In recent years, the demand for processing of biomedical images has been steadily growing due to an emerging developments of imaging tools in biomedical area. The main task of this book was to reconstruct the 3D image of a mouse axon from its 2D cross-section images. New mathematical methods were designed to achieve this. The 3D reconstruction involves three steps: preprocessing, segmenting and tracking of the images. For each step, commonly used methods have been applied but the results were unsatisfactory, hence a new method for each step was designed. The newly designed methods not only work well in the mice axon reconstruction, but also can be applied to other images of similar tasks. The flowcharts provided in this book could be generalized to many application, and therefore, will be of importance to academics, researchers and practitioners in a wide range of disciplines that require 3-D reconstruction as well as image segmentations.