Materials for the "ImageJ/Fiji Level 2: Automation and batch processing using macros" course taught at the Wolfson Bioimaging Facility, University of Bristol.
Download course materials (.zip) here
NEW! Watch on YouTube:
- Part 1: General introduction to programming with a focus on ImageJ/Fiji macros (~78 mins)
- Part 2: Practical guide to writing macros in ImageJ/Fiji (~70 mins)
This workshop is suitable for anyone acquiring microscopy data as part of their research. Familiarity with ImageJ/Fiji will be necessary; in particular the content covered in the Introduction to ImageJ/Fiji course (materials available here). No prior knowledge of programming is necessary. The practical components are designed to enable attendees to work at their own pace.
The workshop begins with a presentation introducing fundamental concepts of programming with a specific emphasis on the ImageJ macro language. Attendees then learn how to run an automated image processing and segmentation routine on microscopy images by carrying out a series of hands-on exercises using provided images.
The examples used concentrate on fluorescence microscopy but the techniques used are widely applicable to other types of images.
Training is provided by staff from the Wolfson Bioimaging Facility during the hands on session which covers basic user interface elements, running image processing techniques, plotting data and batch processing multiple images.
