The Apotome 3 is a simple inverted wide-field microscope with three different imaging modes: standard wide-field fluorescent imaging, optical sectioning of fluorescently stained thin samples using the Apotome grid, and color imaging with the color camera. It is suitable for CCD-based image acquisition for both fluorescence and colorimetric staining.

The system is built on a Zeiss Axio Observer inverted microscope stand with motorized X,Y,Z stage for acquiring Z-stacks and images of areas larger than the field of view through tiling of individual images. The stage can accept slides, plates and dishes.