Advanced methods in bioimage analysis – Course and Conference Office

EMBO Practical Course

Advanced methods in bioimage analysis


This conference will take place at EMBL Heidelberg, with the option to attend virtually.

Registration is not yet open for this event. If you are interested in receiving more information please register your interest.

Course overview

Microscopy is a key methodology in life science research, where the reliability of scientific findings based on data generated on microscopes rely on substantiated qualitative and quantitative image data analysis.

Due to the complexity of the data, without expert guidance, it is very likely that image analysis algorithms may be applied incorrectly, possibly even producing erroneous results. Moreover, the diversity of imaging modalities, analysis algorithms and software solutions is growing so rapidly that even experts are overwhelmed. 

This course aims to promote excellence in bioimage analysis, targeting scientists who already work in this area or harbor ambitions to do so – and will instruct on the latest developments in the field with ample group and networking activities with leading experts in the topic.

With hybrid character, the course will not just strengthen but expand the community of professional bioimage analysts who can transfer the knowledge gained as trainers themselves.


This course is aimed at early-career scientists and staff scientists working in microscopy or image analysis facilities who already have experience in bioimage analysis. Moreover, participants should already provide or show a clear intent of providing bioimage analysis support to other researchers with less or no experience in bioimage analysis.

In selecting participants we look for scientific excellence, immediate application of the methods learned, motivation to disseminate and networking skills. We expect a solid background in bioimage analysis and at least basic programming skills.


  • Microscopy image quality control and image restoration
  • Advanced image segmentation and complex cell phenotyping
  • Handling large microscopy images (such as whole slide scans) and big N-dimensional data 
  • Neural-networks for image restoration, segmentation, and object classification.
  • Co-localisation and spatial statistics
  • Train the trainer: how to teach image analysis

Learning outcomes

Participants should be able to apply what they have learnt to their own image data as well as to image data of their colleagues. 

For each module, participants will learn both theoretical and practical aspects of the latest developments in the fields of bio image analysis concepts and tools. 

After this course, they are expected to be able to confidently operate and interface with a representative selection of open and closed-source image analysis software, including Fiji, QuPath, ilastik, morphographX, KNIME, Imaris, and APEER, in a reproducible and shareable manner. 

In addition, participants will gain new insights about how to set up an image analysis course in their own institution.

What past participants say about the course

“The EMBL practical course on Advanced Methods in Bioimage Analysis represents a turning point in my career. As a Ph.D. student, having the opportunity to meet, network, and learn with the most experienced researchers in this topic changed how I analyze my images and speed up my image analysis workflows.”

– Fernanda Garcia Fossa, Institute of Biology, University of Campinas

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

Trainers, speakers, staff

Scientific organisers

Course organisers

Swetlana Krez

Scientific Training Officer

EMBL Heidelberg


Julia Patricia Nohle

Course and Conference Officer

EMBL Heidelberg



Event sponsors

Event supporter:

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.

Date: 14 - 19 Sep 2025

Location: EMBL Heidelberg and Virtual

Venue: EMBL Advanced Training Centre


  • Ignacio Arganda-Carreras
    University of the Basque Country (UPV/EHU), Spain
    • Anna Klemm
      Uppsala University, Sweden

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