Ctan software v1

All datasets were first processed in the CTAn software v1.17 (https://www.bruker.com/products/microtomography/micro-ct-software/3dsuite.html, Bruker Micro-CT, Kontich, Belgium) to remove the Eppendorf Tubes from the images by drawing circular regions of interest (ROIs). Then the datasets were processed with Matlab 2017b (MathWorks, MA, USA) as described below. Different protocols were applied for the spherical and non-spherical microcarriers.

The real density of sponge cakes was determined using a helium stereopycnometer (Quantachrome Instruments, Boynton Beach, FL, USA). Measurements were performed on sponge cake samples weighing ca. 8 g.
The images of the sponge cake’s structure were taken using a Nikon SMZ1500 stereomicroscope equipped with a DS-Fi1 camera at 7.5× magnification.
The microstructure of the sponge cake was measured using a Skyscan 1272 X-ray micro-computed tomography system (v.1.1.7, Bruker Corp., Kontich, Belgium). The X-ray source was operated at a voltage of 40 kV and a current of 222 μA. Images were obtained with a rotation step of 0.4 over an interval of 0–360 and a two-frame average. Two samples were scanned for each type of sponge cake. The scanning time of one sample was 30 min. About 820 images were obtained and processed with the reconstruction software NRecon v. 1.7.3 (Bruker Corp., Billerica, MA, USA) to obtain 2D cross-sectional images (1344 × 896 pixels).
The images were reconstructed and analyzed using CTAn software v. 1.17 (Bruker Corp., Belgium). The following microstructural parameters were obtained: percent object volume (POV), object surface/volume ratio (OSVR), object volume (OV), object surface (OS), structure model index (SMI), anisotropy coefficient (DA), closed porosity, total porosity, the average size of pores, structural thickness (S.Th), and structure separation (S.Sp).

Scans were performed on a Skyscan 1172 instrument (Bruker, Kontich, Belgium) with a 0.5 mm aluminium filter at a voltage of 50kV, a current of 200μA and a resolution of 5 μm/pixel. 2D images were reconstructed into 3D models using NRecon software v.1.6.10.4 (Bruker) and loaded into CTAn software v.1.16.4.1 (Bruker) for analysis. Quantitative data was recorded for bone and vessel regeneration in rectangular regions of interest (ROI) in the Cortex opposite the defect, measuring 1.5 mm long, 0.9 mm wide and 0.6 mm in depth and in the Defect/Medulla measuring 1.5 mm long, 1.0 mm wide and 1.3 mm in depth. Quantitative data for mineralized tissue includes bone volume/tissue volume (BV/TV %), trabecular thickness (Tb.Th. mm x10-3), trabecular separation (Tb.Sp. mm x10-3), open porosity (%) and open pore volume (Po.V Tot mm3). Quantitative data for vascular channels (Bruker micro CT academy 2016 v5.3) includes vascular channel volume/tissue volume (ChV/TV %), vascular channel number (Ch.N), vascular channel thickness (Ch.Th mm x10-3), and vascular channel connectivity density (Ch.Conn.Dn.).