Image analysis for Correlative Light and Electron Microscopy (CLEM)

30th November 2026 - 4th December, Francis Crick Institute

Overview

This five-day course, aimed at researchers and core facility staff, focuses on enhancing participants’ skills in image analysis for Correlative Light and Electron Microscopy (CLEM) using open-source software and publicly available datasets. This course is run in collaboration with the Collaborative Computational Project (CCP) for Volume Electron Microscopy (CCP-volumeEM)

Registration

Registration to this workshop has now closed.

Instructors

• Cameron Shand, Francis Crick Institute
• Candice Roufosse, Imperial College London
• Daniel Krentzel, Universitat Zurich
• Fiona Young, Francis Crick Institute
• Mariam Demir, STFC Scientific Computing
• Martin Jones, Francis Crick Institute
• Matthew Hartley, EMBL EBI
• Sara Salgueiro Torres, Francis Crick Institute
• Stefania Marcotti, Francis Crick Institute

Preparation

1. Please remember to bring your laptop (and charger). A computer mouse will also be helpful.
2. Ensure your laptop can connect to WiFi networks outside your host institute (eduroam would be ideal) - check with your local IT support team if you're not sure.
3. Please install the required software before the workshop - follow the installation instructions on this page.
4. Download the workshop data by clicking on the link to the ZIP archive at the top of this page.
5. PLEASE CONTACT US BEFORE THE WORKSHOP IF YOU ENCOUNTER ANY DIFFICULTIES WITH ANY OF THE ABOVE.

Program

Monday, November 30th 2026
09:00 - 09:15	Registrations
09:15 - 09:30	Welcome to the course
09:30 - 11:00	Session 1	Introduction & Installations
	Martin Jones and Stefania Marcotti Who are you and why are you here? What are we going to cover in the course? Introduction to the virtual machines
11:00 - 11:15	Coffee Break
11:15 - 12:45	Session 2	Introduction to image analysis
	Sara Salgueiro Torres Foundational concepts Traditional vs. machine learning approaches Metadata and scientific reproducibility
12:45 - 13:45	Lunch
13:45 - 15:15	Session 3	Building an analysis pipeline for light microscopy data
	Sara Salgueiro Torres and Stefania Marcotti Counting and quantifying morphology of objects using Fiji Quantifying fluorescence intensities using Fiji
15:15 - 15:30	Coffee Break
15:30 - 17:00	Session 4	Building an analysis pipeline for light microscopy data
	Sara Salgueiro Torres and Stefania Marcotti Extending the analysis to 3 dimensions using Fiji
Tuesday, December 1st 2026
09:30 - 11:00	Session 5	Building an analysis pipeline for light microscopy data
	Stefania Marcotti Segmenting objects using machine learning algorithms in ilastik Other machine learning approaches
11:00 - 11:15	Coffee Break
11:15 - 12:45	Session 6	Building an analysis pipeline for electron microscopy data
	Mariam Demir and Martin Jones Manual segmentation using Labkit Segmenting objects using machine learning algorithms in ilastik
12:45 - 13:45	Lunch
13:45 - 15:15	Session 7	Building an analysis pipeline for electron microscopy data
	Mariam Demir and Martin Jones Performing quantitative measurements
15:15 - 15:30	Coffee Break
15:30 - 17:00	Session 8	Data reuse
	Matthew Hartley Image repositories Using Next Generation File Formats (NGFFs)
Wednesday, December 2nd 2026
09:30 - 11:00	Session 9	Designing scalable pipelines
	Cameron Shand and Martin Jones Implementing machine learning segmentation with AI OnDemand Introducing containers
11:00 - 11:15	Coffee Break
11:15 - 12:45	Session 10	Reconstructing image volumes
	Cameron Shand and Martin Jones Opening and cropping images Visualising image volumes
12:45 - 13:45	Lunch
13:45 - 15:15	Session 11	Reconstructing image volumes
	Mariam Demir and Martin Jones Stitching image volumes
15:15 - 15:30	Coffee Break
15:30 - 17:00	Session 12	Correlating image volumes across modalities
	Daniel Krentzel Image volume registration using CLEM-Reg
Thursday, December 3rd 2026
09:30 - 11:00	Session 13	Data reuse
	Candice Roufosse The science behind the course dataset Alternative biological questions
11:00 - 11:15	Coffee Break
11:15 - 12:45	Session 14	Group work
12:45 - 13:45	Lunch
13:45 - 15:15	Session 15	Group work
15:15 - 15:30	Coffee Break
15:30 - 17:00	Session 16	Group work
Friday, December 4th 2026
09:30 - 11:00	Session 17	Group work
11:00 - 11:15	Coffee Break
11:15 - 12:45	Session 18	Group work
12:45 - 13:45	Lunch
13:45 - 15:15	Session 19	Final presentations from attendees
15:15 - 15:30	Coffee Break
15:30 - 17:00	Session 20	Q&A and closing remarks

Venue

The workshop will take place in the Francis Crick Institute, London, UK.