Currently, estimating the number of dopaminergic neurons in the mouse brain by stereology is the gold standard in the field to get quantitative data about the dopaminergic cell number. Here we developed a new absolute quantification method for fluorescently labeled cells and other structures by performing ultramicroscopy on whole glass-body brains, and applied that for imaging and counting dopaminergic neurons. We made use of the genetic Cre-lox system in mice to strongly fluorescently label specifically dopaminergic neurons which is nicely compatible with the generation and analysis of conditional knockout mice and transgenic mice. This method is not only more precise than stereology but also much faster, less cumbersome and less artefact-producing since no standard histological techniques are required like embedding, cutting, staining, mounting and realigning of the sections for 3D representation. A commercial ultramicroscope setup with a light sheet producing laser, an object table and a camera with objective lenses can replace the need for a microscope for stereology requiring a motorized stage, a stereology program and a fast camera. Rehydration of the tissue after ultramicroscopy preserves the tissue integrity and fluorescent signal in dopaminergic neurons which allows performing classical histology and immunohistochemistry to co-localize other proteins in dopaminergic neurons or label and quantify additional cell types and structures in this tissue.