The basic mathematics tools, Fourier transform and Convolution to illustrate the electron diffraction and imaging theory of transmission electron microscopy (TEM) will be first introduced. The Abbe microscopy theory and lens aberration in Fourier optics will be discussed. Several imaging modes at atomic resolution such as high-resolution TEM (HRTEM) and scanning TEM (STEM) in parallel and focus beam modes, respectively, will be discussed in detail. The physics of electron Beam-Sample Interaction that gives the structural signal and radiation damage will be explained. The electron beam effect on the dose (rate) dependent in-situ TEM experiment will be explored in detail. The theory of electron tomography, energy-dispersive X-ray spectroscopy (EDX), electron energy-loss spectroscopy (EELS), and electron magnetic circular dichroism (EMCD) will be lectured. Virtual laboratory session will be conducted for TEM and related spectroscopy.