We present a novel fuzzy theory based method for the segmentation of images required in histomorphometrical investigations of bone implant integration. The suggested method combines discriminant analysis classification controlled by an introduced uncertainty measure, and fuzzy connectedness segmentation method, so that the former is used for automatic seeding of the later. A thorough evaluation of the proposed segmentation method is performed. Comparison with previously published automatically obtained measurements, as well as with manually obtained ones, is presented. The proposed method improves the segmentation and, consequently, the accuracy of the automatic measurements, while keeping advantages with respect to the manual ones, by being fast, repeatable, and objective.