During several years, we have elaborated a protocol for the quantification of images obtained using confocal scanning laser microscopy, used to answer specific research question. Microscopic images were analyzed and classified similar to satellite images, but the final interpretation of the results is relevant to microbiology. Polymeric microspheres of known sizes were used to create a ground truth. Biological samples consisted of sections through the marine stromatolites, Earth's oldest macrofossils, in an attempt to foster the understanding of prehistoric conditions based on the analysis of their microstructure, result of the complex interactions of bacteria, sediments, and the environment. This presentation focuses on several research aspects, including estimation and reconstruction of biovolumes, and the understanding of the microarchitecture of stromatolites.