8th - 9th April 2025, University of Galway, Ireland

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 and napari, participants will learn to automate image analysis, enhancing the precision, efficiency, and reproducibility of their research. This two-day event, led by experienced core facility staff from the Francis Crick Institute and King's College London, 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, King's College London
• Sara Salgueiro Torres, Francis Crick Institute
• Pascal Paco Farina, University of Galway
• Karolina Salciute, University of Galway

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.

Slides

All of the presentation material for this workshop is available on Zenodo and can be referenced as follows:

Barry, D. J., Jones, M., Marcotti, S., and Salgueiro Torres, S. (2025). Introduction to Image Analysis. Zenodo. doi: https://doi.org/10.5281/zenodo.15212231

Program

Please note that all catering, as well as attendance of the social on the evening of the 8th, is covered by your registration fee.

Friday, June 6th 2025
12:00 - 14:20	Session 1	Image Pre-Processing, Segmentation & Analysis Dave Barry
	Practical Applications: Basic segmentation using thresholding Use of filtering to suppress noise Obtaining numbers from images
14:20 - 14:50	Coffee Break
14:50 - 17:00	Session 2	Assembling Pipelines and Interpreting Results Dave Barry
	Practical Applications: Counting and quantifying morphology of objects Quantifying fluorescence intensities
Friday, June 20th 2025
12:30 - 13:40	Session 3	Introduction to Python and installations Alicja Skórkowska
	Creating Python environments Installing Jupyter notebooks and napari
13:40 - 14:00	Coffee Break
14:00 - 15:10	Session 4	Using Jupyter Notebooks for Reproducible Analysis - Part 1 Alicja Skórkowska
	Variables and arrays
15:10 - 15:30	Coffee Break
15:30 - 17:00	Session 4	Using Jupyter Notebooks for Reproducible Analysis - Part 2 Alicja Skórkowska
	Practical Application: quantify morphology of objects in a 2D image with Jupyter

Venue

The workshop will take place in the G001 Seminar Room, Human Biology Building, South Campus, University of Galway, Galway, Ireland:

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On the evening of Tuesday the 8th, we will walk (about 15 minutes) to Taylor's Bar, 7 Dominick St Upper, Galway, H91 RP48 for food and drinks (all covered by your registration fee). These workshops are a terrific networking opportunity, so please join us!

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Organisers

• Dave Barry, Francis Crick Institute
• Martin Jones, Francis Crick Institute
• Stefania Marcotti, King's College London
• Kerry Thompson, University of Galway

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

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.