The Scanning Electron Microscope (SEM) as 2D imaging instrument has been widely used in biology and material sciences to determine the surface attributes of microscopic specimens. However the SEM micrographs still remain 2D images. To effectively measure and visualize the surface properties, we need to restore the shape model from the SEM images. Having 3D surfaces from SEM images would provide true anatomic shape of microscopic objects which allow for quantitative measurements and informative visualization of the system being investigated.The 3D Microscopy Dataset includes both 2D images and 3D reconstructed surfaces of two biological samples and one micro material object as follows:tapetal cell of Arabidopsis thaliana(.zip, 11.3 MB): This dataset contains five 2D images from a biological sample called tapetal cell of Arabidopsis thaliana and its 3D surface model (.off format). The set of 2D images were obtained by tilting the SEM specimen stage 9 degrees from one to the next in the image sequence.pollen grain from Brassica rapa(.zip, 620 KB): This dataset contains four 2D images from a biological sample called pollen grain from Brassica rapa and its 3D point cloud (.ply format) which could be easily converted to a surface model byMeshLab. The set of 2D images were obtained by tilting the specimen stage 3 degrees from one to the next in the image sequence.TEM copper grid(.zip, 18.9 MB): This dataset contains five 2D images from a material object called TEM copper grid and a part of its 3D surface model (.off format). The set of 2D images were obtained by tilting the SEM specimen stage 7 degrees from one to the next in the image sequence. We will provide more samples in near future.