Introduction to image analysis using Python and Jupyter notebooks

Learn the foundational concepts of image analysis, develop a pipeline to analyse a single image quantitatively and then learn how to batch-process multiple images. 

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Course info

This one-day course combines classroom-based theory and practical sessions to help participants build image-analysis skills. It begins with foundational concepts of image analysis, then guides participants through building a pipeline to quantitatively analyse a single image. Participants finish by learning how to batch-process multiple images, gaining skills they can apply to their own analysis work.

Held at the Francis Crick Institute in London, the course is designed for researchers with basic coding knowledge, in any programming language, who want to learn the skills needed to analyse their imaging data using Python and Jupyter notebooks. 

The course has been developed by experts from the Crick Advanced Light Microscopy (CALM) science technology platform, which provides cutting-edge imaging and image analysis services and training to researchers across the institute. 

By the end of this training, participants will be able to: 

  • Summarise the foundational concepts of image analysis 
  • Perform segmentation of biological objects for further analysis using Python 
  • Design a simple Python pipeline to extract quantitative information from microscopy images 
  • Automate workflows on a batch of images 

Participation in this course is application-based. Candidates are required to apply by completing the application form below. In case of over-subscription and multiple applicants from the same labs, we will attempt to distribute the available places evenly.

Applications will be closed on Monday 4 January 2027, and successful candidates will be notified by Wednesday 13 January 2027. This is a FREE course and open only to staff and students from the Francis Crick Institute and partner universities: Imperial College London, UCL (University College London), and King’s College London. 

By applying and/or registering to this course, you acknowledge that you have read, understood, and agreed to the Terms and Conditions.

Have a question?

Contact our technical training team at techtraining@crick.ac.uk

Programme

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Application form

Your experience

What kind of microscopy do you routinely perform/work with?
Do you already have image data to analyse?
Do you have experience of coding?
Don't worry if you don't - you can still apply!
Source Destination
Ilastik
FIJI/ImageJ
CellProfiler
QuPath
Napari
Imaris

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