We introduce a microfluidic platform for automated on-chip worm culture, creation of synchronized embryo microarrays, and long-term parallel live imaging of Caenorhabditis elegans embryos. Our device allows studying well-defined embryo populations at unprecedented spatio-temporal resolution, via fully automated multi-dimensional imaging, covering six independent dimensions: the 3 spatial coordinates, development time, exposure duration/type (brightfield, fluorescent), and embryo number in the microarray. We successfully employed our platform to investigate the impact of perturbations of the mitochondrial functions on C.elegans embryogenesis. Our analyses revealed that specific mitochondrial stresses trigger a mitochondrial unfolded protein response (UPRmt) in the embryos. These observations are the first proof that the UPRmt molecular pathway is functional during C.elegans embryogenesis.