Noise reduction of serial block-face scanning electron microscopy images in the Fourier domain

Hani Jang1, Hong-Kyu Kim1, Jae Pyung Ahn1, Kyung Eun Lee1*, Dong Sik Kim2*

1Advanced Analysis Center, Korea Institute of Science and Technology

2Department of Electronics Engineering, Hankuk University of Foreign Studies

E-mail: kelee@kist.re.kr

Serial block-face scanning electron microscopy (SBF-SEM) is a technique to generate high-resolution 3D structures for biological specimens using back-scattered electron (BSE) serial images from SEM with ultra-microtome in its chamber. During microtomy or image acquisition process, artifacts from chattering, knife marks, and electron noise occur in images and often cause severe problems in obtaining a 3D structure from serial images. However, it is not easy to suppress the occurrence of these artifacts during the acquisition process. Therefore, to obtain the desired 3D structure, developing pre-processing schemes for reducing the artifacts from serial images is required. In the frequency domain, the artifacts form modulated signals at certain frequencies due to periodical properties of the artifacts in the spatial domain. Hence, to reduce the artifacts, we can apply several filters to the modulated signals yielded from the artifacts. Depending on the artifact types, the shapes of the modulated signals are different and thus determining appropriate filter types and sizes is important. Furthermore, the artifact positions in the frequency domain should be efficiently searched to minimize distortions from filtering. We first apply a Fourier transform to BSE images acquired from SBF-SEM experiments. We then search the modulated signals and apply notch or band-stop filters to the signals in the Fourier domain. Conducting an inverse Fourier transform to the filtered signals produces noise-reduced images. Through extensive comparison between input and processed images, we demonstrate the performance of our approach in artifact reduction.

Keywords: SBF-SEM, Fourier domain filtering, artifact reduction