Further learning

On-demand training

If you work in the life sciences, you may find that you’re spending less time doing experiments and more time analysing huge amounts of biological data. On-demand training is here to help you do this quickly and efficiently.

On-demand training provides free courses on Europe’s most widely used data resources, created by experts at EMBL-EBI and collaborating institutes. You do not need to have any previous experience of bioinformatics to benefit from this training. We want to help you to be a highly competent user of our data resources; we are not trying to train you to become a bioinformatician.

You can use On-demand training to learn in your own time and at your own pace. You can repeat the courses as many times as you like, or just complete part of a course if you want to brush up on how to perform a specific task.

Webinars

Our webinar series is a freely accessible collection of live seminars focused on EMBL-EBI resources. They provide both brief introductions to a range of databases and more in-depth coverage of new features and tools to assist you in your research.

Each webinar is delivered by an EMBL-EBI expert and is followed by a question and answer session. The webinars are recorded and continue to be freely available here.

FTP

All our course material is freely available, to check out materials from all of our previous courses. Please copy and paste the following link into your internet browser and search by year – http://ftp.ebi.ac.uk/pub/training/.

Sessions from previous iterations of this course

You can find materials from previous iterations of this course in EBI’s ftp. Please note that the most up to date methodologies (up to the lates iteration on March 2026) are located in the ‘Course Content‘ page. We thank all supporters, organisers, trainers and delegates for your contributions to this course.

Year	2021	2022	2023	2024	2025
Materials	FTP	FTP	FTP	FTP	FTP
Scientific Organisers	Alvis Brazma, Craig Russell, Jason Swedlow, Virginie Uhlmann	Alvis Brazma, Jean Marie Burel, Matthew Hartley, Craig Russell, Jason Swedlow, Virginie Uhlmann, Soham Mandal	Jean-Marie Burel, Matthew Hartley, Craig Russell, Jason Swedlow, Virginie Uhlmann	Jean-Marie Burel, Matthew Hartley,Craig Russell,Jason Swedlow, Virginie Uhlmann	Jean-Marie Burel, Matthew Hartley, Jason Swedlow, Virginie Uhlmann, Teresa Zulueta Coarasa
Scientific Training Officer	Patricia Carvajal-López, Alex Holinski	Patricia Carvajal-López	Patricia Carvajal-López	Patricia Carvajal Lopez	Patricia Carvajal-López
Events Organiser	Marina Pujol	Juanita Riveros	Shereen Pethania	Meredith Willmott	Anca Belu
Sessions	Introduction to image analysis \| Alvis Brazma & Virginie Uhlmann	Introduction to image analysis \| Alvis Brazma, Matthew Hartley and Virginie Uhlmann	Introduction to image analysis \| Matthew Hartley and Virginie Uhlmann	Introduction to image analysis \| Matthew Hartley and Virginie Uhlmann	General introduction \| Matthew Hartley and Virginie Uhlmann
	ZeroCostDL4Mic – lecture and questions \| Ricardo Henriques, Romain Laine, Guillaume Jacquemet	Deep learning introduction \| Guillame Jacquemet and Soham Mandal	Deep learning introduction \| Guillaume Jacquemet	Deep learning introduction \| Guillaume Jacquemet	Bioimaging introduction, data formats, and metadata \| BIA and IDR teams
	Segmentation with StarDist and SplineDist – lecture and questions \| Soham Mandal, Virginie Uhlmann, Martin Weigert	Segmentation with StarDist and SplineDist – lecture and questions \| Soham Mandal, Virginie Uhlmann and Martin Weigert	Segmentation with StarDist and SplineDist – lecture and questions \| Virginie Uhlmann and Martin Weigert	Segmentation with StarDist and SplineDist – lecture and questions \| Virginie Uhlmann and Martin Weigert	BioImaging data resources at EMBL-EBI – an overview of the BioImage Archive (BIA) and EMPIAR \| Mattew Hartley and Aybuke Kupcu Yoldas
	Segmentation with StarDist and SplineDist – Practical \| Romain Laine, Craig Russell, Virginie Uhlmann, Soham Mandal	ZeroCost – Practical \| Guillame Jacquemet, Soham Mandal, Esti Gómez de Mariscal	ZeroCost – Practical \| Guillaume Jacquemet, Esti Gómez de Mariscal, and Anna Foix	PyTorch introduction \| Craig Russell	Image Data Resource (IDR) – introduction \| Jason Swedlow
	BioStudies – lecture and questions \| Ugis Sarkans & Awais Athar	Terminal for scientific computing (git, bash and more) – Practical \| Craig Russell	BioImaging data resources at EMBL-EBI, an overview \| Matthew Hartley, Craig Russell, Ugis Sarkans, and Awais Athar	ZeroCost – Practical \| Guillaume Jacquemet	Deep learning introduction \| Martin Weigert
	Variety – lecture and questions \| Matthew Hartley & Craig Russell	BioStudies – lecture and questions \| Ugis Sarkans and Awais Athar	EMPIAR introduction and overview \| Simone Weyend	BioImaging data resources at EMBL-EBI – an overview of the BioImage Archive, BioStudies and EMPIAR \| Matthew Hartley, Craig Rusell, Ugis Sarkans and Awais Athar	Cellpose lecture \| Damian Edward Dalle Nogare
	Biostudies and Variety – Practical \| Craig Russell, Romain Laine & Guillaume Jacquemet	BioImage Archive \| Matthew Hartley and Craig Russell	MitoNet and EBI/EMPIAR: How datasets curated for AI helped create SOTA segmentation models for volume electron microscopy \| Kedar Narayan	BioImaging data resources at EMBL-EBI – practicals \| EMBL-EBI Teams, Aybuke Kupcu Yoldas	ZeroCost lecture \| Guillaume Jacquemet
	EMPIAR: past, present and future – lecture and questions \| Gerard Kleywegt	Scientific pipelines – practical session \| Craig Russell and Jean-Marie Burel	Analysing vEM data with napari and EMPANADA \| Ryan Conrad, Kedar Narayan, Simone Weyend, Andrii Iudin, Osman Salih, and Sriram Sundar Somasundharam	CellProfiler – lecture and questions \| Beth Cimini	CellProfiler lecture \| Beth Cimini
	Depositing and accessing data at EMPIAR – lecture and questions \| Osman Salih	ImJoy – practical session \| Wei Ouyang	CellProfiler – lecture and questions \| Beth Cimini	CellProfiler – practical \| Beth Cimini, Le Liu, Paula Llanos, Esteban Miglietta, Suganya Sivagurunathan, Shatavisha Dasgupta and Callum Tromans-Coia	CellProfiler practical \| Beth Cimini, Le Liu, Paula Llanos
	Depositing and accessing data at EMPIAR – practical \| Andrii Iudin, Osman Salih & Simone Weyand	EMPIAR: past, present and future – lecture and questions \| Gerard Kleywegt	CellProfiler – practical \| Callum Tromans-Coia, Nodar Gogoberidze, and Suganya Sivagurunathan	BioImage Model Zoo – lecture and questions \| Anna Kreshuk	Ilastik lecture and practical \| Dominik Kutra
	Image data resource – lecture + Q&A \| Jason Swedlow	Depositing and accessing data at EMPIAR – Practical \| Osman Salih, Andrii Iudin, Simone Weyand, Paul Korir, Sriram Somasundharam	BioImage Model Zoo – lecture and questions \| Anna Kreshuk	Ilastik – practical \| Dominik Kutra	Bioimage Model Zoo lecture \| Estibaliz Gómez de Mariscal
	Image data resource – lecture and questions \| Frances Wong	Distributed/Cloud computing – practical \| Jean-Marie Burel, Petr Walczysko	BioImage Model Zoo – practical \| ilastik team, Esti Gomez de Mariscal, and Dominik Kutra	BioImage Model Zoo – practical (DL4MicEverywhere) \| Estibalis Gómez de Mariscal and Wei Ouyang	Galaxy workflows for image analysis (slides and demo) \| Anne Fouilloux, Leonid Kostrykin, Beatriz Serrano-Solano, Ricardo Messei
	Image data resource – practical \| Jean Marie Burel, Petr Walczysko, Frances Wong	Image data resource – lecture and Q&A \| Jason Swedlow	Ilastik – practical \| ilastik team, Esti Gomez de Mariscal, and Dominik Kutra	Flex Time – Advanced topics (Terminal, Snakemake, pyTorch) – Questions \| Craig Russell	Working with public image data in OME-Zarr format \| IDR and BIA teams
	BioImage Model Zoo – lecture and questions \| Anna Kreshuk	Image data resource – lecture and questions \| Frances Wong	DeepImageJ – practical \| ilastik team, Esti Gomez de Mariscal, and Dominik Kutra	Image data resource – introduction \| Jason Swedlow	Image data resource – practical \| IDR team
	BioImage Model Zoo – practical \| ilastik team, Wei Ouyang, Esti Gomez de Mariscal, Dominik Kutra	Image data resource – practical \| Jean Marie Burel, Petr Walczysko and Frances Wong	Image data resource – lecture and Q&A \| Jason Swedlow	Image data resource – lecture and questions \| Frances Wong	BioImaging data resources at EMBL-EBI – practicals \| BIA team
	CellProfiler – lecture and questions \| Beth Cimini	The EMBL Imaging Centre \| Timo Job Kristian Zimmermann	Image data resource – lecture and questions \| Frances Wong	Image data resource – practical \| Jean-Marie Burel, Petr Walczysko and Frances Wong	Advanced topics in bioimage analysis \| Anna Foix Romero
	CellProfiler – practical \| Nasim Jamali, David Stirling, Barbara Diaz-Rohrer	BioImage Model Zoo – lecture and questions \| Anna Kreshuk	Image data resource – practical \| Jean Marie Burel, Petr Walczysko, and Frances Wong	Distributed/cloud computing – practical \| Jean-Marie Burel and Petr Walczysko
		BioImage Model Zoo – practical \| ilastik team, Esti Gomez de Mariscal and Dominik Kutra	Distributed/Cloud computing – practical \| Jean-Marie Burel, and Petr Walczysko	Cellpose – practical \| Damian Edward Dalle Nogare
		CellProfiler – lecture and questions \| Barbara Diaz-Rohrer, Rebecca Senft, Mario Costa Cruz, Callum Tromans-Coia	Flex Time – Advanced topics (Terminal, Snakemake, pyTorch) – Questions \| Craig Russell

Year	2021	2022	2023	2024	2025
Materials	FTP	FTP	FTP	FTP	FTP
Scientific Organisers	Alvis Brazma, Craig Russell, Jason Swedlow, Virginie Uhlmann	Alvis Brazma, Jean Marie Burel, Matthew Hartley, Craig Russell, Jason Swedlow, Virginie Uhlmann, Soham Mandal	Jean-Marie Burel, Matthew Hartley, Craig Russell, Jason Swedlow, Virginie Uhlmann	Jean-Marie Burel, Matthew Hartley,Craig Russell,Jason Swedlow, Virginie Uhlmann	Jean-Marie Burel, Matthew Hartley, Jason Swedlow, Virginie Uhlmann, Teresa Zulueta Coarasa
Scientific Training Officer	Patricia Carvajal-López, Alex Holinski	Patricia Carvajal-López	Patricia Carvajal-López	Patricia Carvajal Lopez	Patricia Carvajal-López
Events Organiser	Marina Pujol	Juanita Riveros	Shereen Pethania	Meredith Willmott	Anca Belu
Sessions	Introduction to image analysis \| Alvis Brazma & Virginie Uhlmann	Introduction to image analysis \| Alvis Brazma, Matthew Hartley and Virginie Uhlmann	Introduction to image analysis \| Matthew Hartley and Virginie Uhlmann	Introduction to image analysis \| Matthew Hartley and Virginie Uhlmann	General introduction \| Matthew Hartley and Virginie Uhlmann
	ZeroCostDL4Mic – lecture and questions \| Ricardo Henriques, Romain Laine, Guillaume Jacquemet	Deep learning introduction \| Guillame Jacquemet and Soham Mandal	Deep learning introduction \| Guillaume Jacquemet	Deep learning introduction \| Guillaume Jacquemet	Bioimaging introduction, data formats, and metadata \| BIA and IDR teams
	Segmentation with StarDist and SplineDist – lecture and questions \| Soham Mandal, Virginie Uhlmann, Martin Weigert	Segmentation with StarDist and SplineDist – lecture and questions \| Soham Mandal, Virginie Uhlmann and Martin Weigert	Segmentation with StarDist and SplineDist – lecture and questions \| Virginie Uhlmann and Martin Weigert	Segmentation with StarDist and SplineDist – lecture and questions \| Virginie Uhlmann and Martin Weigert	BioImaging data resources at EMBL-EBI – an overview of the BioImage Archive (BIA) and EMPIAR \| Mattew Hartley and Aybuke Kupcu Yoldas
	Segmentation with StarDist and SplineDist – Practical \| Romain Laine, Craig Russell, Virginie Uhlmann, Soham Mandal	ZeroCost – Practical \| Guillame Jacquemet, Soham Mandal, Esti Gómez de Mariscal	ZeroCost – Practical \| Guillaume Jacquemet, Esti Gómez de Mariscal, and Anna Foix	PyTorch introduction \| Craig Russell	Image Data Resource (IDR) – introduction \| Jason Swedlow
	BioStudies – lecture and questions \| Ugis Sarkans & Awais Athar	Terminal for scientific computing (git, bash and more) – Practical \| Craig Russell	BioImaging data resources at EMBL-EBI, an overview \| Matthew Hartley, Craig Russell, Ugis Sarkans, and Awais Athar	ZeroCost – Practical \| Guillaume Jacquemet	Deep learning introduction \| Martin Weigert
	Variety – lecture and questions \| Matthew Hartley & Craig Russell	BioStudies – lecture and questions \| Ugis Sarkans and Awais Athar	EMPIAR introduction and overview \| Simone Weyend	BioImaging data resources at EMBL-EBI – an overview of the BioImage Archive, BioStudies and EMPIAR \| Matthew Hartley, Craig Rusell, Ugis Sarkans and Awais Athar	Cellpose lecture \| Damian Edward Dalle Nogare
	Biostudies and Variety – Practical \| Craig Russell, Romain Laine & Guillaume Jacquemet	BioImage Archive \| Matthew Hartley and Craig Russell	MitoNet and EBI/EMPIAR: How datasets curated for AI helped create SOTA segmentation models for volume electron microscopy \| Kedar Narayan	BioImaging data resources at EMBL-EBI – practicals \| EMBL-EBI Teams, Aybuke Kupcu Yoldas	ZeroCost lecture \| Guillaume Jacquemet
	EMPIAR: past, present and future – lecture and questions \| Gerard Kleywegt	Scientific pipelines – practical session \| Craig Russell and Jean-Marie Burel	Analysing vEM data with napari and EMPANADA \| Ryan Conrad, Kedar Narayan, Simone Weyend, Andrii Iudin, Osman Salih, and Sriram Sundar Somasundharam	CellProfiler – lecture and questions \| Beth Cimini	CellProfiler lecture \| Beth Cimini
	Depositing and accessing data at EMPIAR – lecture and questions \| Osman Salih	ImJoy – practical session \| Wei Ouyang	CellProfiler – lecture and questions \| Beth Cimini	CellProfiler – practical \| Beth Cimini, Le Liu, Paula Llanos, Esteban Miglietta, Suganya Sivagurunathan, Shatavisha Dasgupta and Callum Tromans-Coia	CellProfiler practical \| Beth Cimini, Le Liu, Paula Llanos
	Depositing and accessing data at EMPIAR – practical \| Andrii Iudin, Osman Salih & Simone Weyand	EMPIAR: past, present and future – lecture and questions \| Gerard Kleywegt	CellProfiler – practical \| Callum Tromans-Coia, Nodar Gogoberidze, and Suganya Sivagurunathan	BioImage Model Zoo – lecture and questions \| Anna Kreshuk	Ilastik lecture and practical \| Dominik Kutra
	Image data resource – lecture + Q&A \| Jason Swedlow	Depositing and accessing data at EMPIAR – Practical \| Osman Salih, Andrii Iudin, Simone Weyand, Paul Korir, Sriram Somasundharam	BioImage Model Zoo – lecture and questions \| Anna Kreshuk	Ilastik – practical \| Dominik Kutra	Bioimage Model Zoo lecture \| Estibaliz Gómez de Mariscal
	Image data resource – lecture and questions \| Frances Wong	Distributed/Cloud computing – practical \| Jean-Marie Burel, Petr Walczysko	BioImage Model Zoo – practical \| ilastik team, Esti Gomez de Mariscal, and Dominik Kutra	BioImage Model Zoo – practical (DL4MicEverywhere) \| Estibalis Gómez de Mariscal and Wei Ouyang	Galaxy workflows for image analysis (slides and demo) \| Anne Fouilloux, Leonid Kostrykin, Beatriz Serrano-Solano, Ricardo Messei
	Image data resource – practical \| Jean Marie Burel, Petr Walczysko, Frances Wong	Image data resource – lecture and Q&A \| Jason Swedlow	Ilastik – practical \| ilastik team, Esti Gomez de Mariscal, and Dominik Kutra	Flex Time – Advanced topics (Terminal, Snakemake, pyTorch) – Questions \| Craig Russell	Working with public image data in OME-Zarr format \| IDR and BIA teams
	BioImage Model Zoo – lecture and questions \| Anna Kreshuk	Image data resource – lecture and questions \| Frances Wong	DeepImageJ – practical \| ilastik team, Esti Gomez de Mariscal, and Dominik Kutra	Image data resource – introduction \| Jason Swedlow	Image data resource – practical \| IDR team
	BioImage Model Zoo – practical \| ilastik team, Wei Ouyang, Esti Gomez de Mariscal, Dominik Kutra	Image data resource – practical \| Jean Marie Burel, Petr Walczysko and Frances Wong	Image data resource – lecture and Q&A \| Jason Swedlow	Image data resource – lecture and questions \| Frances Wong	BioImaging data resources at EMBL-EBI – practicals \| BIA team
	CellProfiler – lecture and questions \| Beth Cimini	The EMBL Imaging Centre \| Timo Job Kristian Zimmermann	Image data resource – lecture and questions \| Frances Wong	Image data resource – practical \| Jean-Marie Burel, Petr Walczysko and Frances Wong	Advanced topics in bioimage analysis \| Anna Foix Romero
	CellProfiler – practical \| Nasim Jamali, David Stirling, Barbara Diaz-Rohrer	BioImage Model Zoo – lecture and questions \| Anna Kreshuk	Image data resource – practical \| Jean Marie Burel, Petr Walczysko, and Frances Wong	Distributed/cloud computing – practical \| Jean-Marie Burel and Petr Walczysko
		BioImage Model Zoo – practical \| ilastik team, Esti Gomez de Mariscal and Dominik Kutra	Distributed/Cloud computing – practical \| Jean-Marie Burel, and Petr Walczysko	Cellpose – practical \| Damian Edward Dalle Nogare
		CellProfiler – lecture and questions \| Barbara Diaz-Rohrer, Rebecca Senft, Mario Costa Cruz, Callum Tromans-Coia	Flex Time – Advanced topics (Terminal, Snakemake, pyTorch) – Questions \| Craig Russell

Microscopy data analysis: machine learning and the BioImage Archive

Further learning

On-demand training

Webinars

FTP

Sessions from previous iterations of this course