Joint texture and topography estimation for extended depth of field in brightfield microscopy

Brightfield microscopy often suffers from limited depth of field, which prevents thick specimens from being imaged entirely in-focus. By optically sectioning the specimen, the in-focus regions can be acquired over multiple images. Extended depth of field methods aim at combining the information from these images into a single in-focus image of the texture on the specimen's surface. The topography provided by these methods is limited to a map of the selected in-focus image for every pixel and is inherently discretized, which limits its use for quantitative evaluation. In this paper, we propose a joint texture and topography estimation, based on an image formation model for a thick specimen incorporating the point spread function. The problem is stated as a least-squares fitting where the texture and the topography are updated alternately. The method also acts as a deconvolution operation when the in-focus image has some blur left, or when the true in-focus position falls in-between two slices. The feasibility of the method is demonstrated with simulated and experimental results