structure state %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% The following variables are the ones that typically need to be changed for a new installation.%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% structure init % acquisitionBoardIndex and mirrorOutputBoardIndex must, at present, be the same % They must represent the device name of a National Insturments S-Series Board (e.g. NI PCI 6110) % The device names of installed boards can be determined by calling daqhwinfo('nidaq') from the MATLAB command line. acquisitionBoardIndex='Dev1' % Name of DAQ board for use with PMT acquisition mirrorOutputBoardIndex='Dev1' % Name of DAQ board for use with galvo mirror output. triggerBoardIndex='Dev1' % Name of DAQ board for use as TTL trigger (usually on DIO line 0; line index is set in init.triggerLineIndex) triggerLineIndex=0 % Index of DIO line to use as the trigger signal output, which should be connected to the triggerInputTerminal of each board. triggerInputTerminal='PFI0' % Terminal on which all ScanImage boards receive their input trigger normally externalTriggerInputTerminal='PFI1' % Terminal on which all ScanImage boards recieve their input trigger, when triggered by an external program (e.g. Ephus) externalTriggerTimeout=inf % Time, in seconds, to wait for an external trigger before timing out. Can be set to 'inf'. outputBoardClockTerminal='RTSI6' % (Can be one of 'PFI'<1-9> or 'RTSI'<0-6>) Terminal on which mirror board's sample clock is exported, and Pockels board(s)' sample clock is imported. maxBufferedGrabTime=500 % Length of time, in seconds, above which Grab acquisitions must use 'Save During Acquisition' mode, rather than buffering all the experimental data. This is system RAM dependent. maxFlybackRate=10000 % (RESERVED for r3.6) Maximum rate, in volts/s, which the fast mirror servo can achieve. Used to determine sawtooth waveforms. %ScanOffsetX/Y specify a constant mirror command offset to apply in order to center the scanning field-of-view within the objective and/or microscope's field-of-view. This is typically done using a fluorescent dye sample. %These parameters can be set interactively via 'SET' on MainControls. They are not stored in either CFG or USR files. scanOffsetX=0.00 Config 2 Gui gh.basicConfigurationGUI.xScanOffset Gui gh.mainControls.etScanOffsetX Numeric 1 scanOffsetY=0.00 Config 2 Gui gh.basicConfigurationGUI.yScanOffset Gui gh.mainControls.etScanOffsetY Numeric 1 parkAmplitudeX=5 % Amplitude to supply to X mirror driver when laser beam is parked (also shutter/Pockels are off) parkAmplitudeY=5 % " " (Y mirror) maxOffsetX=2 % Maximum offset value to allow for X mirror; this voltage is also used to determine 'fast' beam parking, such as when changing zoom during Focus maxOffsetY=2 % " " (Y mirror) maxAmplitudeX=3 % Maximum peak amplitude to allow for X mirror scan maxAmplitudeY=3 % " " (Y mirror) pockelsOn=1 % Flag to determine whether Pockels Cell is being used: 1 = yes, 0 = no % Modulator Specifics. Each of N EOMs (Pockels Cells) must have pockelsBoardIndexN, pockelsOuputIdN, pockelsChannelIndexN, photodiodeInputChannelN, % photodiodeInputBoardIdN, powerConversionN, rejected_lightN, maxPowerN, maxLimitN, and photodiodeOffsetN included below. % NOTE: If photodiodeInputBoardIdN is left empty (default), the Pockels Cell will be uncalibrated. % A valid acquisition device ID (e.g. 'Dev1') must be provided for photodiode calibration to be used. structure eom pockelsBoardIndex1='Dev2' % Name of Output DAQ board for use with scan laser pockels cell pockelsChannelIndex1=0 % Index of output DAQ channel for use to drive scan laser pockels cell. pockelsVoltageRange1=1 % Pockels cell control voltage ranges from 0 to this value--typically 1V for high-Z load, or 2V for 50ohm load photodiodeInputBoardId1='' % Name of Input DAQ board where photocurrent is input. If empty, this beam will be left uncalibrated. In many cases, this will be the same as the acquisitionBoard. photodiodeInputChannel1=2 % Channel index on input DAQ board where photocurrent is input. powerConversion1=10 Config 2 % Conversion factor: * = . rejected_light1=0 Config 2 % The calibration input comes from accepted/rejected light. 0==accepted 1==rejected maxPower1=10 % The startup values can be set here... maxLimit1=100 % Same as above. photodiodeOffset1=0 Config 2 % The 'rest' voltage from the photodiode for this beam (this covers amplifier offset, ambient light, etc). %Uncomment next section to add second Pockels Cell (and photodiode, if present) %pockelsBoardIndex2='Dev2' % Nname of Output DAQ board for use with scan laser pockels cell. %pockelsChannelIndex2=1 % Index of output DAQ channel for use to drive scan laser pockels cell. %pockelsVoltageRange2=2 % Pockels cell control voltage ranges from 0 to this value--typically 1V for high-Z load, or 2V for 50ohm load %photodiodeInputBoardId2='' % Name of Input DAQ board where photocurrent is input. If empty, this beam will be left uncalibrated. In many cases, this will be the same as the acquisitionBoard. %photodiodeInputChannel2=3 % Channel index on Input DAQ board where photocurrent is input. %powerConversion2=10 Config 2 % Conversion factor: * = . %rejected_light2=0 Config 2 % The calibration input comes from accepted/rejected light. 0==accepted 1==rejected %maxPower2=10 % The startup values can be set here... %maxLimit2=100 % Same as above. %photodiodeOffset2=0 Config 2 % The 'rest' voltage from the photodiode for this beam (this covers amplifier offset, ambient light, etc). %Uncomment next section to add third Pockels Cell (and photodiode, if present) %pockelsBoardIndex3='Dev2' % Nname of Output DAQ board for use with scan laser pockels cell. %pockelsChannelIndex3=2 % Index of output DAQ channel for use to drive scan laser pockels cell. %pockelsVoltageRange3=2 % Pockels cell control voltage ranges from 0 to this value--typically 1V for high-Z load, or 2V for 50ohm load %photodiodeInputBoardId3='' % Name of Input DAQ board where photocurrent is input. If empty, this beam will be left uncalibrated. In many cases, this will be the same as the acquisitionBoard. %photodiodeInputChannel3=4 % Channel index on Input DAQ board where photocurrent is input. %powerConversion3=10 Config 2 % Conversion factor: * = . %rejected_light3=0 Config 2 % The calibration input comes from accepted/rejected light. 0==accepted 1==rejected %maxPower3=10 % The startup values can be set here... %maxLimit3=100 % Same as above. %photodiodeOffset3=0 Config 2 % The 'rest' voltage from the photodiode for this beam (this covers amplifier offset, ambient light, etc). endstructure endstructure structure shutter shutterBoardIndex='Dev1' % Name of board on which the static DIO lines for the shutter(s) will be employed shutterLineIndex=1 % Line index for laser shutter line (assumed to be on Port 0) epiShutterLineIndex=2 % Line index for epi-lamp shutter line (assumed to be on Port 0) open=0 % Boolean value indicating TTL level used for open state of laser shutter (0=TTL LO, 1=TTL HI) epiShutterOpen=1 % Boolean value indicating TTL level used for open state of laser shutter (0=TTL LO, 1=TTL HI) endstructure % Stage and Z-Focus controls using a Sutter MP285. % ScanImage users employ different MP285 firmware versions, several of which were specially made for early ScanImage users. % Navigate to Setup->Utilities->Info on the MP-285 controller. % Note if there are 2 letters ('KS', 'SA', or 'WD') preceding the version number. If not, this is a 'native' MP-285. structure motor motorOn=0 % Flag (1 = yes, 0=no) to determine whether MP285 is being used (by any user) port='COM2' % Serial port for MP285 communication baud=9600 % Baud rate - this MUST match the value set on the MP-285 controller timeout=5 % period till timeout in seconds firmware='native' % One of: 'native','KS','SA','WD' posnResolution=0.05 % Resolution, in microns, of positioning commands. Positional errors greater than this amount will be flagged. %Velocity values for movement commands velocityFast=2000 % Velocity used for most of large moves, before slowing down for final 100um. Value is roughly in um/sec. velocitySlow=400 % Velocity used for movements < 100um (e.g. stack steps) and at end of large moves for fine control. Fine resolution mode is used for 'slow' moves, so slow velocity units are not identical to fast velocity units (approx. one-half). endstructure %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% End of section commonly edited on new installation %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%