Amsterdam Advanced Cytometry course

Why an advanced course in cytometry?

Cytometry has become a fundamental technology that enables application in multiple disciplines including fundamental (Cell Biology), translational (Immunology) and clinical research (Hematology and Oncology). The last 10 years have witnessed an explosion in the development of both fluorescence- and mass-based detection methods that are revolutionizing the field. An integral part of the responsibilities of cytometry core facilities is to provide educational support and technical training to facilitate access to cytometry-based methods, in order to ultimately ensure the generation of reproducible quality data and an optimal use of existing resources.

General Learning Objectives

This is a comprehensive course that covers the fundamentals of flow cytometry analysis and sorting, as well as mass cytometry in a lecture format supplemented by practical lab and data analysis sessions. The course is designed to gain in depth knowledge on general technical aspects of the different types of cytometers available in the market and how the different components and their configuration influence data acquisition. Special emphasis is placed on basic concepts of lasers and fluorescence emission, how to properly set up a cytometer for standardized performance, how to optimally prepare cells for a cytometry experiment, the principle of FACS-based cell sorting, and other specialized applications, including data analysis. 
Interactive sessions on data analysis will build up upon basic concepts on compensation, data processing and gating and will focus on the analysis of medium-large multicolor panels. Basic understanding of flow cytometry packages is a not prerequisite, but will help a great deal. We emphasize on providing a wide overview of the different modalities of cytometry currently available and all specialized applications that can be of used for the PhD students in the fields of Immunology, Hematology, and Oncology. The course will conclude with a feedback session with cytometry experts where a selected group of students will present special cases and discuss important aspects of their own PhD projects.


The course consists of three types of sessions; interactive classroom teaching, data analysis sessions, and lab demonstrations. For the data analysis sessions, attendants are expected to use their own laptops equipped with the latest version of R Studio[1] and the freely available software cytosplore[2] ( ). We will pay special attention to the R packages flowcore[3] and cytofkit[4].

[1] Download software here, see also this useful tutorial 
[2] It can be downloaded here: and this is the original publication: T. Höllt, et al. Cytosplore: Interactive Immune Cell Phenotyping for Large Single-Cell Datasets. Computer Graphics Forum (Proceedings of EuroVis), 35(3): pp. 171—180, 2016.
[3] Flowcore can be downloaded for installation here, it contains a tutorial. 
[4] Cytofkit can be downloaded for installation here, it contains a tutorial.

Target audience
Registration deadline

To be announced
9:00 – 17:00 h
PhD students, post-docs and technicians
1,5 ECTS
Juan J Garcia Vallejo, MD, PhD, MBA
O2 Lab building, location VUmc
Free of charge for OOA members
The course is not yet open for registration