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FlowJoTM Advanced Workshop

Workshop description

This beyond the basic workshop shows participants how to analyze flow cytometry data using FlowJoTM.  In the morning, the software is explained theoretically using examples. In the afternoon, participants practice FlowJo in pairs using own data. There is enough time to discuss specific issues.



  • Introduction & help resources
  • General overview of FlowJoTM including the following:

    • Loading samples
    • Sample quality check & time gates
    • Keywords and groups
    • Gating
    • Adding statistics
    • Creating and exporting tables
    • Creating a layout and batching
    • Overlays - grouping by panel or keyword
    • Overlays - compare against a control
    • Heat mapping statistics in the Table and Layout Editors
    • Saving your work

For "power users":

  • Compensation
  • Creating a compensation matrix using the Wizard
  • Editing an existing compensation matrix
  • Saving compensation matrices
  • Deleting compensation matrices
  • Cell cycle
  • Proliferation
  • Concatenation and export
  • Creating templates
  • Using R-dependent plugins with FlowJoTM
  • Using R-independent plugins with FlowJoTM
  • PCA/t-SNE

Theoretical and practical input by the trainer, showing examples, analyzing own data using FlowJoTM with the help of the trainer, discussing own issues, feedback from the trainer.

Target audience, number of participants:
Doctoral students, postdocs and clinician scientists who already know the basics of FlowJoTM.

Maximum number of participants: 14

Please read the FlowJoTM description, which will be sent to you after your registration. Please bring your own data with you in order to analyze them.

Next workshop: to be announced

For the workshop 1 CP for scientific skills training can be credited (0.5 CP for participating only in the theoretical part).

This workshop is co-organized by TransMed and the Core Facility Flow Cytometry (CFFC):

About the Core Facility Flow Cytometry (CFFC):

Everyone is welcome to use FlowJoTM on the CFFC workstations, currently free of charge.
If you are sorting in the CFFC you will receive step-by-step tuition and guidance leading you to being able to work with the FACSAria sorter independently and operator-free. This service is currently free of charge, too.


Ivonne Dietzel
Program Coordinator
Bldg. 907, Room 01-212
University Medical Center
Langenbeckstr. 1
55131 Mainz

Tel. +49 6131 17-7631