On the Formal Representation and Annotation of Cellular Genealogies.

Time-lapse microscopy is a primary experimental tool for biologists to study development: the dynamic process by which an entire organism forms from an individual cell. The domain of these cellular dynamics is quite complex, and thus, demands a conceptual and computational architecture to support the integration of knowledge obtained across experiments and theories. In previous work, we have addressed the conceptual level and developed an axiomatic theory of cellular genealogies. In this work, we will address the other fundamental part of theory formation: the experimental level, where we have to deal with actual observations and discoveries. In the case of experiments from time-lapse microscopy, we need to go from the individual images taken at discrete time points to a full conceptual description of the underlying continuous cellular processes. In this work, we take a first step to bridge the general theory T(CO) and the experimental level by investigating individual cases. Any time-lapse experiment is linked to a real spatiotemporal genealogy, and we assume that these entities are particular instances of the general theory. We will investigate how this individual experimental information can be organised and represented.