Thank you for your suggestion.
It does seem like a Hough transform could be of help. However I found out this kind of transform works with binary images. Finding the right treshold for each image can be tricky.
I did follow a link on the wikipedia page you suggested that helped me a lot. Here is the link http://en.wikipedia.org/wiki/Blob_detection The first method suggested in this page enabled me to detect the structures I was looking for. It even helped me with some images I thought were not clear enough (like the first figure). An additional benefit to the blob detection method is information on the size of the structure in question.
Thank you again for your help. I would be happy to share my code with anyone interested.