I have images of various stages of the cancer. I want to analyse the relative area of the certain bio-marker.
Is want to know the list of available open source software for academia use, along the best and relative easy one to use
Depends a bit also about what kind of images you have.... For MRI scans I'd suggest different software than for stained cell images!
Fiji includes a lot of macros plus ImageJ. There are several open source image processing libraries in python.
Image J would be a good place to start. There are many plugins for this type of work and a large user community.
There is a recent Nature Methods special issue on bioimaging:
Might contain some useful hints. Though I agree with the first comment - some more info on the type of images you have would be useful.
This review also lists some software that can be used for image processing:
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