Advanced image analysis

Automating your image processing

Getting useful information out of our image data often requires analysis with computer programs like Fiji/ImageJ. However, when we have very large amounts of data, or particularly complex analyses we need to be able to use those programs in more sophisticated ways. This course looks at ways to automate analyses and develop more complex processing tools.

Next session: June 2021


  • Matthew Hartley
  • Tjelvar Olsson


This course is aimed at those who either have substantial quantities of image data that they're interested in processing using automated methods, or those whose image analyses stretch the limits of what is possible in Fiji without developing custom analysis code or plugins.


Processing bioimage data often involves repetitive tasks. This can occur when there are lots of similar files to be processed, or certain processing steps need to be run lots of times. This course will look at ways to automate processing of images, including making macros and batch processing. We'll also look at what to do when the analyses we want aren't possible with standard tools, and we need to develop custom analyses, either by extending Fiji or using programming languages like Python.


9:30 Start
11:30 Coffee break
12:30 End

Learning outcomes

By the end of the course you should be able to:


This course assumes a good working knowledge of how to use Fiji for basic image processing.

Full course syllabus

Course materials

Course book