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Amorphous silica-based nanotubes (SBNTs) were synthesized from phosphoryl triamide, OP(NH2)(3), thiophosphoryl triamide, SP(NH2)(3), and silicon tetrachloride, SiCl4, at different temperatures and with varying amount of the starting material SiCl4 using a recently developed template-free synthesis approach. Diameter and length of the SBNTs are tunable by varying the synthesis parameters. The 3D mesocrystals of the SBNTs were analyzed with focused ion beam sectioning and electron tomography in the transmission electron microscope showing the hollow tubular structure of the SBNTs. The reconstruction of a small SBNT assembly was achieved from a high-angle annular-dark field scanning transmission electron microscopy tilt series containing only thirteen images allowing analyzing beam sensitive material without altering the structure. The reconstruction revealed that the individual nanotubes are forming an interconnected array with an open channel structure. (C) 2016 Elsevier Ltd. All rights reserved.