In this paper we present a new approach to sequencing of 2-D slide images with the goal of 3-D object reconstructions. We focus our attention mostly on microscope images obtained from serial sections of biological tissues. For adequate 3-D body reconstruction the correct sequence of section should be available. We propose a modified SOM Kohonen networks with open chain topology for true sequence estimation based on based on 2-D image features invariant to section image translation and rotation, but sensitive to a scale of an object on the slide. We provide an experimental validation of the proposed method using artificial section images of a mechanical device and real microscopic histological section images.