title: Autofocus using adaptive prediction approximation combined search for the fluorescence microscope in second-generation DNA sequencing system.
abstract: Autofocus is an important technique for high-speed image acquisition in the second-generation DNA sequencing system, and this paper studies the passive focus algorithm for the system, which consists of two parts: focus measurement (FM) and focus search (FS). Based on the properties of DNA chips' images, we choose the normalized variance as the FM algorithm and develop a new robust FS named adaptive prediction approximation combined search (APACS). APACS utilizes golden section search (GSS) to approximate the focus position and engages the curve-fitting search (CFS) to predict the position simultaneously in every step of GSS. When the difference between consecutive predictions meets the set precision, the search finishes. Otherwise, it ends as GSS. In APACS, we also propose an estimation method, named the combination of centroid estimation and overdetermined equations estimation by least squares solution, to calculate the initial vector for the nonlinear equations in APACS prediction, which reduces the iterations and accelerates the search. The simulation and measured results demonstrate that APACS not only maintains the stability but also reduces the focus time compared with GSS and CFS, which indicates APACS is a robust and fast FS for the fluorescence microscope in a sequencing system.
authors.forename: Hancong
authors.initials: H
authors.lastname: Xu
authors.forename: Jinfeng
authors.initials: J
authors.lastname: Liu
authors.forename: Yang
authors.initials: Y
authors.lastname: Li
authors.forename: Yan
authors.initials: Y
authors.lastname: Yin
authors.forename: Chenxu
authors.initials: C
authors.lastname: Zhu
authors.forename: Hua
authors.initials: H
authors.lastname: Lu
mesh_terms: D000465:Algorithms; D004247:DNA / Q000235:genetics*; D005246:Feedback; D007089:Image Enhancement / Q000295:instrumentation / Q000379:methods*; D017403:In Situ Hybridization / Q000295:instrumentation / Q000379:methods*; D007909:Lenses; D008856:Microscopy, Fluorescence / Q000295:instrumentation / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000295:instrumentation / Q000379:methods*
chemical_list: D004247:DNA