# 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)

• 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.

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:


### 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,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,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,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,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,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,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,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,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,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,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,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,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


Discussion page for Setup_UTSW_SD imported from old wiki