Aberration-corrected optics have made transmission electron microscopy a widespread and essential tool for 2D/3D material characterization at the atomic scale. With the rapid development of hardware and novel experimental techniques, there is an increasing demand for advanced algorithms to work with new experimental data or improve existing techniques. In this dissertation, we investigate a variety of image reconstruction algorithms for tomography and ptychography - two fast growing areas in electron microscopy. Using experimental and simulated data, we examine the limitations of advanced reconstruction algorithms and propose new methods to improve existing methods. Chapter 1 provides an overview of transmission electron microscopy and introduces some basic concepts in imaging science. Chapter 2 takes a more in-depth discussion of elastic scattering in STEM and how beam propagation can be described analytically and computationally. The next two chapters focus on electron tomography, a technique that reconstructs the 3D structure of the object. Chapter 3 describes the experimental setup and demonstrates an efficient Fourier-based reconstruction framework that works well with novel experimental techniques, including dual-axis tomography and through-focal tomography. In Chapter 4, we investigate the popular sparsity-exploiting reconstruction algorithms - exploring their practical limitations in the context of electron tomography. Chapter 5 introduces electron ptychography, a diffractive imaging technique that is enabled by the recent development of a high dynamic range detector. Here we demonstrate a full-field ptychographic reconstruction that doubles the spatial resolution of the traditional lens limitations. Finally, in Chapter 6 we further study the practical limitations of ptychography and propose new strategies for reconstructions.