Optical microscopy is one of the most important techniques for modern science. As the microscopy technology has developed in recent decades, the microscopy system becomes more and more complex. The accuracy of the results obtained by the microscopy systems is more easily to be influenced by the imperfections of the system in the real-life experiment. Therefore, the modeling and analysis of the complex microscopy systems in details, like the tolerance of the misalignment of the lenses, are on demand to improve the research efficiency. The widely used modeling technique: ray tracing, is limited by the absence of various optical effects, e.g. the diffraction, polarization, coherence, etc. Therefore, the vectorial physical-optics modeling of the microscopy system was proposed and developed. However, it was restricted to aplanatic lens models, or to the presumed aberrations. The vectorial physical-optics modeling of the microscopy system based on the real lens has not been investigated in the literature to the best of the author's knowledge. Furthermore, the modeling of the real-lens-based system with inclusion of the micro-/nano-structures has also not been investigated. In this work, the author does the vectorial physical-optics modeling of microscopy systems with inclusion of the micro-/nano-structures in the framework of field tracing. The full modeling techniques are formulated by the connection of different solvers of Maxwell's equations, e.g. solvers for the lenses and solvers for the micro-/nano-structures. The accuracy and limitations of these solvers are investigated in details. Then, three types of microscopy systems are modeled and analyzed: 1) a system of focusing through a micro-/nano-particle, 2) a Fourier microscopy system, 3) a microscopy system with the structured illumination.
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