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In this thesis, we describe the implementation of a cavity-microscope system for cold atoms experiments. This technology combines a high-finesse optical resonator and a high-resolution imaging system. Stability and alignment are crucial aspects of the setup. A cavity holder has been specifically designed to answer the mechanical demands of the cavity-microscope, ensuring its stability. Furthermore, an assembly and alignment procedure has been carefully planned to bring together the bare optical and mechanical components which form the apparatus. We concretely show the efficacy of the defined technique by constructing an updated setup for the Microscope Experiment in the Laboratory for Quantum Gases. The device has been adapted to address the specifics of the experiment with careful attention to the features needed for its long-term goal. Finally, we demonstrate that the implemented procedure maintains intact the optical properties of the system and that it meets the mechanical requirements discussed above. These tests validate the reliability and the integrity of the devised technique. Through the implemented device, two main benefits emerge. Firstly, it enables the detection of atom numbers in a continuous and high-resolved way, two features that are typically challenging to be incorporated together. Secondly, it provides a method to spatially and temporally control the atom-cavity coupling, which is collective in standard cavity QED setups. Ultimately, this technology opens up stimulating prospects for controlled simulations of long-range interacting physical systems.