Understanding how animals generate and regenerate cell diversity: integrating live imaging, lineage tracking, deep learning and big image data visualization – DeepLineage

Multicellular organisms are made of a wide diversity of cells, all generated from a single cell during development. These cells are generated in the context of a cell genealogy (lineage), which plays an important role in determining their ultimate fate and plasticity. Some animals can also regenerate their body throughout their lifetime, from progenitor cells whose identity/properties are largely unknown. Our goal is to provide a generalised framework for determining and analysing cell lineages, to reveal how cell genealogy impacts cell fate in embryos and regenerating adults. On the experimental side, we will develop genetic and live imaging approaches to record cell lineages, focusing on the crustacean Parhyale hawaiensis, an experimental model where regeneration occurs with exceptional fidelity. On the computational side, we will develop an integrated framework for cell tracking (including deep learning), visual rendering and analysis of cell lineages.