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This two-day workshop is suitable for all MSD postgraduate research students and postdoctoral early career researchers involved with bright field and fluorescence microscopy. (COURSE IS FULL)

This course takes place over two consecutive days and participants are expected to attend both sessions.

6 February 2020 @ 09:30 - 16:30

7 February 2020 @ 09:30 - 16:30

Venue information for each session can be accessed via 'My Resources' once you are booked on the course. Booking confirmation and course reminder emails provide the link to 'My Resources'.

Course aim

This image analysis course 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 and will also learn where and how to access additional help in the future.  

Course format

Two full day interactive workshop.

Course content

This course will cover the following topics:

-          The basic principles of Image Analysis and how it applies to imaging/microscopy.

-          How to interact with the Fiji/ImageJ interface and functions.

-          Best practise with regard to microscopy image analysis and also learn how to avoid common pitfalls.

-          The basic approaches to segmentation and intensity measurements.

-          They will learn to manage measurements on their images through curating regions of interest.

-          The theory behind image filtering and how to perform colocalisation analysis.

-          How programming and scripting work in Fiji/ImageJ

-          How to record macros and will start writing scripts.

-          The best and most important plugins from across industry and academia.

-          How to keep Fiji/ImageJ up-to-date and how to install plugins.

-          What the best resources are online for their continued development.

Course length

Two-day workshop

Number of participants



The course will be held in the Computer Assisted Learning (CAL) Lab in the MSTC, so computers will be provided to all attendees with all the necessary software, image files and practical instructions.

If you wish, you can read the following book ( and/or this book ( before or after attending the course. Reading these books is not compulsory.