MarkerDetector: A method for robust fiducial marker detection in electron micrographs using wavelet-based template

Gaoxin Hou; Zhidong Yang; Dawei Zang; Jose-Jesus Fernández; Fa Zhang; Renmin Han

doi:10.1016/j.jsb.2023.108044

MarkerDetector: A method for robust fiducial marker detection in electron micrographs using wavelet-based template

J Struct Biol. 2024 Mar;216(1):108044. doi: 10.1016/j.jsb.2023.108044. Epub 2023 Nov 14.

Authors

Gaoxin Hou¹, Zhidong Yang², Dawei Zang³, Jose-Jesus Fernández⁴, Fa Zhang⁵, Renmin Han⁶

Affiliations

¹ Research Center for Mathematics and Interdisciplinary Sciences, Frontiers Science Center for Nonlinear Expectations (Ministry of Education), Shandong University, Qingdao 266237, China.
² High Performance Computer Research Center, Institute of Computing Technology, CAS, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
³ High Performance Computer Research Center, Institute of Computing Technology, CAS, Beijing 100190, China.
⁴ Spanish National Research Council (CINN-CSIC), Health Research Institute of Asturias (ISPA), Av. Hospital Universitario s/n, Oviedo 33011, Spain.
⁵ School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China. Electronic address: zhangfa@bit.edu.cn.
⁶ Research Center for Mathematics and Interdisciplinary Sciences, Frontiers Science Center for Nonlinear Expectations (Ministry of Education), Shandong University, Qingdao 266237, China; King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal 23955, Saudi Arabia. Electronic address: hanrenmin@sdu.edu.cn.

PMID: 37967798
DOI: 10.1016/j.jsb.2023.108044

Abstract

Fiducial marker detection in electron micrographs becomes an important and challenging task with the development of large-field electron microscopy. The fiducial marker detection plays an important role in several steps during the process of electron micrographs, such as the alignment and parameter calibrations. However, limited by the conditions of low signal-to-noise ratio (SNR) in the electron micrographs, the performance of fiducial marker detection is severely affected. In this work, we propose the MarkerDetector, a novel algorithm for detecting fiducial markers in electron micrographs. The proposed MarkerDetector is built upon the following contributions: Firstly, a wavelet-based template generation algorithm is devised in MarkerDetector. By adopting a shape-based criterion, a high-quality template can be obtained. Secondly, a robust marker determination strategy is devised by utilizing statistic-based filtering, which can guarantee the correctness of the detected fiducial markers. The average running time of our algorithm is 1.67 seconds with promising accuracy, indicating its practical feasibility for applications in electron micrographs.

Keywords: Electron microscopy; Fiducial marker detection; Template matching; Wavelet transform.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Electrons*
Fiducial Markers*
Microscopy