Flow Cytometry Courses

Keeping up with researchers needs and improving instrument performance requires technical advancements to take place. The Technology section describes some of the current and past Technical Development Projects of the Imaging Unit involving the Flow Cytometry Core Lab.

The following sections provide information on several current and past technological projects developed at the Imaging Unit, involving the Flow Cytometry Core Facility.

Based on the high rate of new user arrivals and the speed that the technology evolves, there is a continuous demand to provide users with the necessary theoretical and practical background. Therefore, there is a an increasing need to organize specific workshops to meet these demands, and give people the chance to become as independent as possible in their research.

We regularly schedule dates and open applications for the respective courses below. When that happens will announce them through e-mail, but you can also check the course status in the table below. You can then find more information about the course in the respective tab (including the registration link).

Flow Cytometry: Fundamentals and Applications

Final Program (dates altered: 18 - 22 January).

Course room: Democritus (above the Canteen)

Click Image to Enlarge


The course will cover the fundamentals of Flow Cytometry, but will mostly focus on the main applications run at the IGC.Topics include Planning a Flow Experiment, Cell Dynamics (cell death, cell cycle, proliferation), Multicolor Flow, Small Particle analysis, High Throughput Flow, Cell Sorting as well as Data Analysis and Publishing. Both experienced and inexperienced researchers are encouraged to attend. There won’t be hands on sessions, but there will be group exercises and discussions as well as acquisition demos done remotely to the Flow Lab.

This course will be supported by several vendors, which includes some of the course material and main speakers that will be later announced.



  • Internals: Free (includes coffee breaks and course materials)
  • Externals: 100€ (includes coffee breaks, Lunch and course materials)

To register, simply fill out this form:

Registration .

Due to space restrictions we are limited to registrations. There are seats left.

Instructions on how to proceed with payment will be sent Jan 5 2016. Please note that your registration is not complete until payment has been received.

Introduction to Flow Cytometry Course

Presentation Files

Hands-on Tutorials

The aim of the Hands-on tutorials is for user to get acquainted with handling the equipment, while at the same time learning a few basic protocols for flow cytometry acquisition, such as DNA cell-cycle analysis and Multicolor immunophenotyping. We will provide as much time as possible for the user to run the machines by himself. For this, it is important to read beforehand the information provided below.

DNA Cell Cycle Analysis

Cell Cycle analysis is one of the most applied protocols in flow cytometry, most commonly to measure frequencies of cells that are either in G0/G1, G2/M, or in the S-phase of the cell cycle. This can be done using a general DNA intercalating dye, such as Propidium Iodide (PI), to quantify the amount of DNA present in each cell. Cells in G0/G1 will typically have half of the DNA signal than cells in G2/M, and those in S-phase will have an intermediate signal between that of G0/G1 and G2/M cells.

During the Hands-on, we will learn how to setup and run a cell-cycle experiment, using HeLa cells previously stained with PI. There will be two different types of samples, with cells either expressing or not expressing GFP. Additionally, we will provide samples with nocodazole to arrest cells in the G2 phase of the cell cycle, so that we can analyze differences in cell cycle distribution.

A general protocol for setting up the analysis in FACSCalibur or FACScan is provided in the following link: Cell Cycle Analysis using CellQuest

Multicolor Immunophenotyping

Immunophenotyping is one of the most common applications in flow cytometry. The need to measure multiple cellular markers simultaneously has been increasing, as researchers dig deeper into more accurate forms of characterizing cellular subpopulations. Conceptually, analyzing samples with two or three fluorescent markers is exactly the same as four, five or more colors. However, as more fluorescent markers are used simultaneously, the need for proper staining and compensation controls becomes increasingly relevant.

In this Hands-on session, we will learn strategies to setup a multicolor analysis, using spleenocytes stained with five fluorescent markers. We will go through the procedures to measure staining and compensation controls to adequately analyze a 5-color sample (CD3-Alexa488; CD8-PE; CD4-PerCP; CD25-Cy5; B220-Pacific Blue).

Due to time restrictions, the multicolor analysis will be done in the FACSAria only, though we will emphasize whenever possible the differences between analyzing in the FACSAria and the FACSCalibur, since the latter is the most commonly used for 4 or less colors.

A general protocol for setting up a multicolor analysis is provided in the following link: Multicolor Analysis.pdf

FACSAria Training Course

Coming Soon.