Getting Trained

[Updated 7/31/2020] Due to the on-going Covid-19 restrictions, the usual MIC Training protocols have been modified. Please see this link for full Covid rules.

New steps for getting trained (Phase 2, July 1, 2020 – Present):

  1. Any non-UC Berkeley researchers or any UCB researchers from a non-open building (Phase 2): Fill out the VCR form here in order to get approval for work in the MIC: VCR Form.
  2. Everyone: Fill out the MIC Use During COVID form.
  3. New Users: View these videos:
    1. Intro to the MIC (Coming soon!)
    2. Image Formation on iBiology (Dan Fletcher, UC Berkeley) and Optical sectioning on iBiology – Laser scanning confocal microscopy & spinning disk confocal (Kurt Thorn, UCSF) or Holly’s MIC Lecture (ask her for link).
    3. How to NOT damage the objective lenses (by Jennifer Waters, Harvard):
    4. For more detail on objective lenses (optional):
  4. Everyone: Review this video:
  5. New Users: Take the Quiz:
  6. New Users: Fill out the MIC User Registration Form (Give us a description of your samples & imaging needs. This is required prior to the Zoom call. If you don’t know some of the questions, just answer as best you can and we will discuss in the call.)
  7. New Users: Sign-up for an iLabs/Kiosk account. This is where we schedule all reservations and we will not schedule a training for you if you are not in iLabs. It is also where you will login to Kiosk to start your session each time you come to the scope – this is the new logbook! (Your lab manager/PI will need to add you to their lab.)
  8. Everyone: Make sure you have appropriate controls prepared:
    • It’s advised to check that your staining worked prior to coming to the facility. If you have a fluorescence microscope in your lab, please check there. If you don’t have access to a scope in your lab, ask to get trained on our scope Bender for checking prior to coming to the confocal or slide scanner! (Bender training is very quick & easy!)
  9. New Users: Email Holly AND Feather to setup a short Zoom meeting (15 – 30 mins) to discuss your imaging goals. We will work out a training plan together on this call. (Please email us both in 1 email so we can respond to you together or delegate to one of us.)
    • Due to Covid restrictions, in-person training time will either not be possible or will be severely limited. 
    • Because of this, we may ask to image your sample for you while you Zoom in to watch remotely. This option allows us to setup settings for your sample which you can re-use when you come to the scope. It will also give you an idea of the workflow for the system and let you see how the software looks. In other cases, we may meet you for 5-15 minutes to show you the instrument and how to mount your sample. This will require you to have an N95 or KN95 mask. 
    • We will likely ask you to watch certain instrument-specific training videos before coming to the MIC so you know what to expect. 
    • The first time you come to the scope, we will Zoom in with you to complete the training. There is a camera we can use to direct you while placing your specimen or for any other questions. 
    • Each instrument has a posted Start Up and Shut Down Sheet in the room. Dial into the Zoom call when you get to the facility and we will walk you through the Start up and getting your first image!
  10. New Users:  Read the MIC rules and regulations to which all users must adhere. By gaining access and using the equipment at the MIC, you are agreeing to abide by these rules. Please print out a copy, sign it, and bring it to your training appointment!

*Note: some instruments require additional training, such as EH&S Laser Safety Training, or FLIM training, while a select few require shorter training sessions at reduced or no cost. You may also have advanced experimental needs that we cannot cover in the initial training, such as live cell imaging, spectral unmixing, or 2-photon imaging. Filling out the MIC User Form will help us determine what kind of training you’ll need.

Frequently Asked Questions:

Who may use the Molecular Imaging Center?
The Molecular Imaging Center is open to all scientists from within the University and outside. Outside users are charged a greater recharge rate to use the facility, generally 2x the UCB rate. ALL users must be trained before accessing the equipment. Only in very rare cases can we do imaging for you (for an additional surcharge). 

What should I know before coming to the MIC?
You should know what your goals are for imaging. Are you looking for just a pretty picture, or do you want to do longterm time-lapse imaging, or quantification of fluorescence intensity, tracking of particles, counting of nuclei, etc.? You should know what dyes/fluorophores you are using and what excitation and emission peaks those dyes have. If you don’t know, check out:

In addition, you should know how to prepare your samples for imaging. You should know if your samples are live or fixed and whether or not they are biohazardous. We are happy to consult with you about your imaging goals and requirements at any time.

How much is training?
Standard training costs $250 per person and includes lecture, hands-on training with your sample, and additional trainings as needed on the same or similar instrument. Outside users are charged $500 for training. Some instrument training fees are reduced or slightly increased, so please consult the iLabs MIC website for the most up-to-date information on training costs:

Do I need to attend the training lecture? And why?
Yes, everyone must attend the training lecture. The lecture is meant to give everyone a basic understanding of fluorescence imaging and laser-based confocal imaging, as well as to share tips for successful imaging early on in the microscopy data collection process. We will also give an overview of the resources available at the MIC and can answer any burning microscopy questions you may have. Additionally, we want to meet our users and get to know what your imaging goals are, which will help in directing your training and guiding you to the best instrument for your needs. 

I know everything about confocal microscopy, do I need to be trained?   Yes, everyone must be trained by MIC staff. While some of our microscopes may be similar to ones you have used in the past, each instrument is unique and our core may have different rules than another core or your previous lab. On the upside, your training could be quite quick if you really do know the microscope and the software.

What should I bring to training? Bring a typical sample that you plan to image.  For fixed samples, make sure to use glass slides with number 1.5 coverslips that are sealed, dry, and clean.  We do not recommend training on live samples, as we want to focus on instrument settings and setup and not the health of the precious sample. If you can bring a fixed sample that is similar to your live sample, that is ideal. Or if you must bring a live sample, for an inverted systems, please use a coverglass-bottom dish (again, #1.5 coverslip), such as those available from MatTek or ibidi, and please use culture media without phenol-red or riboflavin to reduce background fluorescence. For upright instruments, please check in, as the clearance and depth of focus varies depending on the instrument. For lightsheet, please email us for the sample prep guide! Don’t hesitate to ask if you have any questions regarding sample prep.

What happens during training? 
You will receive one-on-one hands-on training with your sample on the most appropriate microscope system for your experiment. You will be taught how to start up and shut down the system safely.   If you have specific expectations or goals, please let us know ahead of time

Ideally, you will sign up to starting imaging on your own a day or two after receiving training so you can really learn the system. 

On select systems, you may also be trained on laser alignment (1-3 hours typical, more with laser training).

What happens after training?
You will receive calendar access to schedule the instrument on iLabs, as well as the necessary door-codes or building access (forms & signatures required for LKS and LSA; after-hours access only available to UCB graduate students & postdocs.).  Additional training/guidance is available after the initial session on an as-needed basis and is non-billable (i.e. FREE). Please email us ahead of time if you would like to meet at the scope and ask more questions. 

I attended training a year ago and have not been back since, why can’t I just jump on the instruments? 

Well, the primary reason is because you have likely forgot a few things. Also, systems change – we upgrade parts, replace or move things and entire systems around. The microscope may be in a different building from the last time you used it! We also update start-up and shutdown protocols and so you should check back in with us before signing up if it’s been a while!

How much does it cost to use MIC instruments?
Hourly charges on most MIC instruments range from $8-46/hour for campus users.  All prices are listed on iLabs. Outside user rates are generally 2x, unless posted elsewhere on iLabs. 

What other services does the MIC offer?

  1. We offer a slide scanning service for limited projects.
  2. We can train you on your own instrument at $250 for the first 2 hours and $65/hr for each additional hour. 
  3. We are available for consultation regarding all matters microscopy.
  4. We can help write or edit your Methods Section for your publication.
  5. We host and present online tutorials for the community – ask us if you have topics you want to learn about!
  6. We are happy to write letters of support for grants and fellowships.

How do I get trained for laser safety?
If you need laser safety training (check with Holly), you’ll need to:

I used one of the MIC’s instruments to obtain data for a publication.  How should I acknowledge that information in my manuscript?
Congratulations on your paper and thank you for remembering us! Please consult the Acknowledging the MIC page for grant and citation information.  When your paper is in press, contact Feather so we can feature it on our MIC Publications page!

Can I get after-hours access to the scopes?
After hours access may be granted to UC Berkeley graduate students and postdocs after appropriate training. Undergraduates may not request after-hour access. Non-campus parties must also work during the 9-5M-F time period. To request access to Weill, fill out the form outside 165 LSA and have Holly sign it for you, then return to the building manager in 165 LSA. You will need your ID and need to go during the posted hours for keycards. For Barker Hall, email Greg Vitan (and cc Holly): vitan at

Have additional questions? Please ask – email Feather or Holly or setup a time to come chat.