Hands-on flow cytometry: learning by doing! – Course and Conference Office

EMBL Course

Hands-on flow cytometry: learning by doing!


Course overview

Flow cytometry is a highly effective method for analysing individual cells that has become widely used in the fields of life sciences and medicine. By utilising flow cytometry, researchers can accurately identify and measure specific cell populations within complex mixtures, as well as assess cell cycle progression, proliferation status, and expression of fluorescent markers.

Our course aims to provide a comprehensive understanding of the underlying principles of flow cytometry, while also emphasising practical considerations related to the most frequently used assays. Through a combination of theoretical instruction and hands-on training, students will gain the knowledge and skills necessary to effectively design, execute, and interpret flow cytometry experiments.


The course is designed for researchers at any step of their career and will cover the subject from basic principles to complex assays. Prior basic working knowledge of flow cytometry, data acquisition or analysis software (DIVA + FlowJo)  is of advantage, but not strictly a must.


  • In-depth principles of Flow Cytometry
  • Quality assessment and instrument validation
  • Analysis of cell cycle profiles in fixed cells
  • Particles counting
  • Apoptosis assays
  • Tissue staining of cell surface and intracellular antigens
  • Principles and guidelines for experimental design, especially for multi-colour Flow Cytometry
  • Essential of gating and gating controls
  • Detailed multi-sessions on analysing data from Flow Cytometers in cooperation with FlowJo
  • Guidelines to prepare flow cytometry data for publication 

Learning outcomes

Our goal for this course is to teach the basic of this technology with a very big emphasis on practical work at the instruments. Nothing is better than learning by doing! We have a great set of experienced trainers in this technology delivering lectures and accompanying you into the lab doing flow on your own. We will have support from FlowJo delivering the basics and some advanced features in multiple sessions. This in-depth five-day course will push your knowledge and skills preparing you for any flow projects ahead on your research path.

What past participants say about the course

My experience at EMBL was lovely and stimulating. The knowledge I acquired through this short time has improved my learning and practical skills. EMBL is a great place for scientific resources; a friendly environment both socially and professionally.” – Ibrahim Malami, Usmanu Danfodiyo University Sokoto

The course was excellently organized, with high quality theoretical and practical sessions! It is a must for everyone interested in basic and more specific aspects of flow cytometry techniques.” – Filipe Olim, University of Madeira

“I enjoyed the course a lot and learned what I was looking for: an opportunity to learn the principles of flow cytometry that are important for planning and performing experiments. Besides the theoretical part, I was able to run samples at the instruments by myself which was a great starting point to perform experiments by myself in the future.” – Maya Funk, German Cancer Research Center


Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course.

Speakers and trainers

Speakers, trainers and staff

Jochen Barths



Ioannis Panetas

FlowJo Informatics, BD


Neda Tafrishi

Sony Biotechnology Inc.


Scientific organisers

Course organisers

Swetlana Krez

Training Lab Technician

EMBL Heidelberg


Nathalie Sneider

Course and Conference Manager

EMBL Heidelberg


Final programme

Are you on social media? Post using #EMBLCytometry and don’t forget to tag @EMBLEvents

  • Some pre-course work (such as watching pre-recordings, protocol reading and computational exercises) with estimated time 0-10 hours will be required and will be shared in advance of the course.
  • Some speakers may need to join virtually to give their lecture or Q&A, and the programme is subject to change.
Day 1 – Monday 13 November 2023
Time (Europe/Berlin)SessionLocation
08:40Bus from hotel to EMBL ATC EntranceISG Hotel
09:00 – 09:30Welcome, Introduction and Safety briefingATC Flex Lab
09:30 – 10:45Participants flash talksATC Flex Lab
10:45 – 11:15Coffee BreakATC Flex Lab
11:15 – 12:00Lecture: Fluidics and optics
Gelo dela Cruz – Novo Nordisk Foundation Center for Stem Cell Medicine – reNEW, Denmark
ATC Flex Lab
12:00 – 12:45Lecture: Fluorescence and PMTs detectors
Steffen Schmitt – German Cancer Research Center, Germany
ATC Flex Lab
12:45 – 13:45LunchEMBL Canteen
13:45 – 14:30Lecture: Data generation and data display
Gelo dela Cruz – Novo Nordisk Foundation Center for Stem Cell Medicine – reNEW, Denmark
ATC Flex Lab
14:45 – 15:45Lecture: The Essentials of gating, FMO and gating controls
Beata Ramasz – EMBL Heidelberg, Germany
ATC Flex Lab
15:45 – 16:15Coffee BreakFlex Lab A & B
16:15 – 18:00Practical Session 1: Assessing instrument performanceTraining Lab B
18:00 – 19:00DinnerEMBL Canteen
19:00Departure to HotelATC Entrance
Day 2 – Tuesday 14 November 2023
Time (Europe/Berlin)SessionLocation
08:40 Bus from hotel to EMBL ATC Entrance
09:00 – 10:00Lecture: Fluorescence spillover and compensation
Gerald Pfister – EMBL Heidelberg Rome
ATC Flex Lab
10:00 – 10:30Coffee BreakATC Flex Lab
10:30 – 12:00Practical Session 2: Absolute countingTraining Lab B
12:00 – 13:00LunchEMBL Canteen
13:00 – 14:00Lecture: Experimental design for multi-color flow
Diana Ordonez – EMBL Heidelberg, Germany
14:00 – 16:00Practical 3: Multi- color staining (Group 1)

Practical 4: Data analysis with FlowJo (Group 2)
Group 1: Training Lab B

Group 2: Computer Training Lab
16:00 – 16:30Coffee BreakATC Flex Lab
16:30 – 18:30Practical 4: Data analysis with FlowJo (Group 1)

Practical 3: Multi- color staining (Group 2)
Group 1: Computer Training Lab

Group 2: Training Lab B
18:30Departure to hotel
19:00 – 21:30Offsite dinner
Day 3 – Wednesday 15 November 2023
Time (Europe/Berlin)SessionLocation
08:40 Bus from hotel to EMBL ATC Entrance
09:00 – 09:30Q&A sessionATC Flex Lab
09:30 – 10:30Lecture: Spectral Flow Cytometry
Neda Tafrishi – Sony Biotechnology Inc., Germany
ATC Flex Lab
10:30 – 11:00Coffee breakATC Flex Lab
11:00 – 12:00Lecture: Cell Cycle Analysis
Diana Ordonez – EMBL Heidelberg, Germany
ATC Flex Lab
12:00 – 13:00LunchEMBL Canteen
13:00 – 15:00Practical 5: Cell cycle samples (Group 1)

Practical 6: Data analysis with FlowJo session 2 (Group 2)
Group 1: Training Lab B

Group 2: Computer Training Lab
15:00 – 15:30Coffee breakATC Flex Lab
15:30 – 17:30Practical 6: Data analysis with FlowJo session 2 (Group 1)

Practical 5: Cell cycle samples (Group 2)
Group 1: Computer Training Lab

Group 2: Training Lab B
17:30 – 18:30DinnerEMBL Canteen
18:30Departure to hotel and free evening
Day 4 – Thursday 16 November 2023
Time (Europe/Berlin)SessionLocation
08:40Bus from hotel to EMBL ATC Entrance
09:00 – 10:00Lecture: Publishing your flow cytometry data
Marcus Eich – German Cancer Research Center, Germany
ATC Flex Lab
10:00 – 10:30Coffee BreakFlex Lab A & B
10:30 – 12:00Practical 7: Preparing Flow Data for Publication – FlowJoComputer Training Lab
12:00 – 13:00Lunch
13:00 – 14:00Lecture: Assessing cell death
Steffen Schmitt – German Cancer Research Center, Germany
ATC Flex Lab
14:00 – 15:30Practical 8: Measuring apoptosisTraining Lab B
15:30 – 16:00Coffee BreakFlex Lab A & B
16:00 – 17:30Practical 9: Data acquisition/Data AnalysisTraining Lab B / Computer Training Lab
17:45Departure to restaurantATC Entrance
18:00 – 22:00Social Activity and Dinner
Day 5 – Friday 17 November 2023
Time (Europe/Berlin)SessionLocation
08:40Bus from hotel to EMBL ATC Entrance
09:00 – 10:00Lecture: Basics of cell sorting
Jochen Barths – ProSort, France
ATC Flex Lab
10:00 – 10:30Coffee BreakFlex Lab A & B
10:30 – 12:30Practical 10: Cell sorting and reanalysis of sorted cellsTraining Lab A & B
12:30 – 13:30Lunch
13:30 – 14:30Lecture: High-dimensional data analysis with FlowJo
Ioannis Panetas – BD, Germany
ATC Flex Lab
14:30 – 15:00Feedback and GoodbyeATC Flex Lab
15:00 Departure to Heidelberg Train StationATC Entrance

Practical information

Registration fees and motivation letter

The course is limited to 16 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.


Registration fees include admission, course materials, COVID-19 safety measures, meals and coffee breaks. Participants are expected to book and pay their own accommodation and travel expenses. 

PhD Student€600

A letter to support your visa application will be issued, on request, once payment of the registration fee is confirmed. We recommend that you book your visa appointment as soon as possible, to avoid any delay with your visa application.

Confirmation and payment

The registration fee should be paid only after acceptance to the course. The results will be announced approximately 2-3 weeks after the application deadline.

Motivation letter submission

After you have logged in and successfully registered, you will receive an email asking you to submit your motivation letter. Click on the link provided and enter your motivation letter in the text box provided. Alternatively you can submit your motivation letter by clicking on the link on the confirmation page directly after registering.


  1. Include your relevant skills, experience and qualifications showing why you would be suitable for the course.
  2. Explain why you would like to attend, including what you can contribute and how you think you will benefit from the course.

Please note:

  • The limit of 2000 characters refers to manually typed text and excludes spaces. If an error occurs try using a different web browser (preferably Google Chrome or Mozilla Firefox).
  • If you copy-paste the text into the form, hidden formatting might still be included which may cause the text to exceed the 2,000 character limit resulting in an error message. We recommend you clear all formatting before pasting in the text.
  • If you have special symbols in your text, make sure you are using Unicode characters, otherwise these will not be recognised.

For detailed instructions, please watch our video on how to submit a course motivation letter.

Further details

For further information about registration and motivation letter submission please refer to the FAQ page.

Financial assistance

Financial assistance

Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of both registration fee waivers and travel grants. Availability is limited to participants attending on-site EMBL Courses and virtual or on-site EMBO Practical Courses in Heidelberg, and will be indicated during the motivation letter submission process.

Your place in the course is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.

Registration fee waiver

The fee waiver will cover the registration sum that you have paid to attend the course.

Travel grant

The travel grant will cover the cost of travel (airfare, train, bus, taxi, accommodation, visa, and/or registration fees*) and is provided up to specified caps which are normally as follows:

– up to €400 for participants travelling to an EMBL Course within Europe.

– up to €1000 for participants travelling to an EMBL Course from outside Europe.

– up to €500 for any participant travelling to an EMBO Practical Course.

– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course.

– up to €700 for any participant working in Croatia, Czech Republic, Estonia, Greece, Hungary, Italy, Lithuania, Luxembourg, Poland, Slovenia, and Turkey travelling to an EMBO Practical Course.

*Registration fees are only covered for EMBO Practical Courses

The organisers may reduce the grant cap to accommodate more participants. Recipients will be notified of their travel cap amount when they are informed of the outcome of their application. Original receipts must be provided with your signature for all costs incurred within two months of completion of travel. Scanned copies cannot be accepted.

Childcare grant (EMBO Practical Courses only)

For EMBO Practical Course participants with children, there is the possibility to apply for a childcare grant to offset child care costs incurred by participants or speakers when participating at a course. Eligible costs include fees for a babysitter or child-care facility, travel costs for a caregiver, or travel costs for taking the child to the meeting etc. Please note that priority will be given to early-stage researchers. A maximum amount of €500 can be awarded per participant applying for an EMBO childcare grant. 

Boehringer Ingelheim Fonds travel grant

Applies to selected courses only. Availability will be indicated during the motivation letter submission process.

This grant covers costs related to your attendance at the course (registration, travel and accommodation costs). The grant is restricted to PhD students and postdocs who conduct basic biomedical research.

Whether you are eligible to apply for a travel grant, depends on when you received your university entrance qualification (e.g. Abitur, A-Levels, High School Diploma, Final State Examination):

– for PhD and MD students, as well as graduates, the university entrance qualification must not have been obtained more than 11 years ago at the time of the envisaged course

– for postdocs, the university entrance qualification must not have been obtained more than 13 years ago at the time of the envisaged course


You may apply for financial assistance when submitting your motivation letter for courses. In your application, you will be asked to answer questions regarding why your lab cannot fund your attendance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.

For the Boehringer Ingelheim Fonds Travel Grant, there is a pre-application question during the motivation letter submission process, and if selected you will be requested to complete a standard form and documentation consisting of your travel expense estimation.


The scientific organisers will select the recipients of all financial assistance during the motivation letter selection process. Results will be announced approximately 6-8 weeks before the event start date, however for some events this may be delayed. Selection results do not impact your admission to the course. Selection is based on scientific merit, your current work or study location, the reasons for needing financial support, and the impact this event will have on your career.


Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.

Further details

See our list of external funding opportunities and for further information about financial assistance please refer to the FAQ page.

Accommodation and shuttles


Single rooms have been reserved for 5 nights (Sunday 12 November to Friday 17 November 2023) at the ISG Hotel. After the selection process, selected participants should contact the hotel directly to make a booking (booking code CYT23-01). We recommend that all course participants stay at the ISG Hotel which is the dedicated hotel for the course.

Local transport

Shuttle buses will go from the ISG Hotel to EMBL and back, mornings and evenings. A bus schedule and location of the bus stops will be made available prior to the meeting.

Further details

Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

For further information on getting to EMBL Heidelberg visit our Travel Information page.

For enquiries about accommodation and local transportation please refer to the FAQ page.

Technical requirements and event software

(delete the technical requirements part if it is not a computer based course in the courtyard room, as well as change label of the details section to only Event Software)

Technical requirements

Below you will find the software and technical requirements for this course.

  • Participants need to bring their own laptops, which will be used to remotely access EMBL virtual machines with pre-installed software.
  • You will need admin rights to install the software required to access the virtual machines. If you do not have admin rights, please contact your technical support team in advance to make sure the software can be installed.
  • If you have a non-standard HDMI port (other than type A), you need to bring an adaptor.
  • Keyboard and PC mouse are available for use with a standard USB port. If you have a different port type, such as USB-C, you will need to bring your own.

Event software

The EMBL eCampus learning platform will be used to collaborate, communicate and network with all of the course participants. All participants will receive information on how to join shortly before the course. We recommend using Chrome, Safari or Mozilla Firefox browsers for eCampus. 

Additional information

Please find additional information including FAQs, terms and conditions, COVID-19 safety policy and travelling to EMBL on our Information for Participants page.

COVID-19 related questions

COVID-19 information for on-site events at EMBL Heidelberg can be found in our COVID-19 FAQs.


Event Partners

Event Sponsors

Sponsorship opportunities

We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other events, or contact sponsorship@embl.de for further information.

If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.


EMBL wishes to warn sponsors of EMBL conferences and courses of fraudulent schemes purporting to offer sponsorship opportunities on behalf of EMBL or affiliated with EMBL officials. One current scam campaign of which we are aware is conducted using the name ‘Judy Eastman’ (judy@gopcontact.a2hosted.com) and entails approaches to sponsors offering sponsorship opportunities on EMBL’s behalf. Please be kindly advised that all relevant communication regarding sponsorship of EMBL conferences, symposia and courses is handled by EMBL directly and is sent from an official EMBL account. EMBL does not work with any external providers on sponsorship acquisition.

Please also note that:

  • EMBL never provides attendee lists for purchase. Any offers of such are fraudulent.
  • EMBL will never call or email you to ask for your credit card details or to request a payment.
  • All payments are on invoice.

Suspicious communications purportedly from, for or on behalf of EMBL should be reported to EMBL at the following email address sponsorship@embl.de.

Media kit

Want to let others know you’re attending this event? Take a look at our shareable media and feel free to use them in your social media channels or presentations.

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Date: 13 - 17 Nov 2023

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre




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