Cookies on this website

We use cookies to ensure that we give you the best experience on our website. If you click 'Accept all cookies' we'll assume that you are happy to receive all cookies and you won't see this message again. If you click 'Reject all non-essential cookies' only necessary cookies providing core functionality such as security, network management, and accessibility will be enabled. Click 'Find out more' for information on how to change your cookie settings.

This four half day online interactive sessions are suitable for all MSD postgraduate research students and postdoctoral early career researchers involved with bright field and fluorescence microscopy.

You are expected to attend four sessions:
  • Monday 19 June, 09:30 - 12:00
  • Tuesday 20 June, 09:30 - 12:00
  • Wednesday 21 June, 09:30 - 12:00
  • Friday 23 June, 09:30 - 12:00


This course consists of four 2.5 hour live interactive online sessions that aims to provide the basic skills necessary to tackle the most common image analysis tasks. Attendees will be shown a variety of techniques and worked examples. They will also learn where and how to access additional help in the future.  

At the tutor’s discretion, some of the scheduled sessions may run into the afternoon if extra time is needed.


This course will cover the following topics:

  • How to interact with the Fiji/ImageJ interface and functions
  • The basic approaches to segmentation and intensity measurements in 2D and 3D
  • How to manage measurements through curating regions of interest
  • How to use image filtering
  • How to perform colocalisation analysis
  • Recommended plugins and image analysis tools
  • How to keep Fiji/ImageJ up-to-date and how to install plugins.
  • How programming and scripting works in Fiji/ImageJ
  • How to use machine learning for image segmentation and de-noising
  • Best practise with regards to microscopy image analysis and how to avoid common pitfalls
  • Where to find online resources for continued development


 At the end of the course, participants will be able to

  • Interact with the Fiji/ImageJ interface and functions
  • Understand the basic principles of Image Analysis and apply them to their images
  • Use machine learning for image segmentation and de-noising
  • Undertake programming and scripting in Fiji/ImageJ
  • Keep Fiji/ImageJ up-to-date and install plugins.




Booking confirmation and reminder emails will send you the link for the live interactive sessions (held in Teams) and joining instructions. To join the session, you can click on the link 15 minutes before the session. Once the tutor has started the session they will tell you what to do. The tutor will share his screen with the slides. At the end of the lecture there will be exercises - the tutor will then go through the exercises and the solutions. Questions and responses will also be managed in the chat. 


A good internet connection, uninterrupted time, camera and microphone enabled on your PC.
Having a computer with two monitors may be beneficial. Before the course, you will need to download Fiji. An email with the instructions will be sent to you.


It is now a requirement that you complete the three short questions in the survey you receive after attending the course. Once you have submitted the survey, you will be sent an email with a link to your attendance certificate. This is to ensure we receive the feedback we need to evaluate and improve our courses. Survey results are downloaded and stored anonymously.


Where no cost is indicated in the shopping trolley, no deposit is required. However, more than two non-attendances or late cancellations without good reason will be logged and may mean you cannot attend any further MSD training that term. Please refer to our Terms and Conditions for further information.