Policies - Microscopy Center

Users of the UCSC Life Sciences Microscopy Center are required to abide by all rules detailed on this page.


The facility is open to researchers inside and outside the life sciences community; however, investigators conducting life sciences research are given priority when reserving microscope time.

Permission and training from the microscopy center director is sufficient to use scopes owned in common. For lab-owned scopes, users must receive specific use permission.

Access to any equipment purchased on NIH instrumentation grants is subject to the terms of those grants and may require approval by the instrument advisory committee. Contact the center director if you wish to use a shared instrument in the facility or request services.


Training and account set up is MANDATORY for all systems before they can be used independently. If you would like training, please start by contacting the microscopy center Director using this form .

If it has been more than 9 months since you have used a particular microscope, before resuming use please contact the facility director for refresher training and updates. You are encouraged to reach out with questions at any time, regardless of how recently you trained.

Training practices have changed under COVID-19, the current training workflow is as follows: After the training request form is received the trainee will be contacted by the facility Director to schedule an appointment. Prior to that appointment the trainee will be given access to a training guide and training movie for the target instrument and an account will be set up on the appropriate acquisition computer. The trainee must watch the movie before the live session. The trainee will bring their laptop or cell phone to the training session where they will be guided through instrument operation by the facility Director over Zoom.

Please see our Fee Schedule page for questions regarding training fees.

General Use

  • Be sure to read, understand an adhere to any policies posted by this facility, especially including all augmented polices surrounding use during COVID-19.

  • Be careful not to slop immersion oil around; it will create a sticky, dust-collecting mess. Clean the microscope stages and working area at the end of each section. Be sure to dispose of your used slides in the provided glass waste container. Spills or broken slides must be reported to the center manager immediately.

  • Treat objectives with respect! Clean your slide before loading it on the stage; mixing different types of immersion oil may result in precipitation that is very difficult to clean.

  • If you turn on the mercury lamp (for epi-fluorescence), it should stay on for at least 30 minutes. If you turn it off, it must stay off for 45 minutes before it can be turned on again.

  • In the unlikely event of a mercury bulb blowing (with a loud pop sound), shut off the bulb power supply and evacuate the room of all users immediately. Put a “Stay Out” sign on the door and contact EH&S (831-459-2553) and the microscopy center manager (831-459-3999) immediately. The room must air out for at least 30 minutes.

  • When you are done with your session, be sure to fill out the paper log next to the scope you are using.

  • At the end of the session, place the objective turret in an empty or low mag position and place the stage in the appropriate position per scope- specific policy.

  • Remember to place the dust cover back on the scope if you turn the scope off. Never place dust covers on the floor.

  • If you experience any problems with a scope it is your responsibility to email the facility manager to report the problem as soon as possible (see also Communications Section).

COVID-19 Precautions

Personal Protective Equipment (PPE) is required in the facility at all times. This includes a mask, glasses and clean gloves. See specific signs posted within the facility.

Glasses must be worn when using the eye pieces. Placing the top rim of the mask nose under the nose bridge of the glasses can help reduce fogging.

At the beginning and end of your session you must soak a paper towel with 70% ethanol and wipe down:

  • Scope focus knobs

  • Computer keyboard and mouse

  • Computer and mouse power switches

  • Scope joystick and touch pad (if applicable)

  • Scope enclosure knobs (if applicable)

  • High breath area immediately below eyepieces

  • Your workspace in front of the the scope

Spay 70% ethanol on a piece of lens paper and wipe down the eyepieces.

Please pay particular attention to your schedule. Scope time is a precious commodity in this time of reduced capacity. Users must vacate the scope room 15min. before the session ends to allow time for air exchange before the next user. Do not show up unannounced or early to your session. Do not allow your session to run over. Book more time if available and necessary.

Facility Biohazard Procedures (BSL2)

All users must have an approved BUA on file and must fill out this safety questionnaire before doing any project in the facility.

UCSC IBSC and SSCF Safety Questionnaire

People working in our Risk Group 2/BSL2 designated areas are also encouraged to take the "Biological Agents in Shared Facilities Awareness Training", which is available through our campus Learning Center (login and "Find a Course" to search).


Once you have been trained and have an active account you will be added to a scope-specific Google group to communicate issues specific to that scope with all other users of the instrument. This may include late changes in reservation status or issues with the hardware or software etc.

It is your responsibility to communicate problems with any scope or with the facility (e.g. missing supplies) with the facility director. You can do so by emailing the director direcly or by emailing the scope-specific Google group.

If you need to contact another user directly, you can find out their email by clicking on their reservation in the reservation calendar and looking at the “Created by:” field. This will display their CruzID and you can add @ucsc.edu to the CruzID to get their email.


  • All microscope sessions must be scheduled through the PBSci Equipment Reservation webpage or Google calendar (for the Solamere spinning disk confocal). Log into the PBSci reservation webpage with your CruzID and password. You must email the center manager to be invited to the Google calendar for the spinning disk confocal. If you are having trouble logging in to the PBSci site, please email mcdhelp@acg.ucsc.edu.

  • When making a reservation please enter your assigned microscopy user ID into the “Client’s name or Status:” field. During COVID-19 you must also enter the name of the instrument you are reserving in the “Full description:” field, see this picture if you have questions.

  • Be realistic with your scheduling. The time that you schedule is time that someone else cannot use the equipment.

  • It is your responsibility to know if someone has booked the scope after you. This policy may differ depending on which scope you are using, so be sure to obey the scope-specific guidelines provided during training. You should check the reservation web page no more than 30 minutes before the start of your session—please be sure that the web page has refreshed. Generally, if you are using a widefield microscope and the next user is coming less than 30 min. after your session ends, leave everything on (see additional note about LEDs below). If it will be more than 30 min before the next user, turn everything off. If you are using a confocal microscope and the next user is coming less than 2 hours after your session ends, leave everything on (see additional note about LEDs below), otherwise turn everything off—this will help maintain the health of lasers and other light sources.

  • If you add a new reservation for a scope while another user is on that scope, or less than 30 minutes before the start of that user’s session, it is your responsibility to tell that user and to ask them to leave the scope on for you.

  • It is always OK to turn LED light sources off at the end of your session since they don't require warm-up or cool down time.

  • If you receive instrument-specific instructions about this during training, those instructions supersede the information in this policies section.

  • While COVID-19 precautions are in place you must vacate the scope at least 15min. before your session ends to allow time for air exchange in the facility. Do not show up unannounced or early to your session. Do not allow your session to run over. Book more time if available and necessary.


  • If you must cancel a reservation please do so at least 24 hours before the scheduled session. If you finish early, please notify the next user.

  • If you must cancel a reservation less than 24 hours before it is scheduled, please be considerate of other users and let them know by sending an email to the scope-specific Google group (mentioned above). Please adhere to the last-minute cancellation guidelines below.

  • If you cancel your reservation less than 30 minutes before another person’s scheduled start time, it is your responsibility to make sure that the scope gets turned off after they are finished (they are expecting to leave it on)—either by turning the scope off yourself or by asking the previous user if he or she can do it for you.

  • If you cancel your reservation less than 30 minutes before another user’s session is scheduled to end, it is your responsibility to turn the scope off.

Data Transfer and Disk Space

  • The microscopy facility assumes NO responsibility for data storage. All hard drives will eventually fail. It is impossible to protect data from viruses with 100% confidence. It is the user’s responsibility to backup data.

  • If you need to use the scope for data transfer to a portable hard drive, please reserve it as you would normally. This is the only way to ensure its availability. You should consider doing the data transfer while you are imaging to maximize scope availability and minimize your cost.

  • It is recommended that you get a USB 3.0 drive (transfers ~10x faster than 2.0) and format that drive with ExFAT, this format is readable and writable by Windows and MacOS and has a larger than 4GB single file size limit.

  • Users are encouraged to back up files frequently to reduce data transfer time.

  • When saving data be sure to save it to the specified location on the specific computer that you are using - generally [Drive location] -> Image Data Folder -> Lab specific folder -> Your user folder.

  • Effective December 1, 2021: User data must be removed from the acquisition computer within 90 days of collection. Data may need to be removed sooner if the drive gets full. Data that is older than 90 days may be deleted without further notice.

Citing the Facility and Instrumentation Grants

Please help us secure future funding resources. All publications containing research performed at the center must acknowledge the facility as:

“Technical support from Benjamin Abrams, UCSC Life Sciences Microscopy Center, RRID: SCR_021135 ."

Please alert the facility director when citing the facility so the publication can be recorded.

If you are using an instrument purchased with an instrumentation grant you must cite that grant number. See the instrument descriptions for specific information. This currently applies to users of the Zeiss 880 Confocal.

If you are publishing data generated on the 880 confocal please include the statement in your acknowledgements or methods section :

"Purchase of the Zeiss 880 confocal microscope used in this research was made possible through the National Institutes of Health s10 Grant 1S10OD23528-01."

Additional guidelines about when acknowledgement vs. co-authorship is warranted can be found here.

Food and Drink

Absolutely no eating or drinking in the microscope rooms.


Use the following links to request brass key access to Sinsheimer rooms

or key card access to BioMed.

Please be sure to list your P.I. as your supervisor on your key requests, not the Microscopy Center Director.