English: Animated 3D reconstruction of mitochondrial structure in Hip tissue of APP/PS1 mouse 24 weeks of age. For 3D reconstruction of the mitochondrial structure, the grayscale of the individual EM section images was first inverted so that the organelle became bright objects. The inverted images were then sequentially co registered using the Normalized Mutual Information 2D registration program in Analyze [84]. This is an automated procedure that aligns similar images based on the statistical distribution of paired pixels compared to the distribution in either image alone. The inverted, co-registered stack was then rendered using Maximum Intensity Projection. Each pixel in the rendered image represents the brightest voxel in a ray from the viewers' eye through the entire stack of sections.