A scaling index based segmentation (SIBS) method is proposed in order to improve visualization and interpretation of data obtained by electron tomography. Based on the interpretation of the scaling index as a measure for dimensionality, the pixels/voxels of an image/volume are subdivided into different categories according to the kind of structure they belong to. Using the weighted scaling index method proposed by Räth1 in conjunction with morphological operators, the approach was adapted to the field of electron microscopy, especially to three-dimensional application as needed by electron tomography. The method turns out to be quite effective for linear structures and membranes. Theory, implementation, parameter settings and results obtained with different kinds of data are presented and discussed.
In this contribution, we propose a novel approach to the segmentation of tomographic image data considering topological properties of binarized image components expressed in terms of the Minkowski Functionals in 3D. Electron tomography is a non-invasive method for three-dimensional (3D) reconstruction of cellular sub-structures from a series of projection images (i.e. from a tilt series) recorded with a transmission electron microscope. Data obtained by electron tomography provide a rich source of quantitative information concerning the structural composition and organization of cellular components. It allows to obtain 3D information on structural cellular arrangements at a significantly higher resolution than any other of the currently available imaging modalities. A major challenge, in this context, is the segmentation of the image data with respect to the identification macro-molecular structures such as the actin-cytoskeleton or cell organelles. We introduce a morphological filtering algorithm based on the Minkowski Functionals in 3D for segmentation of macromolecular structures in intact eukaryotic cells depicted by cryo-electron tomography. In mathematical topology, multi-dimensional convex objects can be characterized with respect to shape, structure, and the connectivity of their components using a set of morphological descriptors known as the Minkowski functionals. In a 3D-Euclidian space, these correspond to volume, surface area, mean integral curvature, and the Euler-Poincare characteristic. The morphological filtering procedure is applied to a 3D image data of an intact, ice-embedded Dictyostelium cell obtained by low dose transmission electron microscopy using a tilt series of -50° to +41.5° with an increment of 1.5°. Our method allows to separate cellular components with predefined textural properties, e.g. filamentary or globular structures, from the image data, which may then be studied and interpreted further.