UCSF Flow Cytometry Training Program

If you analyze or sort infrequently and feel that it is not worth learning how to use these instruments, an option is to request Operator Assistance to have a Flow Core Staff member run your samples for you. Keep in mind, the Team's availability can be limited, this option will offer you less flexibility.

The Core provides a variety of educational options to meet the Basic Training requirements, here is the summary information:

Onboarding Session:

All New Users of Parnassus Flow Cytometry CoLab (PFCC) to make sure all users are aware of the facility policies and instrument procedures.  Please visit the New Users page for the initial steps to get started. Onboarding is considered the Basic Requirement for all Experienced Users who feel comfortable operating the instrument independently and collect quality and reproducible data. At the end of this session you should know:

  • Next steps to complete the New Users workflow
  • Facility and Scheduling policies
  • Basic training requirements
  • Core Contacts

Recommendation: If you plan on using any of the self-use equipment less than once per month, you may consider utilizing the Operator Assistance service instead.

Class (1) Principles of Flow Cytometry Class:

For those new to flow cytometry, or would like reinforcement of flow cytometry fundamentals. The PFCC is partnering with the CIL which provides a lecture designed to cover the basics and theory of flow cytometry. This session is recommended for all Flow users, even if you plan requesting the Operator Assistance service. At the end of this session you should know the basics of flow cytometry and experimental design, these include:

  • Fluorescence emission and detection
  • Fluidics
  • Operation
  • Panel design
  • Controls
Class (2a) CF FACSDiva:

To familiarize users with the conventional flow (CF) workflow and operation of the flow cytometers and the software in BD analyzers and sorters "FACSDiva". The LSRII, Fortessa, X-20, and Symphony appear different, but the operation and workflow are performed in the same manner on all instrument types. Includes one hour of hands-on training. At the end of this session you should know:

  • (coming soon)
Class (2b) FS SpectroFlo:

To familiarize users with the full spectrum (FS) workflow and operation of flow cytometers and the SpectroFlo software in Cytek's Aurora analyzer. Attendance and completion of <PFCC-Cytek's UCSF Spectral Training> is mandatory before signing up to this session. Includes one hour of hands-on training. At the end of this session you should know:

  • (coming soon)
Class (3) Cell Sorting:

Fundamentals about cell sorting and to familiarize users with the workflow on a FACSAria / SH800 sorter. Although the machines have different names (Aria 2, 3u, Fusion), their setup, operation, and workflow are performed in the same manner on any Aria type instrument in the Core. Having experience with other flow cytometers, the workflow, and FACSDiva software will ease the learning curve on the Arias.  It is very beneficial if you have already previous experience in other BD flow cytometer analyzers and using the FACSDiva software. Does NOT include hands-on training. At the end of this session you should know:

  • (coming soon)

*Please note Since Feb 1, 2020 all training registrations are done through iLab using <Scheduling Equipment> tab unless otherwise specified.

For access to additional Educational material and tips and tricks about the technologies the PFCC provides access to additional Resources on our website. There you can view online tutorial before your scheduled trainings, and other material that will help you understanding many flow cytometry basics. We highly recommend the tutorial which is excellent for beginners and even advanced users might learn a few things.


Basic Training Requirements 

We allow you to evaluate your skill level (Novice, Competent, Experienced).

Depending on your experience level and needs of your project you will need to sign up for some or all the classes mentioned below. We highly recommend following the order of the sessions as there is a the logical order to the material covered and gain experience in the field. All classes registration are done through iLab (under <Schedule Equipment> tab, Training category). 

Reminder, after completing your training on your first self-use reservation a Proficiency Assessment appointment is mandatory both at PFCC and CIL. Please note, if we observe you need additional help, you will be required to take supplementary training.

Summary Diagram of Recommended Training at PFCC/CIL
  • All NEW USERS first register and attend the initial Onboarding Session.
  • Novice: we recommend you signup for class (1), class (2a) (and 2b if using the Aurora), and if Sorting class (3).
  • Competent or needs a refresher: signup for class (2) (and 2b if using the Aurora), and if Sorting class (3)
  • Experienced: attend the initial Onboarding Session and schedule the Proficiency Assessment appointment upon the first self-use appointment (plan for a simple pilot experiment). The Flow team will gauge your level of independence and cover site specific procedures and your iLab permission level will be updated to <Trained> after this appointment.

Click on the respective link on iLab to find out the available dates for each class (available in the schedule's header) for an overview you may also visit Staff and Events Calendar. Each class is hosted at least once a month, but space is limited. Save a seat as soon as possible. If you wish to cancel please do it promptly on iLab (FYI late cancellation fees may apply).

Reminder: after completing your training upon your first self-use appointment you are required to schedule Proficiency Assessment appointment with a member of the Core. This helps reinforce the theoretical concepts from the classes, practice the workflow and assess your proficiency. Your iLab permission level will be updated to <Trained> after this appointment. Same rate as appropriate instrument charge, fee is included with the training charges. Click HERE to see class Rates.

Our Proficiency Assessment general checklist is: 
  • Review Before Use and Change Over procedures
  • Create New Experiment with the desired panel (recommendation: do pilot experiment, up to 10 markers -- less is better)
  • Label markers and/or use the Experiment Layout
  • Confirm or Adjust voltages as needed (proper sensitivity & resolution)
  • Run Compensation (if you have multicolor panel)
  • Edit and build your Global Worksheet and Population Hierarchy (gating)
  • How to Export Data
  • For Sorters only: setup Sort Layout, Collection Vessels, and how to monitor cell sorter
  • *reminder: cleaning procedure after each use & check scheduler


Should you have any questions about the Training classes, please do not hesitate to contact [email protected].

You can also find additional Educational Resources on our website HERE


Advanced Flow Training options

There are several advanced training options available to onboarded or trained users at PFCC. All training requests are submitted through iLab, the typical workflow is:

  1. In iLab go to <Request Services> tab
  2. Expand the Training category 
  3. Scroll to respective training session, click <Initiate Request>
  4. After submission, keep an eye out for a follow up email to schedule the training. If you don't hear from our Team within a week please contact us by emailing [email protected].
  5. Your iLab permission status will be updated to after completion of these sessions.
FACSAria Advanced Training - SuperUser

For users who would like to sort, or setup the instrument on their own, during non-normal work hours (Monday-Friday from 7pm-8am, weekends, and holidays), or become super users for their lab, Advanced Training is highly recommended.  In addition to reviewing what was covered under Basic Training, users will be trained on "Aria-Setup" which focuses on instrument startup.     

1)  You must have completed the standard Basic Training requirements, and it is highly recommended to have performed and gained experience during regular Business Hours for at least several months.

2) If you are an exisiting user of PFCC, please submit your training request through iLab.

3) This training may be spread out over a couple of weeks and will involve a minimum of 5 Aria setups where you are trained under the supervision of a Core staff member. You should plan for about an hour a day during morning QC (8-10am). After passing this course, you will be able to setup the FACSAria, run a sort, troubleshoot the most common issues, and shutdown the instrument. You will become a super user for your lab, and will be able to setup the instrument on your own at any time. Cost = click HERE.

BD HTS Training

For users who would like to run 96-well plate format on BD Fortessa at the Core.

1) You must have completed the standard Basic Training requirements, and it is highly recommended requesting this training after onboarding, and gaining for 1-2 months experience using standard Tube acquisition mode.

2) The HTS training is taught one-on-one while on one of instruments which currently have an HTS available (http://flow.ucsf.edu/instrument-status )

3) There are several things to keep in mind when setting up and using the HTS, so it usually takes us about 1 hour to go through the all the information. Here’s the reference link for the PFCC User Guide for the HTS that you can download and print for your reference (under PFCC Fortessa HTS SOP)

4) Cost = click HERE.

Malvern NanoSight NS300 Training

For users who would like to run the NS300 NanoSight at the Core. This session is one-on-one.

1) Training should take at most 3 hours. The training includes how to setup and QC the machine, and if you have available 1 sample titration. On the day of, please bring your practice sample and filtered PBS 0.01um, filtered milliqH20, and filtered 10% bleach.  

2) Cost = click HERE.

Additional options from Affiliates

see Affiliates website linked through main Training page.