To define the biophysical pathways of cellular life and to elucidate the molecular mechanisms that carry out cellular and biological functions is one of the current significant scientific challenges in the intersection field of life and physical sciences. The novel application of optical techniques, sensing physiological changes in the details of individual cells, can help to meet these requirements. Bacterial spores belong to a cell type responding to adverse growing conditions, and the germination of spores from dormant to vegetative state is a special process of physiology. The application and development of optical techniques and single-cell analysis has played an extremely important role in understanding the mechanism of spore germination and heterogeneity. Raman spectroscopy, differential interference contrast microscopy, fluorescence imaging and Raman imaging are reviewed, and major unanswered questions are also discussed.