title: A marker-free automatic alignment method based on scale-invariant features.
abstract: In electron tomography, alignment accuracy is critical for high-resolution reconstruction. However, the automatic alignment of a tilt series without fiducial markers remains a challenge. Here, we propose a new alignment method based on Scale-Invariant Feature Transform (SIFT) for marker-free alignment. The method covers the detection and localization of interest points (features), feature matching, feature tracking and optimization of projection parameters. The proposed method implements a highly reliable matching strategy and tracking model to detect a huge number of feature tracks. Furthermore, an incremental bundle adjustment method is devised to tolerate noise data and ensure the accurate estimation of projection parameters. Our method was evaluated with a number of experimental data, and the results exhibit an improved alignment accuracy comparable with current fiducial marker alignment and subsequent higher resolution of tomography.
authors.affiliation: Key Lab of Intelligent Information Processing and Advanced Computing Research Lab, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Renmin
authors.initials: R
authors.lastname: Han
authors.affiliation: Key Lab of Intelligent Information Processing and Advanced Computing Research Lab, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China. Electronic address: zhangfa@ict.ac.cn.
authors.forename: Fa
authors.initials: F
authors.lastname: Zhang
authors.affiliation: Key Lab of Intelligent Information Processing and Advanced Computing Research Lab, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China.
authors.forename: Xiaohua
authors.initials: X
authors.lastname: Wan
authors.affiliation: National Centre for Biotechnology, National Research Council (CNB-CSIC), Campus UAM, C/Darwin 3, Cantoblanco, 28049 Madrid, Spain.
authors.forename: Jose-Jesus
authors.initials: JJ
authors.lastname: Fernández
authors.affiliation: Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Sun
authors.affiliation: State Key Lab for Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D000818:Animals; D021941:Caveolae / Q000648:ultrastructure; D002502:Centrioles / Q000648:ultrastructure; D055032:Electron Microscope Tomography / Q000379:methods*; D057918:Fiducial Markers; D022781:Hepatocytes / Q000648:ultrastructure; D007091:Image Processing, Computer-Assisted; D051379:Mice; D008930:Mitochondria, Liver / Q000648:ultrastructure
keywords: Alignment; Bundle adjustment; Electron tomography; SIFT