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Flow Cytometry Education

Upcoming Seminar(s)
  • Design Panels with Confidence using Cytek's New Intelligent Panel Design Algorithm (Dr. Paul Dascani, Cytek)
  • BD Seminar of S8 Imaging Spectral Sorter
    • This seminar is in preparation for an on site demo of the sorter, planned for 8/19 - 9/4.
    • Friday, August 9, 11:30-12:30
      • In Assembly room 4001 and online.
      • Free pastries and Q&A time with presenter after presentation if you come in person.  This is an excellent opportunity to discuss an experiment you might want us to try for you when the demo sorter arrives.
    • S8 registration link: https://pitt.co1.qualtrics.com/jfe/form/SV_8kSYHDUfrZGV2Zw
    • BD Information page on S8 Sorter
  • How to get the Most out of Sorting:
    • Planned for September, specific day/time TBA.
  • Please send requests for future seminar topics to flowcore@pitt.edu. 
  • 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. 
ImageStream
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 https://qupath.github.io/  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: https://youtu.be/WTAgXpuuqNY  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: flowjo@bd.com
    • 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