This dataset includes 70 sets of 3D confocal high-resolution images. All images were imaged using an LSM800 Zeiss microscope with a Plan-apochromat 1.40-NA, 63× objective, and Zeiss ZEN Blue 2.6 software was used to acquire the images. Three channels were used to acquire transmitted light (TL), SYBR GoldTM- (Thermo Fisher Scientific, Inc.) labeled (nuclear and mitochondrial DNA), and TMRM-labeled (mitochondria) images. Each confocal image consists of 32 slices with an interval of 0.15 µm and a YX resolution of 917 × 917 pixels.