To understand the structure-function correlation of engineered and natural nanosystems there is a growing need for three-dimensional (3D) characterization. We apply transmission electron microscopy (TEM) tomography (in TEM, STEM, at room temperature and cryo temperatures) to decipher the 3D structure of various organic, inorganic and hybrid systems. We use and develop advanced algorithms and analysis tools for image reconstruction, 3D visualization, and image analysis to probe beyond 2D imaging.