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Many recently developed high-resolution morphological methods promise further breakthroughs in the study of insect morphology. At the same time, the high resolution of these methods often imposes limitations on the size of the studied organism. Therefore, miniature insects are of particular interest for such studies, because they possess all the physiological, cognitive and ethological capabilities found in larger insects and, at the same time, their smaller bodies allows complete reconstruction of all sensory organs using methods that can be applied to other insects only for small parts of one particular sense organ. This is why parasitoid wasps Megaphragma amalphitanum, which have a body size as small as 240 µm, can be used as the key model organism for successful reconstruction of biological networks. We examined the head of M. amalphitanum under a dual beam microscope (FIB-SEM) with a isotropic resolution of 8 nm per voxel. Based on a large array of data, we prepared the first complete 3D reconstruction of the compound eye, including cells and subcellular structures. This reconstruction considerably contributes to our knowledge of the 3D organization and spatial orientation of cells in miniature compound eyes, to the conception of insect vision, and to our understanding of the processing of visual information in animals. Comparative morphological analysis shows a high degree of similarity of the eye of the studied wasp with that of the honeybee in some general points, such as the cell arrangement in the retinula and cell structure. In spite of this, the unique morphological adaptations that were described in the Megaphragma eye in our earlier study have also been confirmed. Analyses of cell volumes and of subcellular components have also been performed, yielding results that can be explained in the light of possible morphofunctional adaptations.