Inverted microscopes can handle all kinds of samples

Core Guidelines




Slides can go in sharps box; plates back to your lab for disposal

All instruments must have an active booking before they are used.  If additional hours are vacant, you are welcome to continue to work, so long as you report the extra time within 24h.

Inverted microscopes can handle all kinds of samples including disposable cell counting slides, LabTec square dishes, Willco dishes with wide #1.5H bottoms, multi well plates, and our own custom 48-well gasket plates.  Slides containing Arabidopsis seedlings may be disposed of in the sharps containers provided, which are autoclaved before disposal. Plates and larger waste should go back to the originating lab for disposal.  

If you wish to bring in anything that other users may consider a potential hazard, contact the Academic Coordinator beforehand. Many people are uncomfortable around dissected mammalian tissue, so please be discreet with animal work.

Leave the work space clean and tidy, and report any problems with the instruments so they can be addressed. If any glass, (including cover slips) is dropped on the floor or inside an instrument, contact the Academic Coordinator for help removing it.

Always collect data to a folder with your name on it.  No user data is backed up, so please remove it to a safe place in your own lab.  Storage space is sufficient but not infinite, and the biggest files will be deleted first when more space is necessary.  The Zeiss systems have large "Deleted Monthly" drives for staging very large experiments.  You can also stream data to a connected second computer (Zeiss)  or pull the data from the Bitplane computer (Leica) for immediate access when your booking is over.


Lenses, Cleanup and Shutdown

Always clean all immersion lenses used in your session with a single folded kimwipe and blue cleaning fluid.  For water immersion lenses, sop up surplus water first, to avoid diluting the cleaning fluid.  

Oil objectives need to be wiped from wet to dry with new kimwipes 4 times to remove the more viscous immersion oil.

For dipping objectives, rinse with distilled water to remove sample buffer, then immerse in a large drop of blue cleaning fluid for 30 seconds, then wipe dry with the corner point of a clean folded kimwipe.

Dry objectives should not need to be cleaned. If an optic is contaminated, please contact David Carter for corrective action.  

Lenses are designed to work for confocal with #1.5 cover slips ; and #1.5H for higher tolerance Airyscan or Airyscan Fast on the Zeiss 880 systems.  The "1.5H"  means 170µm + 5µm borosilicate glass.  Dry and oil lenses are more forgiving, but resolution improvement will be less with the wrong coverslips. If you adjust the lens correction collar, for a different thickness or immersion fluid, please set it back for the next user.

When passing an instrument on to the next user, please indicate which lasers have been turned on, and what other settings are different (e.g. is the SP5 stage homed?). Shut down unwanted lasers yourself before leaving the instrument.

Dust covers are an essential component of the microscope and must be in place when the instrument is not in use. Do not drop them on the dusty floor.

Wait 5 minutes for Argon lasers to cool down before shutting off power.  You will hear the fan go quiet when its cold enough.  There are also flow meters for a visual check on the cooling fan flow rate, which show the laser is cool when the lower air-flow number rapidly drops.


Report Problems Promptly

Things break, often because there is a weakness in their design.  Please report problems with the instruments immediately to, so they can be remedied.  Include all details of symptoms, so the method of failure can be determined, and the repair completed more quickly.  Dr. Carter works closely with vendors to help them diagnose and fix problems as quickly as possible, and knowing more about what happened is extremely helpful to speed up the repair.  Saved data which show a problem are extremely helpful in determining what went wrong.

The Zeiss 880 Airyscan Upright has sharp edges on its piezo Z-drive, which can easily damage the backwards-facing objective lenses.  Please use the very front of the slide holder slot on this instrument, and watch carefully when approaching the sample, to be sure the lenses are safe. To provide more protection, a "crash helmet" has been fitted to the especially fragile oil immersion lens.  Remove it immediately before use, then replace it after the oil lens has been cleaned.  Lenses may be unscrewed to make more room, but put them back in the position they came from, so the instrument selects the right magnification and pinhole size.

The Zeiss 880 Airyscan Inverted has too many fail-safe switches on its incubator box.  If one of them trips, the orange light on the back Elyra scan head goes dark, and no laser light reaches the sample.  A quick work-around is to push the recessed button on the laser deck to the left of the microscope, so the right bank of green LED status lights blink simultaneously.  Laser will then reach your sample, and you can complete your work.

The Leica SP5 HyD detectors sometimes do not activate.  Simply select a different detection mode (BrightR), then go back to standard detection, and this problem should resolve.  Always start using HyD detectors with low laser and small spectral range as they are fixed at maximum sensitivity and can overload.

Firmware glitches are quite common on all these big systems, so a full shutdown and reboot will often fix error messages or unexpected problems.


After-Hours Access

Every user needs their own electronic key fob, which is issued by IIGBadmin and renewed every September.  Do not share fobs, as they are an essential part of the Keen Hall security system, which also features security cameras, and open-door alarms.  During the Covid-19 pandemic, fob records may also be useful for contact tracing, so please bloop your fob when you leave a room, so we know who to contact if a case is reported.

Key fobs are administered through IIGB.  Fill out the form and get it countersigned by your PI and by the core manager; then return it to the IIGB administration office. Since Covid-19, email authorizations has been offered more conveniently by CC'd email, instead of requiring signatures on paper. 


FOB Authorization Form







Let us help you with your search