3rd - 5th June 2026, Francis Crick Institute

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, offers a practical approach to mastering quantitative analysis and workflow automation, essential for advancing research across multiple domains.

Registration

This workshop is open to internal attendees only. Registration is currently open on Workday.

Instructors

• Dave Barry, Francis Crick Institute
• Deniz Bekat, Francis Crick Institute
• Martin Jones, Francis Crick Institute
• Sara Salgueiro Torres, Francis Crick Institute
• Stefania Marcotti, Francis Crick Institute

Preparation

1. Please remember to bring your laptop (and charger).
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. You will be assigned to a specific group, with whom you will be sitting - your group number will be displayed in the training room.
6. PLEASE CONTACT US BEFORE THE WORKSHOP IF YOU ENCOUNTER ANY DIFFICULTIES WITH ANY OF THE ABOVE.

Program

Wednesday, June 3rd 2026
09:00 - 10:30	Session 1	Introduction & Installations
	Sara Salgueiro Torres 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
10:30 - 10:45	Coffee Break
10:45 - 12:15	Session 2	Image Pre-Processing, Segmentation & Analysis
	Sara Salgueiro Torres Basic segmentation using thresholding Use of filtering to suppress noise Obtaining numbers from images Counting and quantifying morphology of objects Quantifying fluorescence intensities
12:15 - 13:15	Lunch
13:15 - 14:45	Session 3	Extending Analyses to Three Dimensions
	Dave Barry Counting and quantifying morphology of three-dimensional objects Quantifying fluorescence intensities of three-dimensional objects
14:45 - 15:00	Coffee Break
15:00 - 17:00	Session 4	Getting Started with Automating Analysis
	Sara Salgueiro Torres Fiji macro language Automating batch analyses
Thursday, June 4th 2026
09:00 - 10:30	Session 5	Napari for Image Visualisation
	Martin Jones Napari GUI and plugins Visualising complex image datasets using napari
10:30 - 10:45	Coffee Break
10:45 - 12:15	Session 6	Improving Reproducibility
	Stefania Marcotti Version control using GitHub Data repositories Introduction to Jupyter notebooks Scripting foundational concepts
12:15 - 13:15	Lunch
13:15 - 14:45	Session 7	Using Jupyter Notebooks for Reproducible Analysis
	Deniz Bekat Quantifying morphology of objects in a 2D image
14:45 - 15:00	Coffee Break
15:00 - 17:00	Session 8	Introduction to Batch Processing with Jupyter Notebooks
	Deniz Bekat & Stefania Marcotti Practical application: analysing all the images in a folder Integrating napari in a Jupyter notebook
Friday, June 5th 2026
09:00 - 10:30	Session 9	Introduction to Machine Learning for Image Analysis - Part 1
	Dave Barry Traditional vs. machine learning approaches Considerations and common pitfalls Available open-source tools
10:30 - 10:45	Coffee Break
10:45 - 12:15	Session 10	Introduction to Machine Learning for Image Analysis - Part 2
	Dave Barry Practical application: using machine learning for segmentation
12:15 - 13:15	Lunch
13:15 - 14:45	Session 11	Q&A and wrap-up

Venue

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