Users must go through training to be able to use the facilities microscopes. The 780 NLO confocal users must also pass a practical test. If you are unsure or have questions about how to operate the system, please get help from the facility staff. Inappropriate use of this facility will result in the revocation of access. The cost for the Zeiss LSM 780 NLO Confocal microscope system was ~$760,000. It is your responsibility to use it appropriately.

Log Books

  • Log all usage time. You must fill out all the logbooks prior to and after using the confocal microscope.
  • Problems: If you have any problem whatsoever with the microscope, record the problem in the logbook AND send an email to staff. Contact a staff member. Even if a problem just seems like a minor glitch, the problem is not fixable unless we know about it.

Calendar Sign Up

  • Must be a certified user with valid index on file in order to sign up.
  • To maximize usage of the confocal system, sign-up immediately adjacent another user (helps extend laser life).
  • During busy times, limit use to (8 hours) per week in the 8:30 am - 5:30 pm times. Exceptions granted by microscope staff. If there is increased demand for the confocal, the number of slots per user may be reduced. There are hours available outside the workweek for experienced users.
  • As a courtesy to others, don't overbook time on the confocal.
  • Change or Cancel your calendar signup time promptly. Even if cancellation is the same day, cancel on the calendar. Change your start time if you will be late.
  • If user has not shown up 30 minutes into their time slot they forfeit their time. Excessive misuse of signup and cancellation can result in revocation of signup privileges.
  • Staff retains the right to reschedule sessions in the unlikely event of system malfunction or some other unexpected event, you will be notified as soon as possible, but you may also want to call to confirm the status your session

User Courtesies

  • If you are finishing up a session, please make sure the next person is coming by giving them a phone call. If you cannot get a hold of them, let Anne-Marie know that they have not yet showed up. If you can't get a hold of the staff, shut the system down. We don't want the system left on overnight.
  • It is also good policy to call if you will be late to a session to let the person before know to leave the system on, or if you might need more time during your session to see if the next person would be willing to come later.
  • Answer the phone in the confocal/LCM room. It may be for you. Someone may be trying to tell you they will not be coming to their session or will be late. If the phone call is for Anne-Marie (737-3413) give them our other posted phone number.

Mail List

  • Keep informed by signing up on the confocal users mail list. All updates to this policy, system downtimes and glitches will be sent to users signed up on this list. In addition, the list can be used as a users’ forum for sample preparation or operation questions

Data Backup and Transfer

  • Save your data to the D: Drive. Do not save directly to the network.  Do not delete data from the D drive.
  • CQLS will back up all LSM 780 data transferred to the ZFS space. We recommend that you make a secondary backup of all your data. Data generated on the LSM 780 System will be periodically deleted from the system's hard drive to maintain space for image generation. 
  • ZFS storage space is for images only collected using the LSM780 or Axiovert 200 M. Storage of files unrelated to image acquisition may result in the suspension of ZFS storage privileges.
  • LSM 780 and Axiovert 200 M data is not backed up.  You are responsible for transferring and backing up this data
  • DON'T plug anything into the USB ports. Transfer data over the network. We don’t have any virus protection on these computers.
  • Use alternate computers for checking calendar systems or email or browsing.


  • Please take great care in using the objectives. They are very expensive.
  • Size 1 ½ coverslips must be used with all objectives for best resolution. Exception is the 40x Water lens which has a correction collar to adjust for coverslip thickness.
  • Take great care that the dry and water lenses do not come in contact with oil. If they do, clean them right away and contact a staff member immediately. After your session is finished, wipe all excess oil from the lens with lens paper.
  • There is special oil for use with a Water Lens for lengthy time periods. Cleanup with lens cleaner is needed before using water.  Water is preferable for the objective.

Confocal Lasers Usage

  • Lasers may take up to one-hour warm-up time before use in order to assure stable laser power.
  • Main system switch must not be turned off until the Argon laser fan has stopped, approximately a five-minute cool down time.
  • Chameleon laser is generally on standby.  If laser is off contact facility staff before use.

X-Cite Lamp Use (LSM 780 NLO Confocal System)

  • The X-Cite 120 PC Lamp on the Zeiss LSM 780 NLO Confocal should be on at least 20 minutes when used. It is a proprietary 120W Mercury Vapor Short Arc Lamp.
    • Unit should not be turned off unless the lamp has been on for a minimum of twenty minutes. The lamp will automatically turn on within 20 seconds and the lamp indicator LED on the front panel will illuminate. The display will flash for the warm-up period of 90 seconds. The display will stop flashing when the warm-up cycle has been completed. Wait until the warm up cycle has been completed before using the X-Cite 120 PC to perform an exposure. Lumen Dynamics recommends 20 minutes to ensure a stable output.
    • If the lamp is turned off, and an attempt is made to turn it back on before it has fully cooled, the “cool” message will appear on the display. The lamp will automatically re-strike when the lamp has cooled.
  • The X-Cite 120 LED provides broad-spectrum excitation (370-700nm) on the Axiovert 200 and has no restrictions on time or frequency of On/Off.