Advanced methods in bioimage analysis

Overview

This course 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.

Audience

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.

Modules/resources

• 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

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Trainers, speakers, staff

Speakers, trainer, and staff

Philippe Andrey

INRAE, Versailles

France

Ignacio Arganda-Carreras

University of the Basque Country (UPV/EHU)

Spain

Beth Cimini

Broad Institute

USA

Robert Haase

University of Leipzig

Germany

Anna Klemm

Scilifelab & Uppsala University

Sweden

Anna Kreshuk

EMBL Heidelberg

Germany

Peter Majer

Bitplane

Switzerland

Mackenzie Mathis

EPFL

Switzerland

Matthew McCormick

Kitware

USA

Perrine Paul-Gilloteaux

CNRS UAR BioCore Nantes University

France

Norman Rzepka

scalable minds

Germany

Jean-Yves Tinevez

Institut Pasteur

France

Pavel Tomancak

Max Planck Institute of Molecular Cell Biology and Genetics

Germany

Christian Tischer

EMBL Heidelberg

Germany

Virginie Uhlmann

EMBL-EBI

United Kindgdom

Britta Velten

Heidelberg University

Germany

Carolina Wählby

Uppsala University

Sweden

Scientific organisers

Ignacio Arganda-Carreras

University of the Basque Country (UPV/EHU)

Spain

Anna Klemm

Scilifelab & Uppsala University

Sweden

Perrine Paul-Gilloteaux

University of Nantes

France

Christian Tischer

EMBL Heidelberg

Germany

Course organisers

Julia Patricia Nohle

Course and Conference Officer

EMBL Heidelberg

Germany

Irena Provaznikova

Senior Scientific Training and Digital Learning Manager

EMBL Heidelberg

Germany

Sponsors

Media partners

Imaging and Microscopy, a Wiley magazine

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.

Media kit

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