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Index

0.   Notices - SCSI fails to initialize, turn on/off UV AOTF manually
1.   Operating the system (a step by step guide to basic operation of the confocal)
2.   The System
3.   First time use (new user)
4.   Known Bugs
5.   Viewing Leica Files - getting viewing software for Windows
6.   Leica confocal file analysis and processing
7.   Links
8.   Reporting Problems
9.   Password problems/German key board
10. Dealing with software crashes and microscope stand lockups

00. Booking Calendar

• Trained users are issued an account on the online booking calendar - 

0.  Notices

• Changing Passwords:
  • Logon with your existing, even expired, password - How to change passwords
• Post Clean Install Notes - same as:
  • New user setup
• System Crashes & Recovery
  • There are multiple CPUs in the scan head, microscope stand and main PC, which can individually crash causing the system to lockup in various ways.  The quickest route to recovery is to determined which subsystem has locked up.
    • Microscope stand freezes - e.g. focus drive and filter shutter or changer does not respond: Shut down LCS software on PC, power down stand (controller [2]), wait 15s, restart stand, then the LCS software
    • LCS software can not initialize the hardware - window with yellow diagonal line appears on computer screen: Check that objective turret rotation is in a click position, shut down LCS softwarSe and restart it.
    • Scanning freezes or scanning can not be stopped - shut down LCS software, power down Scan electronics ("scanner" [5]), power down microscope stand (controller [2]), restart stand, restart scan electronics, run LCS software
    • If the above fails - shutdown LCS software, turn off scan electronics ("scanner" [5]), turn off microscope stand (controller [2]), if any error involves the SCSI system, shut down Windows and power off the PC computer, but leave lasers running.  Restart the system following the standard start up procedures.
  • Please make a brief note of what happened in the log book for each crash!  This helps us keep appraised of the system's health.
  • More words on dealing with crashes and lock ups.
• Erratic movement of the motorized stage
  • On very rare occasions the motorized stage will move up unexpectedly if the objective turret is turned, even slightly.  In order to avoid injury when cleaning immersion fluids off the objective used, move it to two positions to the right (or left) away from the optical path
    1. Lower stage down using coarse focus button on right side of microscope stand
    2. Remove slide
    3. Turn objective to be cleaned from the light path to two positions to the right (or left)
    4. Gently clean objective with lens tissue.  Blot on the glass front element.  Rub slowly on the metal around the glass element.
• Please sign the log book in the room and note any problems.
• Switching to dual monitor mode if single screen mode comes up
• Due termination of the service contract Leica support is no longer available at 1-866-830-0735.
• Here is the SP2 TCS software manual (10 MBytes)
  • (An MHmicroscopy account may be required for access.  Remember to put mhmicroscopy\ before your user name)
• Upper Wollaston prism (objective Wollaston) will exacerbate reflections during scanning especially with dry (non immersion) objectives.  Switch objective prism wheel to bright field position BF when not doing DIC/Nomarski. 
• Transmitted light scanning through the condenser can only be done with visible laser illumination.  It can not be performed with the UV excitation laser alone.  Turn on a visible laser even if the wavelength is not required for fluorescence.
• For DAPI scanning please make sure the UV correction lens is set to the 63X. Note that it will set automatically for the 40X 1.25 NA and 10x/20x objectives, but needs manual intervention when the 63x 1.4 NA objective is selected.  This is a work around.  

1.  Operating the system

Power up, setting up microscope, starting software, scanning, saving, shutting down, special scanning modes

2.  The System

• Laser Spot Scanning Confocal Microscope
• Upright microscope with DIC (Nomarski and epi-fluorescence) DM-RXA2
• Visible (blue, green & red) and UV excitation lasers switched/modulated using an AOTF
• Simultaneous transmitted light or DIC imaging while scanning confocally
• AOBS for splitting of excitation lines from emission bands
• Photo Multipliers Tube (PMT) light detectors with spectral discrimination
• High precision galvanometer z-axis positioning stage

• "UV" 351/364nm for e.g. DAPI, Hoechst, Alexa 350, Kaeda photoactivation, Indo-1
• "Blue" Argon 458/476/488/514nm  e.g. 488 nm FITC, Bodipy,  Alexa 488. GFP, CY2, Fluo-4, Calcein; 458 nm CFP, 514 nm YFP
• "Green" Solid State Diode Pump 561nm  e.g. Texas Red, CY3, Alexa 568, Alexa 594, will excite Rhodamine, TRITC, DsRed & Alexa 543
• "Red" HeNe 633nm  e.g. CY5, Alexa 633, Alexa 647, TO-PRO-3, Draq-5

2.2  Objectives:

* Note: exact objective installed should be confirmed by looking at the microscope
** dipping lenses use no cover slip.  All other lenses prefer a number 1.5 (170 um) glass cover slip.
*** When not using DIC the objective Wollaston should be in the blank (BF) position and the Analyser should be out
Use only Leica immersion oil

*Counter-clockwise= increasing position number ↑
clockwise= decreasing position number ↓

2.3  Detection:

• Filtering through an Acoustical Optical Beam Splitter (AOBS)
• Spectral separation through a prism
• Three tunable detection bands with adjustable spectral windows before the three Photo Multiplier Tubes (PMT)
• Standard XY scanning with zoom and rotation (N.B. image rotation is not available with UV excitation)
• XZ rapid scanning using galvanometer stage (range +/-85 um)
• XZ scanning using microscope stand's fine focus (range mm's)
• Transmitted light and DIC (non confocal)
• FRAP, Emission Spectra, ratio imaging

2.4  Analysis:

• Intensity profiles, FRAP, FRET, fluorograms, 3D renders, maximum projection, average projection

3.  First time use (new user)

Copy LCS parameter files from d:\users\_typical\lcs to d:\users\username\lcs
Do not use factory default settings since most parameters are not appropriate for our system

4.  Known Bugs

• Parameter window zoom factor and several other factors does not update when loading an old image.  To see these parameters, just right click on the image name in the experiment window to get a table of scan information.  This information can also be gleaned from the .txt file in the image database directory.

5.  Viewing Files

• LAS-AF lite v 2.6
  • Runs in Windows 7 & Vista & also WinXP
  • Get the LAS AF lite software installer from here (LAS AF lite v2.6.3) or (v2.6.0) or the Leica ftp site: ftp://ftp.llt.de/softlib/LAS_AF_Lite/
  • Using LAS AF 2.6.3 a quick guide
  Leica LCS Light v 2.6 (Looks and somewhat runs like the LCS software on the confocal \\Laplace computer)
  • This program runs under WindowsNT4/WindowsXP
  • It is available from Users' Web pages (http://malus.med.unc.edu/). 
  • Note that LeicaLCS lite does not run under Windows2000, Vista or Win 7/8 (Use LAS AF lite instead)
  • A simple guide with an example image file on using Leica LCS lite
• Volocity 3D/4D image viewing, process & measurement will import Leica image data bases and run Mac or Windows
  • For information about getting access to Volocity see: http://microscopy.unc.edu/volocity
• ImageJ
  • There are several plug ins for Leica image stacks/databases
  • LOCI ImageJ plug ins
  • FIJI ImageJ plug ins

Note: Read/Write permission may be required required to open a Leica Image Database: Image data base files must be in a location with read & write permissions.  Since CD/DVDs are read only, copy the whole database to the hard drive, and open it from the hard drive if necessary.  Depending on the operating system permissions may need resetting on the hard drive after copying from CD/DVDs. 

8.  Leica confocal Image analysis and processing

• Scale bars

7.  Links

      www.leica-microsystems.com
       LeicaLCS-lite software FTP site - ftp://ftp.llt.de

8.  Reporting Problems

     Please contact facility personnel

     Leica Confocal Service and Support is NO LONGER available
     866-830-0735    8:00 A.M. to 5:00 P.M. EST/EDT
     confocal@leica-microsystems.com
     serial number 195353
     Installation date: 23 April 2002 

9.  German Keyboard mappings can prevent passwords from being recognized

German keyboard mappings translates some keyboard keys to other characters.  Basically some keys have a different meaning to the label embossed into the key cap.  Characters to avoid include: !  @  #  '   there are others.  These characters may be found in other unusual positions on the keyboard. 

10.  Dealing with software crashes and Microscope Stand Lock Ups

• Exit software and wait for black window to close.  Then restart LCS software.  Try this twice, then try exiting software
• See here for information

11. Applications:

• Indo-1
  • Chroma suggested filters
  • Omega suggested filters

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