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Setup UTSW SD

Summary

Version 1.4.13 (64-bit)
Operating System Windows 7 Professional 64-bit
Facility UT Southwestern Live Cell Imaging Facility (Prof. Kate Luby-Phelps, Abhijit Bugde)
End User Salman Banani, et al
Vendor Micro-Manager setup by Pariksheet Nanda (Andor)
Dates Setup 2013-03-19 to 2013-03-21
Total Time Spent 8 hours (4 of those hours on external Python scripts)
Comments Green Flags Red Flags
  • Searching nabble (mailing list) answered most questions.
  • Beanshell scripting is powerful- less time hunting; more time coding.
  • Not enough time left over to optimize system- jitter when streaming in MDA.
(A) Optical train of spinning disk system (B) Full system (C) Microscope
Components

Experience gained

  • Should not use > 4GB circular buffer for AndorSDK3 camera with MM version 1.4.13 (issue fixed in nightly build).
  • During setup, it's useful to occasionally backup the configuration file with Tools > Save Configuration Settings as.
  • It's not a good idea to enable Tools > Options > Do not ask for config file. While changing around COM ports and presets, the startup errors would not launch the software. Without an earlier backup, the configuration file needed many lines commented out. If there was a backup one could use the "none" configuration to start and then diagnose the problem with the offending hardware setup (e.g. by loading it one at a time).
  • Learned that one has to put the MMStartup.bsh startup script in the µManager root folder. First instinct was to put it in the "scripts" folder, which didn't work.
  • exec() command in Beanshell startup script was useful in fixing hardware annoyances.
  • Beanshell silently won't run a script with exec() if the library it's loading has already been loaded by the Java VM. Workaround found was using a sub-shell (CMD /C on Windows).

Wishlist

  • AndorLaserCombiner: ability to create Group shortcuts for laser intensities. This is not possible since the laser on/off state is tied with the laser intensity, so if having multiple lasers set to a non-zero intensity turns all those lasers on! Maybe create shutters for each individual laser?
    • Changing laser intensity could be done with one drag of the mouse slider with this change.
    • Right now, adjusting laser intensity requires editing the preset, waiting for the associated hardware to move, changing the value, and then saving the preset.
  • New DeviceAdapter for FRAPPA galvo
  • Example MMstartup.bsh script with useful commands, (commented out, of course).
  • Automated bug reporting and product registration does not work since the IT department at UT Southwestern blocks whatever port is requires.
  • Some Plugins not documented in wiki.

Appendix

Startup Script (MMStartup.bsh)

   // Set FRAPPA galvo position to 6.5 degrees for this system's light
   // path.
   //
   // However the script won't run inside Micro-Manager since
   // tillimic.dll also uses log4j.  Therefore use a sub-shell as a
   // workaround (i.e. the `CMD /C` prefix).
   exec("CMD /C C:/Python27/python C:/MM/frappa_bypass.py 6.5 2>&1");
   // Laser shutter does not open on initialization, so as a workaround
   // this Python script keeps trying till it opens.
   exec("C:/Python27/python C:/MM/alc_shutter_toggle_until_open.py");
   // Home the Z Piezo to the center of its range.
   mmc.setPosition("NanoScanZ", 50);
   // Crop sCMOS to spinning disk aperture.  If you need to change the
   // ROI values if the camera is moved, run `show_roi_coordinates.bsh`
   default_camera = mmc.getProperty("Core", "Camera");
   mmc.setProperty("Core", "Camera", " sCMOS");
   mmc.waitForSystem();
   mmc.setROI(526, 582, 1622, 1142);
   mmc.waitForSystem();
   mmc.setProperty("Core", "Camera", default_camera);
   mmc.waitForSystem();
   // Startup with DIC channel.
   mmc.setConfig("Channels-Confocal", "DIC");
   gui.refreshGUI();  // Shows above selected channel.
   // For Emacs to understand this beanshell file
   // Local Variables:
   // mode: auto-fill
   // mode: java
   // End:

Python scripts

Configuration File (spinning-disk.cfg)

   # Generated by Configurator on Wed Mar 20 18:52:39 CDT 2013
   
   # Reset
   Property,Core,Initialize,0
   
   # Devices
   Device,COM5,SerialManager,COM5
   Device,COM6,SerialManager,COM6
   Device,COM7,SerialManager,COM7
   Device,COM3,SerialManager,COM3
   Device,COM4,SerialManager,COM4
   Device,EMCCD,Andor,Andor
   Device,TIScope,NikonTI,TIScope
   Device,TINosePiece,NikonTI,TINosePiece
   Device,TIFilterBlock1,NikonTI,TIFilterBlock1
   Device,TIZDrive,NikonTI,TIZDrive
   Device,TIPFSOffset,NikonTI,TIPFSOffset
   Device,TIPFSStatus,NikonTI,TIPFSStatus
   Device,TITIRF,NikonTI,TITIRF
   Device,TIEpiShutter,NikonTI,TIEpiShutter
   Device,TIDiaShutter,NikonTI,TIDiaShutter
   Device,TILightPath,NikonTI,TILightPath
   Device,TIAnalyzer,NikonTI,TIAnalyzer
   Device,CSUX-Hub,CSUX,CSUX-Hub
   Device,CSUX-Dichroic Mirror,CSUX,CSUX-Dichroic Mirror
   Device,CSUX-Shutter,CSUX,CSUX-Shutter
   Device,CSUX-DriveSpeed,CSUX,CSUX-DriveSpeed
   Device,Wheel-sCMOS,CSUX,CSUX-Filter Wheel
   Device,AndorLaserCombiner,AndorLaserCombiner,AndorLaserCombiner
   Device, sCMOS,AndorSDK3,Andor sCMOS Camera
   Device,XYStage,Prior,XYStage
   Device,Wheel-EMCCD,SutterLambda,Wheel-A
   Device,Shutter-Transmitted,SutterLambda,Shutter-A
   Device,NanoScanZ,Prior,NanoScanZ
   
   # Pre-init settings for devices
   Property,COM5,AnswerTimeout,500.0000
   Property,COM5,BaudRate,9600
   Property,COM5,DelayBetweenCharsMs,0.0000
   Property,COM5,Handshaking,Off
   Property,COM5,Parity,None
   Property,COM5,StopBits,1
   Property,COM5,Verbose,1
   Property,COM6,AnswerTimeout,500.0000
   Property,COM6,BaudRate,9600
   Property,COM6,DelayBetweenCharsMs,0.0000
   Property,COM6,Handshaking,Off
   Property,COM6,Parity,None
   Property,COM6,StopBits,1
   Property,COM6,Verbose,1
   Property,COM7,AnswerTimeout,500.0000
   Property,COM7,BaudRate,9600
   Property,COM7,DelayBetweenCharsMs,0.0000
   Property,COM7,Handshaking,Off
   Property,COM7,Parity,None
   Property,COM7,StopBits,1
   Property,COM7,Verbose,1
   Property,COM3,AnswerTimeout,5000.0000
   Property,COM3,BaudRate,115200
   Property,COM3,DelayBetweenCharsMs,0.0000
   Property,COM3,Handshaking,Off
   Property,COM3,Parity,None
   Property,COM3,StopBits,1
   Property,COM3,Verbose,1
   Property,COM4,AnswerTimeout,500.0000
   Property,COM4,BaudRate,9600
   Property,COM4,DelayBetweenCharsMs,0.0000
   Property,COM4,Handshaking,Off
   Property,COM4,Parity,None
   Property,COM4,StopBits,1
   Property,COM4,Verbose,1
   Property,EMCCD,Camera,| iXon Ultra | DU897_BV | 7389 |
   Property,CSUX-Hub,Port,COM3
   Property,Wheel-sCMOS,WheelNumber,1
   Property,AndorLaserCombiner,MultiPortUnitPresent,1
   Property,XYStage,Port,COM5
   Property,Wheel-EMCCD,Port,COM4
   Property,Shutter-Transmitted,Port,COM7
   Property,NanoScanZ,Port,COM6
   
   # Pre-init settings for COM ports
   
   # Hub (parent) references
   Parent,TINosePiece,TIScope
   Parent,TIFilterBlock1,TIScope
   Parent,TIZDrive,TIScope
   Parent,TIPFSOffset,TIScope
   Parent,TIPFSStatus,TIScope
   Parent,TITIRF,TIScope
   Parent,TIEpiShutter,TIScope
   Parent,TIDiaShutter,TIScope
   Parent,TILightPath,TIScope
   Parent,TIAnalyzer,TIScope
   
   # Initialize
   Property,Core,Initialize,1
   
   # Delays
   
   # Roles
   Property,Core,Camera,EMCCD
   Property,Core,Shutter,AndorLaserCombiner
   Property,Core,Focus,TIZDrive
   Property,Core,AutoShutter,1
   
   # Camera-synchronized devices
   
   # Labels
   # TINosePiece
   Label,TINosePiece,5,6-      
   Label,TINosePiece,4,5-ApoTIRF 100x na 1.49
   Label,TINosePiece,3,4-ApoTIRF  60x na 1.49
   Label,TINosePiece,2,3-SPlanFLuor  40x na 0.60
   Label,TINosePiece,1,2-SPlanFLuor  20x na 0.45
   Label,TINosePiece,0,1-PlanFluor  10x na 0.30
   # TIFilterBlock1
   Label,TIFilterBlock1,5,6------
   Label,TIFilterBlock1,4,5-CFPHQ
   Label,TIFilterBlock1,3,4-YFPHQ
   Label,TIFilterBlock1,2,3-TxRed
   Label,TIFilterBlock1,1,2-GFPHQ
   Label,TIFilterBlock1,0,1-ANALY
   # TILightPath
   Label,TILightPath,3,Left80
   Label,TILightPath,2,Right100
   Label,TILightPath,1,Left100
   Label,TILightPath,0,Eye100
   # CSUX-Dichroic Mirror
   Label,CSUX-Dichroic Mirror,2,Quad
   Label,CSUX-Dichroic Mirror,1,488-568
   Label,CSUX-Dichroic Mirror,0,405-488-561-594
   # Wheel-sCMOS
   Label,Wheel-sCMOS,5,440-521-607-700
   Label,Wheel-sCMOS,4,542-27
   Label,Wheel-sCMOS,3,484-35
   Label,Wheel-sCMOS,2,607-36
   Label,Wheel-sCMOS,1,525-40
   Label,Wheel-sCMOS,0,447-60
   # Wheel-EMCCD
   Label,Wheel-EMCCD,9,Blocked-9
   Label,Wheel-EMCCD,8,Blocked-8
   Label,Wheel-EMCCD,7,Open
   Label,Wheel-EMCCD,6,440-521-607-700
   Label,Wheel-EMCCD,5,542-27
   Label,Wheel-EMCCD,4,484-35
   Label,Wheel-EMCCD,3,607-36
   Label,Wheel-EMCCD,2,525-40
   Label,Wheel-EMCCD,1,447-60
   Label,Wheel-EMCCD,0,512-630
   
   # Configuration presets
   # Group: Channels-Confocal
   # Preset: 561
   ConfigGroup,Channels-Confocal,561,TIFilterBlock1,Label,6------
   ConfigGroup,Channels-Confocal,561,CSUX-Dichroic Mirror,Label,Quad
   ConfigGroup,Channels-Confocal,561,Wheel-sCMOS,Label,607-36
   ConfigGroup,Channels-Confocal,561,AndorLaserCombiner,PowerSetpoint405,0.0000
   ConfigGroup,Channels-Confocal,561,AndorLaserCombiner,PowerSetpoint445,0.0000
   ConfigGroup,Channels-Confocal,561,AndorLaserCombiner,PowerSetpoint488,0.0000
   ConfigGroup,Channels-Confocal,561,AndorLaserCombiner,PowerSetpoint515,0.0000
   ConfigGroup,Channels-Confocal,561,AndorLaserCombiner,PowerSetpoint561,3.0000
   ConfigGroup,Channels-Confocal,561,AndorLaserCombiner,PowerSetpoint594,0.0000
   ConfigGroup,Channels-Confocal,561,AndorLaserCombiner,LaserPort,A
   ConfigGroup,Channels-Confocal,561,Core,AutoShutter,1
   ConfigGroup,Channels-Confocal,561,Core,Shutter,AndorLaserCombiner
   ConfigGroup,Channels-Confocal,561,Wheel-EMCCD,Label,607-36
   ConfigGroup,Channels-Confocal,561,TILightPath,Label,Right100
   
   # Preset: 488
   ConfigGroup,Channels-Confocal,488,TIFilterBlock1,Label,6------
   ConfigGroup,Channels-Confocal,488,CSUX-Dichroic Mirror,Label,Quad
   ConfigGroup,Channels-Confocal,488,Wheel-sCMOS,Label,525-40
   ConfigGroup,Channels-Confocal,488,AndorLaserCombiner,PowerSetpoint405,0.0000
   ConfigGroup,Channels-Confocal,488,AndorLaserCombiner,PowerSetpoint445,0.0000
   ConfigGroup,Channels-Confocal,488,AndorLaserCombiner,PowerSetpoint488,3.0000
   ConfigGroup,Channels-Confocal,488,AndorLaserCombiner,PowerSetpoint515,0.0000
   ConfigGroup,Channels-Confocal,488,AndorLaserCombiner,PowerSetpoint561,0.0000
   ConfigGroup,Channels-Confocal,488,AndorLaserCombiner,PowerSetpoint594,0.0000
   ConfigGroup,Channels-Confocal,488,AndorLaserCombiner,LaserPort,A
   ConfigGroup,Channels-Confocal,488,Core,AutoShutter,1
   ConfigGroup,Channels-Confocal,488,Core,Shutter,AndorLaserCombiner
   ConfigGroup,Channels-Confocal,488,Wheel-EMCCD,Label,525-40
   ConfigGroup,Channels-Confocal,488,TILightPath,Label,Right100
   
   # Preset: DIC
   ConfigGroup,Channels-Confocal,DIC,TIFilterBlock1,Label,6------
   ConfigGroup,Channels-Confocal,DIC,TILightPath,Label,Right100
   ConfigGroup,Channels-Confocal,DIC,CSUX-Dichroic Mirror,Label,Quad
   ConfigGroup,Channels-Confocal,DIC,Wheel-sCMOS,Label,440-521-607-700
   ConfigGroup,Channels-Confocal,DIC,AndorLaserCombiner,LaserPort,A
   ConfigGroup,Channels-Confocal,DIC,AndorLaserCombiner,PowerSetpoint405,0.0000
   ConfigGroup,Channels-Confocal,DIC,AndorLaserCombiner,PowerSetpoint445,0.0000
   ConfigGroup,Channels-Confocal,DIC,AndorLaserCombiner,PowerSetpoint488,0.0000
   ConfigGroup,Channels-Confocal,DIC,AndorLaserCombiner,PowerSetpoint515,0.0000
   ConfigGroup,Channels-Confocal,DIC,AndorLaserCombiner,PowerSetpoint561,0.0000
   ConfigGroup,Channels-Confocal,DIC,AndorLaserCombiner,PowerSetpoint594,0.0000
   ConfigGroup,Channels-Confocal,DIC,Wheel-EMCCD,Label,Open
   ConfigGroup,Channels-Confocal,DIC,Core,AutoShutter,1
   ConfigGroup,Channels-Confocal,DIC,Core,Shutter,Shutter-Transmitted
   
   # Preset: 445
   ConfigGroup,Channels-Confocal,445,TIFilterBlock1,Label,6------
   ConfigGroup,Channels-Confocal,445,CSUX-Dichroic Mirror,Label,Quad
   ConfigGroup,Channels-Confocal,445,Wheel-EMCCD,Label,484-35
   ConfigGroup,Channels-Confocal,445,AndorLaserCombiner,PowerSetpoint405,0.0000
   ConfigGroup,Channels-Confocal,445,AndorLaserCombiner,PowerSetpoint445,3.0000
   ConfigGroup,Channels-Confocal,445,AndorLaserCombiner,PowerSetpoint488,0.0000
   ConfigGroup,Channels-Confocal,445,AndorLaserCombiner,PowerSetpoint515,0.0000
   ConfigGroup,Channels-Confocal,445,AndorLaserCombiner,PowerSetpoint561,0.0000
   ConfigGroup,Channels-Confocal,445,AndorLaserCombiner,PowerSetpoint594,0.0000
   ConfigGroup,Channels-Confocal,445,AndorLaserCombiner,LaserPort,A
   ConfigGroup,Channels-Confocal,445,Core,AutoShutter,1
   ConfigGroup,Channels-Confocal,445,Core,Shutter,AndorLaserCombiner
   ConfigGroup,Channels-Confocal,445,Wheel-sCMOS,Label,484-35
   ConfigGroup,Channels-Confocal,445,TILightPath,Label,Right100
   
   # Preset: 515
   ConfigGroup,Channels-Confocal,515,TIFilterBlock1,Label,6------
   ConfigGroup,Channels-Confocal,515,CSUX-Dichroic Mirror,Label,Quad
   ConfigGroup,Channels-Confocal,515,Wheel-sCMOS,Label,542-27
   ConfigGroup,Channels-Confocal,515,AndorLaserCombiner,PowerSetpoint405,0.0000
   ConfigGroup,Channels-Confocal,515,AndorLaserCombiner,PowerSetpoint445,0.0000
   ConfigGroup,Channels-Confocal,515,AndorLaserCombiner,PowerSetpoint488,0.0000
   ConfigGroup,Channels-Confocal,515,AndorLaserCombiner,PowerSetpoint515,2.9900
   ConfigGroup,Channels-Confocal,515,AndorLaserCombiner,PowerSetpoint561,0.0000
   ConfigGroup,Channels-Confocal,515,AndorLaserCombiner,PowerSetpoint594,0.0000
   ConfigGroup,Channels-Confocal,515,AndorLaserCombiner,LaserPort,A
   ConfigGroup,Channels-Confocal,515,Core,AutoShutter,1
   ConfigGroup,Channels-Confocal,515,Core,Shutter,AndorLaserCombiner
   ConfigGroup,Channels-Confocal,515,Wheel-EMCCD,Label,542-27
   ConfigGroup,Channels-Confocal,515,TILightPath,Label,Right100
   
   # Preset: 405
   ConfigGroup,Channels-Confocal,405,TIFilterBlock1,Label,6------
   ConfigGroup,Channels-Confocal,405,CSUX-Dichroic Mirror,Label,Quad
   ConfigGroup,Channels-Confocal,405,Wheel-sCMOS,Label,447-60
   ConfigGroup,Channels-Confocal,405,AndorLaserCombiner,PowerSetpoint405,3.0000
   ConfigGroup,Channels-Confocal,405,AndorLaserCombiner,PowerSetpoint445,0.0000
   ConfigGroup,Channels-Confocal,405,AndorLaserCombiner,PowerSetpoint488,0.0000
   ConfigGroup,Channels-Confocal,405,AndorLaserCombiner,PowerSetpoint515,0.0000
   ConfigGroup,Channels-Confocal,405,AndorLaserCombiner,PowerSetpoint561,0.0000
   ConfigGroup,Channels-Confocal,405,AndorLaserCombiner,PowerSetpoint594,0.0000
   ConfigGroup,Channels-Confocal,405,AndorLaserCombiner,LaserPort,A
   ConfigGroup,Channels-Confocal,405,Core,AutoShutter,1
   ConfigGroup,Channels-Confocal,405,Core,Shutter,AndorLaserCombiner
   ConfigGroup,Channels-Confocal,405,Wheel-EMCCD,Label,447-60
   ConfigGroup,Channels-Confocal,405,TILightPath,Label,Right100
   
   
   # Group: Channels-TIRF
   # Preset: TIRF 488
   ConfigGroup,Channels-TIRF,TIRF 488,TITIRF,Mirror,In
   ConfigGroup,Channels-TIRF,TIRF 488,TITIRF,Position,35000
   ConfigGroup,Channels-TIRF,TIRF 488,TILightPath,Label,Right100
   ConfigGroup,Channels-TIRF,TIRF 488,Wheel-sCMOS,Label,440-521-607-700
   ConfigGroup,Channels-TIRF,TIRF 488,AndorLaserCombiner,LaserPort,C
   ConfigGroup,Channels-TIRF,TIRF 488,AndorLaserCombiner,PowerSetpoint405,0.0000
   ConfigGroup,Channels-TIRF,TIRF 488,AndorLaserCombiner,PowerSetpoint445,0.0000
   ConfigGroup,Channels-TIRF,TIRF 488,AndorLaserCombiner,PowerSetpoint488,3.0000
   ConfigGroup,Channels-TIRF,TIRF 488,AndorLaserCombiner,PowerSetpoint515,0.0000
   ConfigGroup,Channels-TIRF,TIRF 488,AndorLaserCombiner,PowerSetpoint561,0.0000
   ConfigGroup,Channels-TIRF,TIRF 488,AndorLaserCombiner,PowerSetpoint594,0.0000
   ConfigGroup,Channels-TIRF,TIRF 488,TIFilterBlock1,Label,5-CFPHQ
   ConfigGroup,Channels-TIRF,TIRF 488,Core,AutoShutter,1
   ConfigGroup,Channels-TIRF,TIRF 488,Core,Shutter,AndorLaserCombiner
   ConfigGroup,Channels-TIRF,TIRF 488,Wheel-EMCCD,Label,Open
   
   
   # Group: Select-Focus
   # Preset: NanoScanZ
   ConfigGroup,Select-Focus,NanoScanZ,Core,Focus,NanoScanZ
   
   # Preset: TIPFSOffset
   ConfigGroup,Select-Focus,TIPFSOffset,Core,Focus,TIPFSOffset
   
   # Preset: TIZDrive
   ConfigGroup,Select-Focus,TIZDrive,Core,Focus,TIZDrive
   
   
   # Group: System
   # Preset: Startup
   ConfigGroup,System,Startup,CSUX-Shutter,State,Open
   ConfigGroup,System,Startup,CSUX-DriveSpeed,State,5000
   ConfigGroup,System,Startup,Wheel-EMCCD,Speed,2
   ConfigGroup,System,Startup,EMCCD,Gain,100
   ConfigGroup,System,Startup, sCMOS,TriggerMode,Software (Recommended for Live Mode)
   
   
   # Group: Select-Camera
   # Preset: sCMOS
   ConfigGroup,Select-Camera,sCMOS,Core,Camera, sCMOS
   
   # Preset: EMCCD
   ConfigGroup,Select-Camera,EMCCD,Core,Camera,EMCCD
   
   
   # Group: Channels-Eye
   # Preset: DIC
   ConfigGroup,Channels-Eye,DIC,TIFilterBlock1,Label,1-ANALY
   ConfigGroup,Channels-Eye,DIC,TILightPath,Label,Eye100
   ConfigGroup,Channels-Eye,DIC,Core,AutoShutter,0
   ConfigGroup,Channels-Eye,DIC,Core,Shutter,Shutter-Transmitted
   
   
   # Group: EM-Gain
   # Preset: 250
   ConfigGroup,EM-Gain,250,EMCCD,Gain,250
   
   # Preset: 200
   ConfigGroup,EM-Gain,200,EMCCD,Gain,200
   
   # Preset: 150
   ConfigGroup,EM-Gain,150,EMCCD,Gain,150
   
   # Preset: 100
   ConfigGroup,EM-Gain,100,EMCCD,Gain,100
   
   # Preset: 300
   ConfigGroup,EM-Gain,300,EMCCD,Gain,300
   
   
   
   # PixelSize settings


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