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The aim of this research is to analyze CT images of stromatolites originated from Salt Lake, RJ, Brazil, with a neural networks tool, called SOM, developed by Kohonen in the 80's. This research analyzed images of various sections of stromatolites and identified three classes: pore, sediment and rock. The automatically, quickly and with high accuracy are the advantages of this technique can be used as an alternative to conventional methods used, generating 3D images.