18th & 19th August 2025, 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 and Jupyter, 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, offers a practical approach to mastering quantitative analysis and workflow automation, essential for advancing research across multiple domains.

Registration

Applications for this workshop are now closed. Keep an eye out for future Image Analysis workshops!

Instructors

• Sara Salgueiro Torres, Francis Crick Institute
• Stefania Marcotti, Francis Crick Institute
  
  

Who will be kindly assisted by:

• Martin Jones, Francis Crick Institute
• Cameron Shand, Francis Crick Institute
• Alicja Skórkowska, Francis Crick Institute

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 SARA 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., Marcotti, S., Salgueiro Torres, S., Jones, M., & Skórkowska, A. (2025, August 19). Introduction to Image Analysis. Zenodo. https://doi.org/10.5281/zenodo.16949737

Program

Monday, August 18th 2025
09:30 - 10:30	Session 1	Introduction - Automated Image Analysis for Reproducible Science
	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 - 12:30	Session 2	Image Pre-Processing, Segmentation & Analysis
	Practical Applications: Basic segmentation using thresholding Use of filtering to suppress noise Obtaining numbers from images
12:30 - 13:30	Lunch
13:30 - 15:30	Session 3	Assembling Pipelines and Interpreting Results
	Practical Applications: Counting and quantifying morphology of objects Quantifying fluorescence intensities
15:30 - 15:45	Coffee Break
15:45 - 17:15	Session 4	Introduction to Batch Processing
	Practical Application: Record commands to form the basis of a script
Tuesday, August 19th 2025
09:30 - 10:30	Session 5	Introduction to Python and installations
	Creating Python environments Installing Jupyter notebooks
10:30 - 10:45	Coffee Break
10:45 - 12:30	Session 6	Using Jupyter Notebooks for Reproducible Analysis
	Variables and arrays Practical Application: quantify morphology of objects in a 2D image with Jupyter
12:30 - 13:30	Lunch
13:30 - 15:30	Session 7	Introduction to Batch Processing with Jupyter Notebooks
	Practical Application: batch processing with Jupyter
15:30 - 15:45	Coffee Break
15:45 - 16:45	Session 8	Introduction to napari, wrap-up, and Q&A

Venue

The workshop will take place in Training Room 1 at the Francis Crick Institute.

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

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 apply.