Atomic structure information is essential for understanding the properties and functions for all materials and molecules. It is also fundamental for research and development in natural sciences, engineering and medicine. X-ray diffraction has made great impact on structure determination, but has limitations when it comes to studying nano-sized crystals, interfaces, phase boundaries and their surfaces. Transmission electron microscopy (TEM) can overcome these limitations and has a strong potential for structural studies of nano-crystals, however, improved methods need to be developed, especially for achieving three-dimensional (3D) structure information because each TEM image gives only two-dimensional (2D) information.