Stereo Scanning Electron Microscopy Dataset

Published: 11-09-2017| Version 1 | DOI: 10.17632/nztd83gxdc.1
Ahmadreza Baghaie,
Heather A Owen


This is the dataset for the paper titled "Slanted Support Window-Based Stereo Matching for Surface Reconstruction of Microscopic Samples" published in Micron. ( For each microscopic sample, a pair of Scanning Electron Microscopy (SEM) micrographs is provided which acquired by a Hitachi S-4800 field emission scanning electron microscope (FE-SEM). This device is equipped with a computer controlled 5 axes motorized specimen stage, enabling movements in X, Y and Z directions as well as tilt (-5 to 70 degrees) and rotation (0 to 360 degrees). Specimen manipulations, such as tilt, Z-positioning, and rotation of the specimen stage are done through the Hitachi PC-SEM software. The working distance was determined at the maximum tilt for every sample at the chosen magnification factor. The SEM image was centered manually while the specimen was tilted in successive 1-degree increments until reaching the final value. Here, the tilt angle between the micrographs in each pair is 7 degrees. It should be noted that the micrograph pairs are not true stereo images as the acquisition is done by tilting the specimen stage. Therefore, an initial step of stereo rectification is necessary, as described in the paper. The dataset is available free of charge for any academic and research purposes. Please cite the following publications if you used the dataset in your research: 1- Baghaie, Ahmadreza, et al. "Slanted Support Window-Based Stereo Matching for Surface Reconstruction of Microscopic Samples." Micron, (2017): 2- Baghaie, Ahmadreza; Owen, Heather A, “Stereo Scanning Electron Microscopy Dataset”, Mendeley Data, v1, (2017), 3- Baghaie, Ahmadreza. Study of Computational Image Matching Techniques: Improving Our View of Biomedical Image Data. Diss. Ph. D. Thesis, University of Wisconsin-Milwaukee (UWM), Milwaukee, WI, USA, 2016. 4- Baghaie, Ahmadreza, et al. "Three-dimensional reconstruction of highly complex microscopic samples using scanning electron microscopy and optical flow estimation." PloS one 12.4 (2017),