UCSF Flow Cytometry Training Program

If you analyze or sort cells (particles) infrequently and do not know how to use our cytometers, there is an option to request Operator Assistance and have a Flow Core Staff member help run your samples. Keep in mind, that the Team's availability can be limited, so using this option alone provides less flexibility.

The PFCC provides a variety of educational resources, and specific monthly training classes (list below), to enable users to acquire the Basic Training and Competency that is needed to run samples independently on our flow cytometers. 

Onboarding Session (runs biweekly, Wednesdays or Thursdays):

Mandatory for ALL New Users of Parnassus Flow Cytometry CoLab (PFCC). This information session makes sure all users are aware of our facility policies, available training classes and iLab procedures (e.g., view/access specific schedules, book, change or cancel time slots).  Please visit the New Users page for the initial steps to get started. At the end of this session you should know:

  • Next steps to complete the New Users workflow
  • Facility and Scheduling policies
  • Basic training and instrument competency requirements
  • How to sign-up for next avaialble PFCC training classes
  • How to request an iLab status update to 'trained' for self-use, IF you are an experienced user
  • Core Contacts

Recommendation: If your plans include only minimal use of any cytometers, e.g.,less than once per month, consider requesting Operator Assistance services instead of, or in advance of, any training.

Class (1) Principles of Flow Cytometry Class:

As of January 2024,this class is no longer offered by the Core Immunology Lab (CIL). A comprehensive introduction to Flow Cytometry, with a review of key principals is provided by the PFCC's Class 2A


Class (2a) Conventional Flow Cytometry & FACSDiva (runs monthly):

Reviews basic principals of conventional flow cytometry (CFC), how it works, what it measures, together with important CFC workflows, experimental design considerations and operation of "FACSDiva" flow cytometer software, that is on BD Biosciences analyzers and sorters. For different BD models, LSRII, Fortessa, X-20, and Symphony, the operation and workflows are similar. After the initial theory session (3hrs, with 2 scheduled breaks), trainees separately sign-up for an additional hands-on training (via a Google Sheet sign-up lin, sent out to the class). By the end of this training you will be familiar with the critical basic information required for carrying out reliable, reproducible flow cytometry experiments and analyses. Class content includes,

  • Principals of Flow Cytometry
  • Basics of Panel Design
  • Appropriate Experiment and Staining Controls
  • Workflows for using Flow Cytometers
  • Introduction to FACSDiva software (BD Biosciences)
  • Best Practice rules for high quality data
  • Additional Resources
Class (2b) Full Spectrum (FS) Flow Cytometry & SpectroFlo (runs monthly):

Reviews full spectrum (FS) flow cytometry principals and workflows, including the use of SpectroFlo software on Cytek's Aurora 5L analyzer and Aurora 5L CS sorter.

PLEASE NOTE, BEFORE signing up for this Spectral REVIEW class in iLab, COMPLETE the pre-requisite self-study materials provided below (takes at least 4-6 hrs):

  1. REVIEW Cytek UCSF Training Slides PDF, divided into three sessions (from Feb. 2023; ~1hr EACH session)
  2. Check University of Chicago Website, Spectral Flow Cytometry introduction; 'Resources for Spectral Experiments' (end of web page) provides useful guides for working through practical aspects of spectral flow cytometry, see Spectral Experiment DesignSample Preparation.

This training class also includes a two hour hands-on cytometer session (separate Google-Sheet sign-up link is sent out after the theory review class). Hands-on training uses samples provided by the PFCC.

Class content includes,

  • Similarities and differences between CFC and FS, including Spectral Unmixing
  • Workflows to Plan/Execute a Spectral Flow Experiment
  • Assessing/testing Staining Panels, Running QC Checks, Evaluating Data
  • Identifying Problems, Unmixing Artifacts etc.
  • QC Steps to Improve, Eliminate or Minimize Specific Issues
  • Assessment of Panel Performance for Spread/Marker Resolution Loss
Class (3) Cell Sorting (runs monthly):

Covers cell sorting fundamentals to familiarize users with the workflow on electrostatic droplet sorters, such as the BD Biosciences Aria Flow Cytometer sorter models. BD Aria 2, 3u, Fusion have the same basic setup, operation, and workflow. Prior experience with BD flow cytometer analyzers, single cell anaysis workflows, and FACSDiva software will ease the learning curve on the Arias. This class does NOT include hands-on training, we recommend requesing at least 1 hr Operator Assistance for your first use of an instrument after taking the training. At the end of this session you should know:

  • Key Flow Cytometry Cell Sorting Principles using Electrostatic Droplet Sorters
  • Experimental Planning Workflows
  • Sample Preparation, Cell Concentrations, and Setting Optimal Flow Rates
  • Sort Considerations and Outcome Performance Metrics
  • Running and Monitoring a Sort

For access to additional Educational material and tips and tricks about the technologies the PFCC provides access to additional Resources on our website. You can view various online tutorials before your scheduled trainings, in addition to other materials that will help you understand many different aspects of flow cytometry. We highly recommend the resources listed, excellent for beginners and even advanced users can certainly improve their outcomes by reviewing best practices and making sure they are reporting the ISAC recommended minimum information about their flow cytometry experiments

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 logical order to the material covered as you gain experience in the field. All class registrations are done through iLab (under <Schedule Equipment> tab, see Training category menu). 

Reminder, AFTER completing any necessary training, on your first use reservation a Proficiency Assessment appointment is mandatory both at PFCC and CIL. Please note, if we observe that 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.