The uncertainty of Transmission Electron Microscopy (TEM) measurement is affected by the stability of acceleration voltage, defocus, lens aberration, repeatability and reproducibility...etc. The current work evaluates that how the pixels of image obtained through charge coupling device and related software influence the uncertainty of TEM measurement. There are three major measuring tools, including line ROI tool, line profile tool, and line tool in the software for TEM measurement. The results of evaluation reveal that line profile tool provides the smallest uncertainty in measurement. By the comparison of measurements in real space and reciprocal space, both can achieve an approximate result for the reduction of uncertainty.
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