Course content

To see details about the live Microscopy data analysis: machine learning and the BioImage Archive course and the original programme, you can refer to the course page and programme.

The contents table below outlines the different sessions that were included in the course, as well as the format of the materials (slides/videos/practicals) and each session’s trainer. Either proceed through the materials using the arrows at the end of each page or pick your topic of interest from the table below to skip straight to it.

 Presentation slides –  View or download the slides

 Recorded lectures – Watch the lecture videos 

 Practicals – View or download the slides, exercises, datasets, analysis scripts and results

Format	Subject	Trainer
	Introduction to bioimage analysis
	Introduction to image analysis	Matthew Hartley, and Virginie Uhlmann
	Deep learning introduction	Guillame Jacquemet
	Segmentation with StarDist and SplineDist – lecture and questions	Virginie Uhlmann and Martin Weigert
	Bioimaging data resources at EMBL-EBI
	BioImaging data resources at EMBL-EBI – an overview of the BioImage Archive, BioStudies and EMPIAR	Matthew Hartley, Craig Rusell, Ugis Sarkans and Awais Athar
	BioImaging data resources at EMBL-EBI – practicals	EMBL-EBI Teams, Aybuke Kupcu Yoldas
	Open access machine learning resources for bioimage analysis
	ZeroCost – Practical	Guillame Jacquemet
	BioImage Model Zoo – lecture	Anna Kreshuk
	BioImage Model Zoo – practical (DL4MicEverywhere)	Estibalis Gómez de Mariscal and Wei Ouyang
	Ilastik – practical	Dominik Kutra
	Cellpose – practical	Damian Edward Dalle Nogare
	CellProfiler
	CellProfiler – lecture	Beth Cimini
	CellProfiler – practical	Beth Cimini, Le Liu, Paula Llanos, Esteban Miglietta, Suganya Sivagurunathan, Shatavisha Dasgupta and Callum Tromans-Coia
	Image Data Resource – Discovery using community repositories
	Image data resource – Introduction	Jason Swedlow
	Image data resource – Data submission and curation	Frances Wong
	Image data resource – practical	Jean Marie Burel, Petr Walczysko and Frances Wong
	Advanced computational topics in the context of bioimage analysis
	pyTorch introduction	Craig Russell
	Advanced topics (Terminal, Snakemake, pyTorch)	Craig Russell
	Distributed/Cloud computing	Jean-Marie Burel and Petr Walczysko