Measuring Percentage of Color Area

[TinaS]

I have an image that shows the antigen staining. The antigen is stained by a brown color, and I would like to know how to calculate the percentage or total amount of brown spots (which are goblet cells) that are present in the image. My first step, which is creating the image into a Binary image, skews and blends the brown and blue (cell membrane) areas, so I'm not getting an accurate reading on these values of Goblet cells. Neither the user guide nor tutorial seems to shed light on this problem, does anyone have any suggestions?

Thanks.