This chapter describes the procedures necessary to create generative models of the spatial organization of cells directly from microscope images and use them to automatically provide geometries for spatial simulations of cell processes and behaviors. Such models capture the statistical variation in the overall cell architecture as well as the number, shape, size, and spatial distribution of organelles and other structures. The different steps described include preparing images, learning models, evaluating model quality, creating sampled cell geometries by various methods, and combining those geometries with biochemical model specifications to enable simulations.
Keywords: Biochemical simulation; Generative model; Spatial organization.