The aim of this project is to develop zebrafish as an in silico system to study the dynamical processes of the innate immune response. The transparent skin of zebrafish embryos made it an ideal model organism to investigate cell migration processes using fluorescent time-lapse microscopy. The innate immune system of zebrafish embryos closely resembles that of humans and is at early stages clearly separable from the adaptive response.

Many different data types, such as cell migration imaging data or transcriptomics data, have been collected over the past years. However, the full potential of such data has not been explored so far. I will perform a detailed network analysis of immune cell signalling pathways in zebrafish. The constructed network will be used to generate an improved model of macrophage and neutrophil migration during acute injury. In particular, the cell dynamics will be described by an agent-based hybrid model, which will capture the internal cellular signalling process of each individual cell, as well as the migration process inside the extracellular matrix. Most cell migration data have been analysed using simple statistics, e.g. the velocity of a cell or the straightness index of a cell. Such statistics fail to describe the detailed migration process. I will further develop random walk models and analysis tools to identify migration patterns in 2D, but even more important in 3D. The developed algorithms will provide powerful tools to study migration processes. The analysis of leukocyte migration in 3D will be the basis to develop a 3D in silico model of the innate immune response in zebrafish. This model will be extended to the whole organism level.