Learning ImageJ and/or Fiji is easy with all the help available. Here are a few places to start:
- An overview of the image processing and analysis concepts: https://www.ibiology.org/online-biology-courses/bioimage-analysis-course/. This doesn’t teach the software, but reviews the concepts.
- It’s highly recommend you start with Ellen Dobson’s workshop videos. She works with Kevin Elicieri: https://imagej.net/Presentations#Living_workshops. All of the videos for Introduction to FIJI; Segmentation in FIJI; Scripting in FIJI are thorough and easy to follow. This may be enough.
- Next, complete the exercises in FIJI in this certificate course on EdX: https://www.edx.org/course/image-processing-and-analysis-for-life-scientists. It’s simple to complete and self-paced.
- For more advanced techniques, check out Robert Hasse’s workshop: https://www.youtube.com/playlist?list=PL5ESQNfM5lc7SAMstEu082ivW4BDMvd0U
When all else fails, go to the ImageJ Forum and ask questions and GET ANSWERS from folks who sit around all day waiting for posts on the forum. Big time saver here. Beginning to Advanced questions. Nothing is too basic or complicated.
In the end, when you publish a paper with your processed images, remember to read a good overview of best practices in image acquisition – and how to write a proper materials and methods section.
