This paper aims to present an experimental study of structured crystals, which has been realized by the integrated use of software products for assessment and analysis of crystal lattices, as well as the building of their three-dimensional color profiles based on the author’s microscopic images with a view to subsequently importing them into agent-based simulation environment models for visualization of crystal growth. The generated results can contribute to extending previous author’s research, united in a methodology for the optimization of structured crystals for telecommunication and scientific-technological applications, in which the object of the microscopic and simulation studies are the quartz crystals and the possibilities of their implementation in technical devices such as quartz filters and resonators. In the present research the focus is placed on simulation methods for the study of ruby crystals after their preliminary optimization. This approach is justified by their possible applications in laser systems, temperature sensor components of modern 3D printers, and medical devices, which aim to increase the efficiency of industrial processes.