Image processing with ImageJ and Python


The Biomedical Informatics Hub team are hosting a workshop to provide training in image processing techniques using imagej (image processing and analysis in Java). The sessions will cover imagej basics, through to recording and writing your own macros and the plugin system. The workshop is open to researchers across the University with interest in image processing.

The Department of Biosciences at the University of Exeter has been gaining global recognition for excellence in research. With this increasing capacity for cutting edge research has come a surge of biological imaging data. The challenge with such data lies in systematic and scientific extraction of relevant information. While manual segmentation and measurement has been the de facto standard for image analysis for many years, recent developments in computer hardware and image processing software have started allowing for image processing automation. Semi-automated to fully automated image processing techniques already exist to perform diverse tasks such as counting cells in a dish, recognising faces in an image, converting a photo of printed text to characters, and even self-driving cars.

While generic image processing software may not suffice to cover the requirements of the spectrum of images captured in research settings within biomedical sciences or other disciplines, the ability to customise these processing pipelines using macros, scripting languages, and/or custom written algorithms allows us to take full advantage of these approaches to analyse our data.

Workshop aims

  • Introduction to basic imagej usage
  • Common image processing tasks such as segmentation and measurement using the point-and-click interface, such as cleaning up data, detecting objects
  • Introduction to macros via the macro recorder functionality
  • Understanding and familiarization with imagej macro syntax
  • Editing existing and writing custom macros
  • Overview of imagej plugin system and the differences between macros and plugins
  • Demonstration of Automated Image Analysis using Python


You should bring a laptop with a working ImageJ install; FIJI is a good, "batteries-included" distribution of ImageJ that includes many useful plugins. 

There will also be laptops at the workshop if you are unable to bring a laptop. 

Programme & Registration

Part 1 - Introduction to the ImageJ GUI (Graphical User Interface) - 16/10/2019

Time: 14:30 -- 17:30

Registration link:

  • Basic UI functionality - from loading images to ROIs and measurements
  • Background Subtraction & thresholding
  • Advanced UI functionality and recording macros

Part 2 - Automated Image Analysis with ImageJ Macros or Python - 23/10/2019

Time: 14:30 -- 17:30

Registration link:

  • Recording and writing/editing Macros
  • Introduction/demo of Python Scripting for Image Analysis; please attend the Introduction to Python workshop in Nov. 2019 for a more complete introduction to the Python programming language.

NOTE: At the end of each session, the workshop team will remain available in order that you can practise your newly learned skills. We recommend that you bring some of your own data so that you can practise the techniques on data that is relevant to your research.


    Wednesday 16/10/2019

Automated Image Analysis:
    Wednesday 23/10/2019


14:30 -- 17:30

Instructors: Dr Jeremy Metz
Location: Hatherly B12 PC Lab