Getting Trained

[Updated 9/30/2021] The MIC is open in full!  Masks are required! Also, you must take the daily screener to come to the MIC: https://calberkeley.ca1.qualtrics.com/jfe/form/SV_3xTgcs162K19qRv

See the full campus Covid restrictions and access rules here

Steps for getting trained:

  1. Non-UC Berkeley researchers: Access to the MIC is now via RICs: https://ipira.berkeley.edu/berkeley-research-infrastructure-commons
  2. Everyone: View training videos:
    1. (~90 mins) Holly’s Intro to MIC Lecture, (email hollya at Berkeley Dot Edu for access).
    2. (~6 mins) How to NOT damage the objective lenses (by Jennifer Waters, Harvard): https://www.youtube.com/watch?v=YAnRHIe2rdY
    3. (Optional, ~30 mins) Image Formation on iBiology (Dan Fletcher, UC Berkeley)
    4. (Optional, ~30mins) Optical sectioning on iBiology – Laser scanning confocal microscopy & spinning disk confocal (Kurt Thorn, UCSF)
    5. (Optional) Some videos on sample prep:
    6. (Optional) For more detail on objective lenses:
  3. Everyone: Take the Quiz:
  4. Everyone: Fill out the MIC User Registration Form (Give us a description of your samples & imaging needs. This is required prior to setting up a Zoom call before training. Failure to do complete the User Registration form will delay your training.)
  5. Everyone: Sign-up for an iLabs/Kiosk account. This is where we schedule all reservations and we will not schedule a training if you do not have an iLabs account. It is also where you will login to Kiosk to start your session each time you come to the microscope – this is the new logbook! (Your lab manager/PI may need to add you to their lab.)
  6. Everyone: Make sure you have appropriate controls prepared: https://expert.cheekyscientist.com/essential-controls-for-reproducible-fluorescent-microscopy-imaging/
    • 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 signal prior to coming to the confocal or slide scanner! (Bender training is very quick & easy – no fee!)
  7. Everyone: Email mictraining@lists.berkeley.edu
    to setup a short Zoom meeting (15 – 30 mins) to discuss your imaging goals with the MIC Team. We will work out a training plan together on this call.
    • Due to the on-going Covid pandemic, you will need to wear a well-fitting mask over your mouth and nose, regardless of vaccination status throughout the training.
    • We may conduct part of the training in person and part via Zoom.
    • We will ask you to watch instrument-specific (or technique specific) training videos before coming to the MIC so you know what to expect and to help the training move along quickly.
    • Each instrument has a posted Start Up and Shut Down Sheet in the room. [If we need to conduct the training entirely remotely, 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! There is a camera at each system you can use to help us direct you while placing your specimen or for any other questions.] 
  8. EveryoneRead 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 and agreeing to site the MIC in any publications resulting from data acquired at the MIC. 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 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 and how many trainings you’ll need. In general, we only charge for the initial training session, or for re-training after 6-months of non-use. 

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 JUST looking for 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 $275 per person and includes access to online training lectures and materials, hands-on training with your sample, and additional trainings as needed on the same or similar instrument. Outside users are charged $550 for training. Some instrument training fees are lower or higher, so please consult the iLabs MIC website for the most up-to-date information on training costs:

Do I need to watch the training lecture? And why?
Yes, everyone must view 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. It also includes an overview of the resources available at the MIC and elsewhere on campus.

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 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 # 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. 

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 (email us your Cal-ID and numbers on the back of the card to get your building access).  Additional training/guidance is available after the initial session on an as-needed basis and is typically non-billable (i.e. FREE). Please email us ahead of time if you would like to Zoom 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 forgotten a few things. Also, systems change – we upgrade parts, replace or move things and entire systems around (we moved 5 systems in 2020-21 so far!). 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 $9 – 52/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 $275 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.

Do I need laser safety?
Nearly all of the instruments are deemed Class-1 use and do not require laser safety. A few systems, however, do. Please check with Holly if you are concerned and think you may require it. 

I used one of the MIC’s instruments to obtain data for a publication.  How should I acknowledge that information in my manuscript?
First – 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 berkeley.edu.

Have additional questions? Email MicTraining@lists.berkeley.edu