I know this an old thread and am not sure if you still need assistance, but I would defintely recommend you visit www.MIPAR.us.
It is very powerful and intuitive 2D/3D image analysis software written by scientists/end-users and is about to be released as a free trial on December 14th. You can sign up on the site as well as submit images/datasets to test.
There are many image analysis options available, but I think you may just find MIPAR to be something special if you give it a try!
Could you please stop spamming this forum with advertising commercial software. Go ahead if you have some segmentation result or if you have something to say about algorithms incorporated in MIPAR that would be able to tackle this problem...
First, please let me apologize for any irritation I may have caused you, with what you call spamming. I sensed a great deal of frustration in your post, and you instilled a great deal in me. Much as I would like, I do not have the time to post a solution to every poster's segmentation problem, although I have for quite a few. Therefore, for the others, I have decided to "advertise" MIPAR to as many members as possible, knowing with great confidence it has the potential to help them, as it has myself and many others.
Contrary to your reaction, I've received many positive responses, and, when those responses included images, have return those images processed, to the gratitude of many community members. I see dozens of repetitive posts of "advertising" freeware solutions like ImageJ, without a single result or follow-up, and strangely I never see your public complaints on those threads. Believe it or not, commercial products and a desire to help others are not mutually exclusive ideas - and MIPAR is currently free. Anyway, I don't want to irritate other members any further, many of whom have been very appreciative of my postings, and have had no desire for your policing. Here is a potential solution to Evren's problem. A masked adaptive threshold, followed by classic morphology and size filter steps. Evren, feel free to contact with any questions, and I'd be happy to share the MIPAR recipe I used if you receive a free copy.
I will continue to positively contribute to this scientific forum.
I agree with you that answers to questions like "use MatLab" or "use ImageJ" are also not very helpful. I probably did not complain about those, because such answers are made by nitwits. I got the impression that you are more knowledgeable in image-processing and therefore worth my criticism. Also I had the impression that MIPAR is commercial software, because you wrote about free trial-versions.
Anyway, I appreciate your scientific contributions, but if you do not have the time to post solutions to problems or suggestions towards solutions, then I would say: don't post an answer.