Automatic slide scanning

Abstract

In this chapter we describe an automatic slide scanning and autofocusing system that consists of three components. First, images are captured at low magnification. This yields a panoramic view of an entire slide which allows the extraction of the positions and sizes of all particles. Then, a particle screening is carried out at medium magnification, in order to eliminate particles that are not diatom-like, i.e. debris that does not comply with pre-defined selection criteria. This method selects about 80% of all usable valves. In a third step at high magnification, images of particles, mostly diatoms, are captured using autofocusing and multifocus fusion. The output of the systems is an annotated gallery of images that can be used for diatom identification. The main limitation of the automatic slide scanning system consists of the mechanical parts. The average time to position the motor-controlled microscope stage and to acquire an image is about 3 seconds.