Counting or measuring objects with strong shadows over an irregular background

I need to compare several image files where a number of blobs appear and change shape and size from one image to the next. Background is irregular and shows rather deep grooves. Objects are rounded, semi-rounded, somewhat irregular and/or diamond shape. They are also large and small (app. bimodal). They all have a strong shadow that makes recognition only partial, and I am not sure how to get rid of it. I have tried several of the examples provided for image analyses but the results are not good. Any suggestion? (ps maybe helpful to some to know that these are atomic force microscopy images.)

---I am attaching an original of these type of images. These are large and I have reduced them and changed their mode (i.e., to grayscale, lab color, etc) before opening them in Matlab.

[Image Analyst]

What would be more helpful is to show us your images. Why make us work blind???