This paper deals with the high resolution X-ray micro-computed tomographical (micro-CT) visualization of a fibrin scaffold intended to be used during medical repairs of various types of human tissue. Due to the cellular nature of scaffolds, it is important to inspect their microstructure in high detail on a volumetric basis. In this work, we demonstrate the micro-CT measurement of a fibrin-based bone scaffold performed using a proprietarily developed tomographical scanner equipped with a large-area imaging device (LAD) composed of 10× 10 Timepix silicon pixel detectors without any gaps between the individual tiles. The fibrin scaffolds are based on organic materials, which may be reinforced by various additives to improve their mechanical characteristics, and their dimensions are generally very small (i.e. micrometer to millimeter scale). As the organic material used in fibrin scaffolds exhibits very low X-ray attenuation, low-energy X-ray radiation is desirable to achieve sufficient contrast in the projections. Moreover, a high resolution is needed to visualize the fine features in the scaffolds. Here, conventional scintillation detectors suffer two problems that make the aforementioned LAD superior for the imaging of the investigated scaffolds: a wide point-spread function and low sensitivity at low energies. Despite the high LAD sensitivity to low-energy photons, it was necessary to apply several correction procedures to achieve the highest possible resolution. Here, a computational procedure was developed to compensate for the drift of the tube's focal spot, geometrical imperfections of the LAD detector assembly, and the effects of its border pixels with different responses and sizes. We demonstrate the results on the final reconstructed images based on uncorrected and corrected projections, where we achieved a 1 μm voxel size.