Advanced scripting with Fiji#

In this course, we will introduce the fundamentals of scripting in Fiji. In the first two days, we will cover introductory topics in programming such as variables, logic, and control flow, and then use this programming knowledge to create Fiji macros to automate processing of data. Some topics that we will cover are batch processing files, making simple graphical user interfaces, segmentation using pixel classification, and using the ROI manager in a script. The third day will be a workshop-style event where participants are encouraged to bring their own data and develop their own image analysis script. This course is targeted toward people who have either already taken the HT “introduction to scientific image analysis” course, or who have a good background in ImageJ/Fiji.