Searching for a comprehensive guide (or links) for beginners

Hi everybody,

i have recently started my bachelor thesis. My topic is “quantitative image analysis with Fiji”. Therefore i looked for tutorials on Fiji on the internet, especially on the imageJ wiki. I have no special background with image processing or programing.

There are so much tutorials though. I, as a beginner, dont know where to start. I cant differentiate what tutorials are helpful etc. So i am asking you to give me some links for guides. They should be detailed and not too simplistic. The format (video, lectures, courses, workshops, etc.) doesn’t matter to me. The more the better.

To give you some informations, I have to focus on ImageJ Macro language, filtering, thresholding, segmentation, measurements etc. of images of semiconductor microstructures.

Thank you!

What is your background, what did you study?

Image processing is a subfield of signal processing which in turn is a study in itself. Consequently, you’d need to study signal processing to become sufficiently fluent …

It would help if you could restrict the field and tell us what exactly you are supposed to do for your bachelor thesis.

… is definitely too broad to help you further.

Hi, thanks for the quick answer.
I am studying microsystems engineering. In particular i have to develop a Macro to segment different layers on chips (REM or Xray images) with Fiji, measure their thickness etc. and make it reproducible.

Please post representative images or part of those in the best quality available (no JPG-format) and explain in detail what should be done.

You can see the different layers. Thats just an example. The macro has to recognize the number of the different layers and their thickness (median). I am right on the beginning of my bachelor thesis, so its hard to give you more information on details because i stuck on the beginner guides.

Thanks for the sample image!

I’m sure you’ve already read the ImageJ User Guide, the description of the ImageJ Macro Language and the list of available Macro Functions.

Everything else is up to you.

Concerning the layer thickness, I shall post a result in the sequel.

Thank you very much! So those two guides are sufficient to get things done concerning my topic ?

Ok Can you give me some keywords you would the topic expect to depend on? Just for orientation

Here are attempts to estimate the thickness of the three layers:




A dedicated ImageJ-plugin for the underlying processing is in preparation.

As I wrote before start with: