Building a 3d image of serial area images and th calculate volume

I have

The image uploaded is the weil myelin stainned rat brain section. This rat has been subjected to stroke. I would like to calculate the area of both the inter ventricular space, and the infarct lesion size on the left side of this brain image. And also, I have a series of these sections and would like to construct a 3 dimensional image. Can some one suggest easy steps in completing this project. I have 900 X 2=1800 brain image hemispheres to calculate in a shot time. please help me with the quick steps involved in doing it.

Best,
Dayalan.S
Texas A&M University