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The Flow Cytometry Facility provides a state of the art flow cytometry service to iMM researchers as well as external groups from other research institutes.

We aim at training researchers in the adequate use of the instruments and also on flow cytometry principles, experiment planning, as well as data analysis and interpretation.

The Flow Cytometry Facility also provides a cell sorting service using two High Speed Cell Sorters (BD FACSAria III and BD FACSAria Fusion) operated by dedicated staff.

More Information:
Flow Cytometry Wiki

Instruments and Services

Our flow cytometers are grouped into two categories: analyzers and cell sorters. Analyzers are instruments for acquisition only, cells cannot be recovered once they are analyzed in the instrument. Cell sorters are capable of physically “sorting” out a population(s) of interest.

The choice of the proper equipment should depend on the aims/applications of your project and the combination of fluorochromes in your samples.

The following table summarizes the excitation optics of all our flow cytometers. To find out more about each instrument's optical configuration, see the individual descriptions bellow.

Cell Sorters

Available for booking from 10am to 6pm from Monday to Friday.

The cell purification service is provided by a dedicated technician upon reservation on the online booking system.

Cell Analyzers

Available 7 days a week, 24 hours a day for use by trained researchers upon reservation on the online booking system.

Imaging Flow Cytometer
  • Amnis ImageStreamX - benchtop multispectral imaging flow cytometerequipped with two CCD cameras that can acquire up to 12 images simultaneously of each cell or object in brightfield, scatter and multiple fluorescent channels.
Data Analysis

For flow cytometry data analysis we suggest FlowJo software.

We have 2 workstations (Mac and PC) and FlowJo is installed on both of them.

On our PC workstation, we also have FACSDiva and ModFit software.

No training is required to use these computers, but you can always ask for assistance and one of our technicians will help you throughout the analysis.

To use it on your own lab computer, the iMM has acquired a site license for FlowJo. For more information get in contact with us.

These services are free of charge, however pre-reservation is required on the online booking system

Training and Support

The Flow Cytometry training at iMM consists of a theoretical introduction and an hands-on training of approx. 2 hours. Before your training session, we strongly recommend you to read our tutorial on Basics of Flow Cytometry, our summarized software tutorials and the e-learning courses we recommend. You can find all these documents and other useful links, such as suggested protocols to prepare your samples, on our Wiki page.

After training you will get access to the booking system and, in the first acquisitions, we will be available to support you until you feel entirely confident with the equipment.

How to use the Service

All new users must contact the Flow Cytometry Facility to get proper training in using the systems and know the Usage Rules. They should also register in our booking system, Agendo, and then request permission to gain access to the calendar of the desired equipment.

After getting in contact with us, we will give you a guided tour through the Flow Cytometry Facility, so that you can have the best experience with our cytometers.

We will give you a theoretical introduction and an hands-on training of approx. 2 hours, and we will provide you important tools to ensure you understand the basic principles of the technique and learn how to perform your experiments according to the best practices.

After training you will get access to the instruments.

To get access to the cell sorters, training is not mandatory, since our technicians are the ones who operate the machines. Talk to use and we will suggest you the best sorting conditions for your experiment.

It is mandatory the compliance with our policies and Guidelines here.


Users are billed for the actual time of usage.


If you used our services and equipment, please acknowledge us on your publications or any other formal presentations. This is one of our key performance indicators and very important for future funding.

You are welcome to use the following examples for reference:

In Materials and Methods: “All experiments were performed at the Flow Cytometry Facility of Instituto de Medicina Molecular João Lobo Antunes.”

In Acknowledgements: “We would like to thank the Flow Cytometry Facility of Instituto de Medicina Molecular João Lobo Antunes for their technical support.”

Thank you!


service directors:
contacts :