Training and Resources 

On-Demand Training Resources 

Flow Cytometry Basics
: Self-paced e-learning courses from BD Biosciences. Focused on flow cytometry theory as employed in classical/conventional BD flow cytometers. 


For Users of BD Instruments 


FACSDiva YouTube Trainings: FACSDiva is the software that runs the Fortessa and the FACSAria. Each video is about 100 min long but goes through both the theory and the hands-on use of the software. These training videos were produced by Open Flow Cytometry, an open access Flow Cytometry education resource. The Open Flow initiative is a collaboration between the Francis Crick Institute (London, England), Memorial Sloan Kettering Cancer Center (NY, NY, USA) and the Whitehead Institute for Biomedical Research (Cambridge, MA, USA). 

Part 1: Experimental Set-up in FACSDiva 


For Users of Cytek Instruments 


Full Spectrum Flow Cytometry: After you have become familiar with basic flow cytometry theory, Open Flow Cytometry has released a training video on YouTube entitled Full Spectrum Flow Cytometry with the Cytek Aurora. The video is about 1h 40 min includes both a good discussion of the theory behind the instrument and a hands-on portion demonstrating how to use the instrument. They also offer a second training on the specifics of panel design for full spectrum flow cytometry. 



Cytek has great videos short videos (~10 minutes each) on their website that demonstrate the basic functions of their cytometers. 


Resources for Designing Panels 


Optimized Multicolor Immunofluorescence Panels (OMIPs) are peer-reviewed panels designed for fluorescent assays. They serve as a great starting point for designing a new panel. 


Cytek has recently released their SpectroLearnportal  and FSP™ Panel Design Series which takes a dive deep into Full Spectrum Profiling™ Technology (FSP™). This video series contains 6 videos covering the following topics: 

Panel Design Step 1: Marker Expression and Co-expression 

Panel Design Step 2: Fluorochrome Brightness 

Panel Design Step 3: Case Study Analysis 

Panel Design Step 4.1: The Importance of Reference Controls 

Panel Design Step 4.2: Selecting Appropriate Controls 

Panel Design Step 5: Evaluation of Marker Resolution in Multicolor Assays 


Resources for Optimizing High Parameter Flow Cytometry Panels 


Once your panel design is completed, you will need to physically optimize the protocol at the cytometer. Here is some info on how to optimize high parameter panels for flow cytometry. 



This is an excellent protocol walking the user through the panel optimization process Panel Optimization for High‐Dimensional Immunophenotyping Assays Using Full‐Spectrum Flow Cytometry - Ferrer‐Font - 2021 - Current Protocols - Wiley Online Library which includes five crucial steps:  

Antibody titration 

Evaluation of reference controls 

Evaluation of unmixing of fully stained samples 

Evaluation of marker resolution 

Assessment of data quality 


The following videos show examples of how to implement the above recommendations. 

Maria Jaimes: Best practices for reference controls optimization. Recording 

Monica DeLay: How to effectively evaluate data quality and performance. Recording 


Addressing Problems with Autofluorescence 


A feature of the Cytek instruments is the ability to extract the autofluorescence. If you are analyzing highly autofluorescent cells, I recommend watching the following brief video Extracting Autofluorescence. 


If you are working with very heterogenous samples with multiple autofluorescent signatures, I recommend watching the following videos: 


For more advanced users, Cytek has a series of presentations on the following topics: 

  • Joanne Lannigan: Entering the submicron world through the gates of best practices.  Recording 

  • Geoff Kraker: Mise en place: Ensuring high quality data for high quality results.Recording 


On-line Tools 

Spectra Viewers 


Tinalyn Kupfer, PhD, SCYM(ASCP)CM

Manager, Flow Cytometry Shared Resource Laboratory


ImmunoMicro Flow Cytometry Shared Resource Lab
University of Colorado Anschutz Medical Campus
Mail Stop 8333 AMC
Research Complex 1 North | Room P18-8207
12800 E 19th Avenue,
Aurora, CO 80045  

Phone: 303.724.8972

Immunology Microbiology (SOM)

CU Anschutz

Research I North

12800 East 19th Avenue

Mail Stop 8333

Aurora, CO 80045


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