7th November 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 Python and Jupyter notebooks, participants will learn to automate image analysis, enhancing the precision, efficiency, and reproducibility of their research. This 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

Registration for this workshop is currently open on Workday

Instructors

• Stefania Marcotti, Francis Crick Institute
• Sara Salgueiro Torres, Francis Crick Institute
• Dave Barry, 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. PLEASE CONTACT STEFANIA BEFORE THE WORKSHOP IF YOU ENCOUNTER ANY DIFFICULTIES WITH ANY OF THE ABOVE.

Program

Friday, November 7th 2025
09:30 - 11:00	Session 1	Introduction and Installations
	Who are you and why are you here? Creating Python environments Why manual analysis is a bad idea Embracing uncertainty What is metadata and why do you need it
11:00 - 11:15	Break
11:15 - 12:45	Session 2	Image pre-processing, Segmentation and Analysis
	Variables and arrays Basic segmentation using thresholding Use of filtering to suppress noise Obtaining numbers from images
12:45 - 13:45	Lunch
13:45 - 15:45	Session 3	Assembling Pipelines and Interpreting Results
	Counting and quantifying morphology of objects Reproducibly analysing multiple images
15:45 - 16:00	Break
16:00 - 17:00	Session 4	Wrap-up and Q&A

Venue

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

FAQ

1. Do I need any prior knowledge of image analysis to attend?

   No, but a basic understanding of image acquisition would be beneficial.

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

   We will start from the basics, but move quite swiftly to coding exercises – therefore, some basic experience in coding in any programming languages (including Fiji macro language) will be beneficial to make the most of this course.