Recently I've started using FIJI. Works well. However I hear that there are such variations called ImageJ2.What is real fundamental difference of ImageJ2 when you compare it with FIJI and/or ImageJ?
Well, Fiji Is Just ImageJ, as it is ImageJ2 with plugins, and this includes ImageJ1 with a compatibility layer. See the ImageJ page for details.
got it. there is no fundamental difference.
Just to clarify again. There is a fundamental difference between ImageJ v1.x and ImageJ2/Fiji, as the latter is a complete rewrite of the former. That legacy layer to which @imagejan refers was to preserve backwards compatibility so that old-style plugins/macros can still run.
You can always read even more details about ImageJ2 and all the goodies it brings here... ImageJ2: ImageJ for the next generation of scientific image data.