Membranes,mitochondria and amoebae: shape models

Most real-world shapes and images are characterized by high variability- they are not rigid, like crystals, for example—but they are strongly structured. Therefore, a fundamental task in the understanding and analysis of such image ensembles is the construction of models that incorporate both variability and structure in a mathematically precise way. The global shape models introduced in Grenander's general pattern theory are intended to do this. In this paper, we describe the representation of two-dimensional mitochondria and membranes in electron microscope photographs, and three-dimensional amoebae in optical sectioning microscopy. There are three kinds of variability to all of these patterns, which these representations accommodate. The first is the variability in shape and viewing orientation. For this, the typical structure is represented via linear, circular and spherical templates, with the variability accomodated via the application of transformations applied to the templates. The transformations form groups: scale, rotation and translation. They are locally applied throughout the continuum and of high dimension. The second is the textural variability; the inside and outside of these basic shapes are subject to random variation, as well as sensor noise. For this, statistical sensor models and Markov random field texture models are used to connect the constituent structures of the shapes to the measured data. The third variability type is associated with the fact that each scene is made up of a variable number of shapes; this number is not assumed to be known a priori. Each scene has a variable number of parameters encoding the transformations of the templates appropriate for that scene. For this, a single posterior distribution is defined over the countable union of spaces representing models of varying numbers of shapes. Bayesian inference is performed via computation of the conditional expectation of the parametrically defined shapes under the posterior. These conditional mean estimates are generated using jump-diffusion processes. Results for membranes, mitochondria and amoebae are shown.