Description
This is a MATLAB .m file that contains parameters that describe the hardware configuration of your microscope. These parameters are expected to rarely change.
It is only read when ScanImage starts; any change during an experiment requires a Matlab restart.
It is required for ScanImage to start. If the file is missing, you'll be asked to configure or locate one. For a fresh installation, choose to create a new file. A new file will be opened in the Matlab editor, and parameters will be added with default values for you to customize. Be sure to save the file when finished.
Sections
| Section | Description |
|---|---|
| ScanImage | General ScanImage behavior (for example, simulated mode). |
| ResonantAcq | The FlexRIO Digitizer Module |
| ResScanCtrl | The system's Scan Control DAQ. |
| Shutters | Shutter(s) used to prevent any beam exposure from reaching specimen during idle periods. |
| Beams | Beam control and calibration channels. Typically used to control Pockels cells. |
| Motors | Motor used for X/Y/Z motion, including stacks. |
| FastZ | FastZ hardware used for fast axial motion, supporting fast stacks and/or volume imaging. |
Parameters
ScanImage
| Parameter | Description |
|---|---|
| simulated | Boolean for activating simulated mode. For normal operation, set to 'false'. For operation without NI hardware attached, set to 'true'. |
| nominalResScanFreq | nominal frequency of the resonant scanner, in Hz |
| primaryPxiChassisNum | Numeric ID of the PXI chassis that contains the FlexRIO FPGA and Digitizer module. |
| scannerHardwareType | One of {'standard' 'ecu1' 'bscope2'}; Used to enable native Thorlabs ECU and BScope 2 support. More details can be found at the following page. |
| digitalIODeviceName | Specify the name of the DAQ board that is used for trigger inputs/outputs. This device must be installed in the same PXI chassis as the FlexRIO Digitizer. |
Example
ResonantAcq
| Parameter | Description |
|---|---|
| pathToBitfile | Name of bitfile to load onto FPGA |
| rioDeviceName | FlexRIO Device ID as specified in MAX. If empty, defaults to 'RIO0' |
| channelsInvert | specifies if the input signal is inverted (i.e., more negative for increased light signal) |
Example
ResScanCtrl
| Parameter | Description |
|---|---|
scanCtrlDeviceName | String identifying the NI-DAQ board to be used to control the resonant/galvo scanner. The name of the device can be seen in NI MAX. |
resonantZoomAOChanID | An integer. The numeric ID of the Analog Output channel to be used to control the Resonant Scanner Zoom level. |
galvoAOChanID | An integer. The numeric ID of the Analog Output channel to be used to control the Galvo. |
| chanCtrMeasResPeriod | counter channel for measuring the resonant scanner period |
| galvoVoltsPerOpticalDegree | galvo conversion factor from optical degrees to volts |
| rScanVoltsPerOpticalDegree | resonant scanner conversion factor from optical degrees to volts |
| refAngularRange | optical degrees for resonant scanner and galvo at zoom level = 1 |
Example
Shutters
| Parameter | Description |
|---|---|
| shutterOpenLevel | Logical or 0/1 scalar/array indicating TTL level (0=LO;1=HI) corresponding to shutter open state for each shutter line. If scalar, value applies to all shutterLineIDs |
| shutterOpenTime | Time, in seconds, to delay following certain shutter open commands (e.g. between stack slices), allowing shutter to fully open before proceeding. |
Example
Beams
| Parameters | Description |
|---|---|
| beamModifiedLineClockIn | an empty string ("") or one of PFI0..15 to which external beam trigger is connected. Leave empty if DAQ device is in main PXI chassis. |
| beamDeviceName | String or cell string array of device name(s) containing beam modulation channels. If single string, applies to all channels in beamChanIDs. |
| beamChanIDs | Array of integers specifying AO channel IDs, one for each beam modulation channel. Length of array determines number of 'beams'. |
| beamIDs | Optional string cell array of identifiers for each beam |
| beamVoltageRanges | Scalar or array of values specifying voltage range to use for each beam. Scalar applies to each beam. |
| beamCalInputDeviceNames | String or cell string array of device name(s) containing beam calibration channels. If single string, applies to all beamCalInputChanIDs. TO BE REMOVED IN FUTURE RELEASES |
| beamCalInputChanIDs | Array of integers specifying AI channel IDs, one for each beam modulation channel. Values of nan specify no calibration for particular beam. |
| beamCalOffsets | Array of beam calibration offset voltages for each beam calibration channel |
| shutterBeforeEOM | Logical or 0/1 indicating if shutter is before EOM. Single value, applying to all shutterLineIDs. (moved to beams class definition. |
Example
Motors
| Parameters | Description |
|---|---|
| motorDimensions | If supplied, one of {'XYZ', 'XY', 'Z'}. Defaults to 'XYZ'. |
| motorControllerType | If supplied, one of {'thorlabs.bscope', 'sutter.mp285', 'sutter.mpc200', 'scientifica', 'pi.e665', 'pi.e816'} |
| motorStageType | Some controller require a valid stageType be specified |
| motorCOMPort | Integer identifying COM port for controller, if using serial communication |
| motorBaudRate | Value identifying baud rate of serial communication. If empty, default value for controller used. |
| motorZDepthPositive | Logical indicating if larger Z values correspond to greater depth |
| motorPositionDeviceUnits | 1x3 array specifying, in meters, raw units in which motor controller reports position. If unspecified, default positionDeviceUnits for stage/controller type presumed. |
| motorVelocitySlow | Velocity to use for moves smaller than motorFastMotionThreshold value. If unspecified, default value used for controller. Specified in units appropriate to controller type. |
| motorVelocityFast | Velocity to use for moves larger than motorFastMotionThreshold value. If unspecified, default value used for controller. Specified in units appropriate to controller type. |
| motor2ControllerType | If supplied, one of {'thorlabs.bscope', 'sutter.mp285', 'sutter.mpc200', 'scientifica', 'pi.e665', 'pi.e816'} |
| motor2StageType | Some controller require a valid stageType be specified |
| motor2COMPort | Integer identifying COM port for controller, if using serial communication |
| motor2BaudRate | Value identifying baud rate of serial communication. If empty, default value for controller used. |
| motor2ZDepthPositive | Logical indicating if larger Z values correspond to greater depth |
| motor2PositionDeviceUnits | 1x3 array specifying, in meters, raw units in which motor controller reports position. If unspecified, default positionDeviceUnits for stage/controller type presumed. |
| motor2VelocitySlow | Velocity to use for moves smaller than motorFastMotionThreshold value. If unspecified, default value used for controller. Specified in units appropriate to controller type. |
| motor2VelocityFast | Velocity to use for moves larger than motorFastMotionThreshold value. If unspecified, default value used for controller. Specified in units appropriate to controller type. |
Example
Fast Z
| Parameters | Description |
|---|---|
| frameClockIn | an empty string ("") or one of PFI0..15 to which external beam trigger is connected. Leave empty if the DAQ device is in the main PXI chassis. |
| fastZControllerType | If supplied, one of {'useMotor2', 'pi.e665', 'pi.e816'}. |
| fastZCOMPort | Integer identifying COM port for controller, if using serial communication |
| fastZBaudRate | Value identifying baud rate of serial communication. If empty, default value for controller used. |
| fastZAODeviceName | String specifying device name containing AO channel used for FastZ control |
| fastZAOChanID | Scalar integer indicating AO channel used for FastZ control |
| fastZAIDeviceName | String specifying device name containig AI channel used for FastZ position sensor |
| fastZAIChanID | Scalar integer indicating AI channel used for FastZ sensor |