | Yes | |
| Enabled | bool | Whether the profile should be acquired. | Yes | |
| ZStack | string | The name of the Z-Stack settings to apply, single plane if null. | No | null |
| Positions | list of string | The list of positions to acquire. If null, all positions are acquired. If empty, no positions are acquired. | No | null |
| Views | enum | The view(s) to acquire. Possible values listed below. | No | 0 |
| View1 | string | View 1 | - | |
| View2 | string | View 2 | - | |
| View1and2 | string | View 1 and 2 | - | |
| DeviceSettings | list of dict | Settings for some devices. Keys of dict listed below. | No | |
| Name | string | The name of the device to set. | Yes | |
| Settings | string | The name of the settings to apply. | No | |
| Channels | list of dict | The list of channel settings. Keys of dict listed below. | Yes | |
| Name | string | The name of the channel. | Yes | |
| Enabled | bool | Whether the channel should be acquired. | Yes | |
| AcquireNthTimePoint | int | Interval at which the channel is acquired. It is acquired at every specified number of time points. | No | |
| Color | enum | The channel default color. Possible values listed below. | Yes | |
| Red | string | Red color. | - | |
| Green | string | Green color. | - | |
| Blue | string | Blue color. | - | |
| Cyan | string | Cyan color. | - | |
| Magenta | string | Magenta color. | - | |
| Yellow | string | Yellow color. | - | |
| White | string | White color. | - | |
| Illumination | string | Name of the illumination settings to apply on acquisition controller device. | No | |
| Exposure | string | Name of the exposure settings to apply on acquisition controller device. | No | |
| Camera | int | The index of the camera to use. | No | |
| DeviceSettings | list of dict | Channel-related settings for some devices. Keys of dict listed below. | Yes | |
| Name | string | The name of the device to set. | Yes | |
| Settings | string | The name of the settings to apply. | No | |
| Photomanipulation | dict | The photomanipulation settings. Keys of dict listed below. | No | |
| Enabled | bool | Whether the photomanipulation should be executed. | No | false |
| IlluminationInternal | bool | Whether to use the internal illumination. | No | true |
| Illumination | string | Name of the illumination settings to apply on acquisition controller device. | No | null |
| IlluminationFilter | string | Name of the illumination filter settings to apply on the filter wheel. | No | null |
| IlluminationIntensityExternal | double | The intensity (as a percentage of the maximum) of the external illumination. | No | 0 |
| Positions | list of string | The list of positions to photomanipulate. If null, all positions are photomanipulated. If empty, no positions are photomanipulated. | No | null |
| TimePoints | list of int | The list of time points to photomanipulate. If both and are null, the photomanipulation is executed at every time point. If empty and is null, no time points are photomanipulated. | No | null |
| AcquireNthTimePoint | int? | Interval at which the channel is acquired. It is acquired at every specified number of time points. If both and are null, the photomanipulation is executed at every time point. | No | null |
| ChannelPresets | list of dict | The list of channel presets. Keys of dict listed below. | Yes | |
| Name | string | The name of the channel. | Yes | |
| Enabled | bool | Whether the channel should be acquired. | Yes | |
| AcquireNthTimePoint | int | Interval at which the channel is acquired. It is acquired at every specified number of time points. | No | |
| Color | enum | The channel default color. Possible values listed below. | Yes | |
| Red | string | Red color. | - | |
| Green | string | Green color. | - | |
| Blue | string | Blue color. | - | |
| Cyan | string | Cyan color. | - | |
| Magenta | string | Magenta color. | - | |
| Yellow | string | Yellow color. | - | |
| White | string | White color. | - | |
| Illumination | string | Name of the illumination settings to apply on acquisition controller device. | No | |
| Exposure | string | Name of the exposure settings to apply on acquisition controller device. | No | |
| Camera | int | The index of the camera to use. | No | |
| DeviceSettings | list of dict | Channel-related settings for some devices. Keys of dict listed below. | Yes | |
| Name | string | The name of the device to set. | Yes | |
| Settings | string | The name of the settings to apply. | No | |