Location & dates EMBL Heidelberg, Germany 3 - 9 Oct 2020
Deadlines Application closed

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EMBL Courses and Conferences during the Coronavirus pandemic

With the onsite programme paused, many of our events are now being offered in virtual formats.

Registration is open as usual for many events, with back-up plans in place to move further courses and conferences online as necessary. Registration fees for any events affected by the COVID-19 disruption are fully refundable.

More information for participants of events at EMBL Heidelberg can be found here.

EMBL has taken the difficult decision to pause our programme of external courses and conferences. As a result, we are postponing the course to 2021 and apologise for the inconvenience.

Course Overview 

Bioimage analysis has become a keystone of biological research: the deluge of data produced by increasingly advanced microscopes calls for experts able to guide life scientists in the methods and software to be used to produce quantitative knowledge from this data. Due to the complexity of the data, without such 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 advanced course concentrates on teaching cutting-edge concepts and tools for quantitative image analysis, and will seek to upgrade the competencies of future bioimage analysis experts on both theoretical algorithm advancements as well as on practical implementation skills.


This course is aimed at early-career scientists as well as staff scientists working in microscopy or image analysis facilities who already have experience in bioimage analysis. Moreover, participants should already provide or show the 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.


EMBL Courses and Conferences are kindly supported by our Corporate Partnership Programme

Founder partners

  • Leica logo
  • Olympus logo

Corporate partners

  • 10x Genomics_120x82
  • Becton Dickinson logo
  • Bio-Rad logo
  • Boehringer Ingelheim logo
  • Eppendorf logo
  • GSK logo
  • Milteniy Biotec logo
  • NetApp logo
  • Stilla logo
  • ThermoFisher logo

Associate partners

  • Merck logo
  • New England Biolabs logo
  • Nikon logo
  • Promega logo
  • Roche logo
  • Sanofi logo
  • Sartorius logo