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Flow Cytometry Education

Upcoming Seminar(s)
  • Wednesday, May 29, 10 - 11 am EDT, online only.  FluoroFinder Demo Webinar - learn how to use new (and newly updated) tools to design panels for flow.
  • Please send requests for future seminar topics to
  • Recordings and/or slides from past seminars can be found at the bottom of this page under "Unified Flow Core Seminars." 
Conventional Flow Cytometry
Spectral Flow Cytometry
  • Cytek (Aurora) Biosciences Resource Page
    • Cytek Cloud - Good place for spectral panel design for Auroras (all of ours are 5 laser).  Can even save an experiment template to save time setting up at the machine!  Account is free.
  • Aurora Training Course
    • This is an EXCELLENT course on spectral flow cytometry by the University of Chicago's Cytology and Antibody Technology facility.
  • Unified Flow Core Aurora Reference Guide
  • Be sure to check out the AF Explorer Tool seminar from November 2023. 
Chip Cytometry Resources


  • We are currently reconfiguring the Zeiss microscope to work with Micro-Manager and will soon offer training to run experiments using this software. Micro-Manager is also ImageJ based and works well with QuPath. 
  • Micro-Manager 2.0 user's guide
  • Canopy ZellScanner Tutorials and Guides
  • Canopy ZellScanner Publications/Webinar Page
    • Webinars require a free account to access.
  • Antibody Resources/Guidelines (Easiest Way):
    • Do a PubMed search for papers using the following terms: multiplex imaging, chipcytometry (one word), etc...
    • Look for papers that use the ZellScanner, your tissue type (frozen or paraffin embedded), species, and tissue of interest (if possible).
    • Check out the methods section for a table of antibodies used, with concentrations, which you will use as a STARTING POINT for your project.
    • Note that the Canopy ZellScanner Publications/Webinar Page also lets you search publications.
    • If you can't find an example of someone using your antibody on the ZellScanner, don't despair, email the Flow Core and we can assist you.  
  • Data Analysis Resources (Chip Cytometry)
    • You're going to want to analyze your data in QuPath (free), which is based on ImageJ, but is designed for large images, including those from multiplex experiments.
    • Download QuPath from  For best results, install it on a workstation, as opposed to an underpowered desktop or laptop.  We have a copy on the analysis computer if needed.
    • Note the VALUABLE resource links under the download link on the QuPath page, including the forum, docs, YouTube channel, etc...  An excellent video to start with is this one:  Be sure to look at the valuable links in that video description as well.
Data Analysis Resources
  • Flowjo
    • Note: no account needed to view educational/reference materials.  Flowjo can be used to analyze spectral and conventional flow data.
    • Flowjo Courses
    • Webinars Scroll down to "Recorded Webinars" if you aren't able to attend a live one. 
    • Flowjo Exchange Download various (free) plugins here.  Especially recommended are: FlowAI, FlowSOM, ClusterExplorer, and check out ezDAFI.  Recommended dimensional reduction plugins in addition to TSNE (which is now part of Flowjo), UMAP, FitSNE (faster TSNE)
    • The support staff at Flowjo is very responsive and helpful.  Feel free email them with questions about the software, plugin installation, or the plugins themselves:
    • Check out the next section as well for background on dimensional reduction. Most tools mentioned are now available as Flowjo plugins.
  • ImageStream Data Analysis 
    • IDEAS - analysis software manual
    • IDEAS Tutorial Series is available on Analysis Computer in Assembly G532
    • Machine Learning Manual - IDEAS v6.3 has the machine learning module (this version is available on analysis computer in Assembly G532).
Flow Cytometry BootCamp Series - Lisa Borghesi (Fall 2021)
Unified Flow Core Seminars