Development and study of cell-cultured constructs, such as tissue-engineering scaffolds or organ-on-a-chip platforms require a comprehensive, representative view on the cells inside the used materials. However, common characteristics of biomedical materials, for example, in porous, fibrous, rough-surfaced, and composite materials, can severely disturb low-energy imaging. In order to image and quantify cell structures in optically challenging samples, we combined labeling, 3D X-ray imaging, and in silico processing into a methodological pipeline. Cell-structure images were acquired by a tube-source X-ray microtomography device and compared to optical references for assessing the visual and quantitative accuracy. The spatial coverage of the X-ray imaging was demonstrated by investigating stem-cell nuclei inside clinically relevant-sized tissue-engineering scaffolds (5x13 mm) that were difficult to examine with the optical methods. Our results highlight the potential of the readily available X-ray microtomography devices that can be used to thoroughly study relative large cell-cultured samples with microscopic 3D accuracy.