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
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: http://www.nature.com/nmeth/journal/v9/n7/full/nmeth.2024.html?WT.ec_id=NMETH-201207
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: http://www.nature.com/nmeth/journal/v7/n3s/full/nmeth.1431.html
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version 2.3.6
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.