Standard Operating Procedures

All CIF users must review the general SOPs available for ACMAL.


Confocal Imaging Facility

Instrument State

The instrument will accompanied by brief operating instructions for basic operations as well as the standard conditions in which the instrument should be left after each use. Failure to execute the shut-down procedures as specified may needlessly confuse the next user. Moreover, due to the electronic log book system, users who failed to execute the shut-down procedures might lose their privileges to use the instrument.

Responsible Use

Non-standard Operating Procedures

All non-standard experiments involving the confocal microscope must be approved in advance


If there is a problem with the instrument, record the problem AND report it to the facility manager immediately. There is no penalty for reporting accidental damage to equipment. Deliberate misuse of equipment will not be tolerated. Deliberate or negligent use of the equipment will result in the assessment of repair charges to the responsible faculty member.


Unauthorized use of the equipment or failure to correctly follow procedures will result in loss of use privileges.

Instrument Care


Please take great care in using the objectives. They are very expensive. The coverslips must be used with all objectives. 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. Do not do any other cleaning without staff present.

Laser Usage

Laser may take up to one-hour warm-up time before use in order to assure stable laser power. The 405 laser in particular will appear to flick off and on during scanning. We have seen this in the first 45 minutes of operation. If you see this at other times please let us know immediately. Main system switch must not be turned off until the system has been given a five-minute cool down time.

Mercury Lamp Use

Once the mercury lamp has been turned on, it must remain on at least 30 minutes. Once it has been turned off, it must remain off at least 30 minutes. The mercury lamp is on another circuit from the system, so you may turn on the mercury lamp at any time.

Saving Images

Session Captures

Images that are saved during the session must be taken with you when you leave. All images on the system will be purged every night at 11:00 pm automatically.

All authorized users can obtain FluoView Viewer Software for their own use to process the images. Please ask facility staff for more information.

CD/DVD Burning

Users must supply their own CDs and DVDs.

Data Backup

Users are responsible for backing up their data. Data generated on the Confocal Microscope will be periodically deleted from the system’s hard drive. Do not expect more than a month of storage on the system. The data on the instrument itself is not backed up. If you do not save your images by transferring them to a server or flash drive or burning them onto a CD or DVD before you leave your session, data may be lost. The data is periodically purged to create space for newer files.

USB Ports

DO NOT plug anything into the USB ports or any other port on the confocal system unless you have shut the software down!! It will completely mess up the entire system! Scan your flash drives for viruses before inserting into the system.