Course Advanced Flow Cytometry

ECTS: 2.9

Course leader: Morten Nørgaard Andersen

Language: English

Graduate school: Faculty of Health

Graduate program: BIO

Course fee: 3,480.00 DKK

Status: Course is open for application

Semester: Spring 2024

Application deadline: 18/03/2024

Cancellation deadline: 01/04/2024

Course type: Classroom teaching

Start date: 29/04/2024

Administrator: Johanne Gregor Nielsen

The course B299/04 Advanced Flow Cytometry is being offered by the Graduate School of Health, Aarhus University, 2024.

Criteria for participation: University degree in medicine, dentistry, nursing, or master’s degree in other fields and/or postgraduate research fellows (PhD students and research-year medical students).

Aim: The course provides detailed knowledge on flow cytometry, with a thorough review of the theoretical foundation necessary for performing state-of-the-art flow cytometry experiments, and includes extensive practical hands-on data analysis exercises covering the most important topics and pitfalls. Thus, the course provides the participant with a broad understanding of how to design multicolour flow cytometry experiments, how to handle sample material, and how to analyse and present flow cytometry data for publication.

Recommended knowledge for participation Some degree of practical flow cytometry experience, completion of the PhD course in Basic Flow Cytometry or comparable knowledge on basic principles in flow cytometry.

Learning outcomes:

  • (i) how to design and optimize a flow cytometry experiment.
  • (ii) how to select the optimal flow cytometry related methodology.
  • (iii) which controls to include (e.g. data quality controls, negative/positive controls, compensation and FMO controls) – and how to interpret the results.
  • (iv) how to analyze flow cytometry data including critically evaluation of the experimental results.
  • (v) how to include high-dimensional data analysis tools (e.g. tSNE)
  • (vi) how to present flow cytometry data for publication.


Presentation of

    • different flow cytometry related applications within biomedical research (incl spectral flow cytometry and image stream).
    • panel design.
    • quality controls, sources of error, validation of different flow cytometry methodologies.
    • optimal panel and experimental design.
    • analysis and presentation of flow cytometry data

Practical exercises (hands-on data analysis).

    • titration experiments and compensation.
    • quality controls and validation on instrument performance.
    • analysis and presentation of flow cytometry data, including for publication.
    • high-dimensional data analysis using FlowJo (incl tSNE).

Workload: The full workload of the course is expected to be 48 hours

Instructors:   Morten Nørgaard Andersen (AU/AUH), Anders Etzerodt (AU), Kasper Lauridsen (AUH), Timothy Bushnell (University of Rochester Medical Center, New York), Debajit Bowmick (Brody School of Medicine, East Carolina), and staff experienced in flow cytometry from the Dept Biomedicine (AU) and Dept Hematology (AUH) 

Venue: Aarhus University, Aarhus.

Participation in the course is without cost for:

  • PhD students, Research Year students and Research Honours Programme students from Aarhus University
  • PhD students enrolled at partner universities of the Nordoc collaboration
  • PhD students from other institutions in the open market agreement for PhD courses


Course dates:

  • 29 April 2024 08:30 - 16:30
  • 30 April 2024 08:30 - 16:30
  • 01 May 2024 08:30 - 16:30
  • 02 May 2024 08:30 - 16:30