CLEM combines the strength of the fluorescence detection in the light microscope with the resolving power of the electron microscope. This allows to find the needle in the haystack, and then get its high-resolution structure.

CLEM requires optimized sample preparation, so that the same location is identifiable by its color or fluoresence, and the identical or an equivalent sample position then has to be identifiable in the electron microscope.

A possible workflow consists of the following:

- A tissue is sectioned into many thin (200nm) sections, which are alternatingly collected on light microscopy glass slides and on EM grids.

- Glass slides are inspected with a light microscope (LM), and an overview image of the section is recorded. The X/Y positions of at least three recognizable features are memorized, such as three corners of the section. The LM is then used to find the objects of interest. Their X-Y coordinates in recorded LM images are also memorized.

- The EM grid is loaded into an electron microscope and the X/Y coordinates of the same three corners of the section are noted. A coordinate transfer software (developed in our group) then can be used to navigate in the LM image to a certain feature of interest, read-out the X/Y coordinates of that position and translate them into the coordinate system of the EM, so that the EM can then directly and precisely navigate to that location.
A high-resolution EM image or EM tomography tilt series can then be collected from that location.