18th - 20th May 2026, University of Cardiff, Wales

Overview

In this workshop, we will bridge the gap between advanced microscopy data generation and the computational skills required for its analysis. By leveraging open-source tools like FIJI, Jupyter notebooks and napari, participants will learn to automate image analysis, enhancing the precision, efficiency, and reproducibility of their research. This three-day event, led by experienced core facility staff from the Francis Crick Institute and the University of Cardiff, offers a practical approach to mastering quantitative analysis and workflow automation, essential for advancing research across multiple domains.

Applications for this workshop have now closed.

Instructors

• Dave Barry, Francis Crick Institute
• Martin Jones, Francis Crick Institute
• Stefania Marcotti, Francis Crick Institute
• Sara Salgueiro Torres, Francis Crick Institute
• Tom Slater, University of Cardiff

Preparation

1. Please remember to bring your laptop (and charger).
2. Please install the required software before the workshop - follow the installation instructions on this page.
3. Download the workshop data by clicking on the link to the ZIP archive at the top of this page.
4. You will be assigned to a specific group, with whom you will be sitting - your group number will be displayed in the training room.
5. PLEASE CONTACT US BEFORE THE WORKSHOP IF YOU ENCOUNTER ANY DIFFICULTIES WITH ANY OF THE ABOVE.

Program (draft)

Please note that all catering, as well as attendance of the social on the evening of the 18th, is covered by your registration fee.

Monday, May 18th 2026
09:30 - 10:00	Registration
10:00 - 11:30	Session 1	Introduction & Installations
	Dave Barry Who are you and why are you here? Stefania Marcotti Creating Python environments Sara Salgueiro Torres Why manual analysis is a bad idea Embracing uncertainty What is metadata and why do you need it
11:30 - 11:45	Coffee Break
11:45 - 13:15	Session 2	Image Pre-Processing, Segmentation & Analysis
	Sara Salgueiro Torres Basic segmentation using thresholding Use of filtering to suppress noise Obtaining numbers from images
13:15 - 14:15	Lunch
14:15 - 15:45	Session 3	Assembling Pipelines and Interpreting Results
	Sara Salgueiro Torres & Dave Barry Counting and quantifying morphology of objects Quantifying fluorescence intensities
15:45 - 16:00	Coffee Break
16:00 - 17:30	Session 4	Extending Analyses to Three Dimensions
	Dave Barry Counting and quantifying morphology of three-dimensional objects Quantifying fluorescence intensities of three-dimensional objects
18:00	Dinner: venue TBC
Tuesday, May 19th 2026
09:00 - 10:30	Session 5	Using GitHub for Code Version Control
	Stefania Marcotti Creating repositories Tracking changes Intro to coding: variables and arrays
10:30 - 10:45	Coffee Break
10:45 - 12:15	Session 6	Using Jupyter Notebooks for Reproducible Analysis - Part 1
	Stefania Marcotti Analysing light microscopy data Quantify morphology of objects in a 2D image
12:15 - 13:15	Lunch
13:15 - 14:45	Session 7	Using Jupyter Notebooks for Reproducible Analysis - Part 2
	Tom Slater Analysing electron microscopy data Quantify morphology of objects in a 2D image
14:45 - 15:00	Coffee Break
15:00 - 16:30	Session 8	Introduction to Batch Processing with Jupyter Notebooks
	Stefania Marcotti Practical application: analyse all the images in a dataset
16:30 - 18:00	Session 9	Extending Analyses to Three Dimensions in Python
	Tom Slater Quantify morphology of objects in a 3D image
Wednesday, May 20th 2026
09:00 - 10:30	Session 10	Using Napari for Image Visualisation
	Martin Jones Introduction to napari interface Integrating napari into Jupyter notebooks
10:30 - 10:45	Coffee Break
10:45 - 12:15	Session 11	Introduction to Machine Learning for Image Analysis - Part 1
	Dave Barry Annotations and metadata Shallow vs. deep learning Example software tools for light microscopy data
12:15 - 13:15	Lunch
13:15 - 14:45	Session 12	Introduction to Machine Learning for Image Analysis - Part 2
	Martin Jones and Tom Slater Example software tools for electron microscopy data Working with multimodal datasets
14:45 - 15:00	Coffee Break
15:00 - 15:30	Session 13	Wrap up

Venue

The workshop will take place in the School of Chemistry, Cardiff University, Cardiff (UK).

Previous Workshops

Date	Venue	Content
8 / 9th April 2024	King's College London	Click here
24 / 25th April 2024	Royal College of Surgeons in Ireland	Click here
21 / 22nd October 2024	Francis Crick Institute	Click here
8 / 9th April 2025	University of Galway, Ireland	Click here
6 & 20th June 2025	Francis Crick Institute	Click here
18 / 19th August 2025	Francis Crick Institute	Click here
27 / 28th October 2025	Francis Crick Institute	Click here

FAQ

1. Do I need any prior knowledge of image analysis, FIJI or napari to attend?

   No, this workshop is aimed at complete beginners, but a basic understanding of image acquisition would be beneficial.

2. Do I need to have any experience of coding?

   While some basic knowledge would be helpful, it's not essential and even if you have no knowledge of python, Jupyter notebooks or FIJI scripts/macros, you should still apply.