title: Model-based 2.5-d deconvolution for extended depth of field in brightfield microscopy.
abstract: Due to the limited depth of field of brightfield microscopes, it is usually impossible to image thick specimens entirely in focus. By optically sectioning the specimen, the in-focus information at the specimen's surface can be acquired over a range of images. Commonly based on a high-pass criterion, extended-depth-of-field methods aim at combining the in-focus information from these images into a single image of the texture on the specimen's surface. The topography provided by such methods is usually limited to a map of selected in-focus pixel positions and is inherently discretized along the axial direction, which limits its use for quantitative evaluation. In this paper, we propose a method that jointly estimates the texture and topography of a specimen from a series of brightfield optical sections; it is based on an image formation model that is described by the convolution of a thick specimen model with the microscope's point spread function. The problem is stated as a least-squares minimization where the texture and topography are updated alternately. This method also acts as a deconvolution when the in-focus PSF has a blurring effect, or when the true in-focus position falls in between two optical sections. Comparisons to state-of-the-art algorithms and experimental results demonstrate the potential of the proposed approach.
authors.affiliation: Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. francois.aguet@epfl.ch
authors.forename: François
authors.initials: F
authors.lastname: Aguet
authors.forename: Dimitri
authors.initials: D
authors.lastname: Van De Ville
authors.forename: Michael
authors.initials: M
authors.lastname: Unser
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D007089:Image Enhancement / Q000379:methods*; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008853:Microscopy / Q000379:methods*; D008962:Models, Theoretical; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity