In this paper, we introduce a novel probabilistic approach to handle occlusions and perspective effects. The proposed method is an object based method embedded in a marked point process framework. We apply it for the size estimation of a penguin colony, where we model a penguin colony as an unknown number of 3D objects. The main idea of the proposed approach is to sample some candidate configurations consisting of 3D objects lying in the real plane. A Gibbs energy is define on the configuration space, which takes into account both prior and data information. These configurations are projected onto the image plane. The configurations are modified until convergence using the multiple birth and death optimization algorithm and by measuring the similarity between the projected image of the configuration and the real image. During optimization, the proposed configuration is modeled by a mixed graph which represents all dependencies between the objects, including interaction between neighbor objects and parent-child dependency for occluded objects. We tested our model on synthetic image, and real images.