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Extended Depth of Field and Specimen Topography Estimation in Brightfield Microscopy

F. Aguet, D. Van De Ville, M. Unser

Proceedings of the CHUV Research Day (CHUV'07), Lausanne VD, Swiss Confederation, February 1, 2007, pp. 226.



Brightfield microscopy suffers from a limited depth of field, often preventing 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. For the analysis of the in-focus image, knowledge of the specimen's topography can be mandatory. Current methods provide only limited topographical information, usually in the form of a map of selected pixel positions. In this work, we present a joint estimation of the in-focus image and the topography, based on a model of the specimen and the microscope's point spread function. The method, which can be likened to an object model-based deconvolution, produces a continuous topography. Promising results from simulated and experimental image stacks of specimens used in embryological studies demonstrate the efficiency of the method.


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