Cryo-TEM and atmospheric SEM (ASEM) have enabled direct observation of protein molecules, cells, and tissues in hydrophilic environments. By using cryo-TEM, we have determined the conformation of receptors and ion channels in thin ice layer under vacuum. For the observation in water, we have developed the ASEM. The resolution near the SiN film is 8 nm. The detachable specimen dish can hold a few ml liquid, and allows various types of cells to be cultured in a stable environment, e.g., in a CO2 incubator. The film surface has glass-like nature, and can be coated variously, which allows different types of cells to be cultured, including primary neurons. The system is an efficient immuno-electron microscope, because antigenicity is protected in hydrophilic environments. Using this system, the distributions of proteins in cells are determined at high resolution, and the time and effort required for these experiments are comparable with those for immuno-fluorescence optical microscopy. This system was applied to microbes, bacterial biofilm, host-microbe interactions and neurons, as well as various tissues including glands e.g. the islet of Langerhans in pancreas and blood cells in the capillaries, and further to cancer metastases.