In this paper, we study the problem of segmenting, reconstructing, and analyzing the structure and growth of thrombi (clots) in vivo in blood vessels based on 2-photon microscopic image data. First, we develop an algorithm for segmenting clots in 3-D microscopic images which incorporates the density-based clustering algorithm and other methods for dealing with imaging artifacts. Next, we apply the union-of-balls (or alpha-shape) algorithm to reconstruct the boundary of clots in 3-D. Finally, we perform experimental analysis on the reconstructed clots and obtain quantitative data of thrombus growth and structures. The experiments are conducted on laser-induced injuries in vessels of two types of mice (the wild type and the type with low levels of coagulation factor VII). By analyzing and comparing the developing clot structures based on their reconstruction from image data, we obtain results of biomedical significance. Our quantitative analysis of the clot composition leads to better understanding of the thrombus development, which is also valuable to the modeling and verification of computational simulation of thrombogenesis.