The oldest known fossils are marine stromatolites. They were built mainly by cyanobacteria more than 3 billion years ago, but are still forming today in Bahamas and Australia. Bacteria dig canals through the sand grains and re-precipitate calcium carbonate elsewhere. Canals abound in some regions and lack almost completely in others. Oar goal is to provide an analytical tool to assess spatial variability within the stromatolite microenvironment.  Following image enhancement and classification, various geostatistical techniques are used to quantify the microstructure of stromatolites. Fluorescent microbeads incorporated in gel capsules are used for calibration. To obtain the capsules, fluorescent polymeric microbeads are incorporated into a gel solution (alginate, kelcogel), and portions of the gel solution are inserted into a CaCl2 solution (dropped or sprayed with a syringe, or using other devices). As a result, gel capsules containing microbeads precipitate. Even though there are some limitations, our standardized methodology introduces the same error, making images classified using the same algorithm become comparable.