Bone ultrastructure studied using correlative nanoscale imaging techniques

In this paper published in the journal Advanced Functional Materials, the authors study the early stages of mineralization in type I collagen-based materials, and find that the mineral spreads between and through the collagen fibrils, forming discrete units called spherulites. These spherulites are composed of a multitude of tiny apatite crystals that are distributed in curved layers, following the protein scaffold provided by the collagen. These spherulites grow radially and longitudinally until imbrication (resulting in complete mineralization of the collagen architecture), and are responsible for the characteristic lacey pattern observed in cross-section in mature calcified tissues. The same ultrastructure is observed in different types of bone, leading the authors to propose a homologous mineralization mechanism for type I collagen materials.

In this study, correlative nanoscale imaging was used, including:

  • Environmental Scanning Electron Microscopy (ESEM) using a FEI Quanta.
  • Focused Ion Beam-Scanning Electron Microscopy (FIB-SEM) 3D imaging and FIB lamella preparation using a Zeiss Crossbeam 540.
  • Scanning/Transmission Electron Microscopy (S/TEM) and STEM-EDS (Energy Dispersive X-ray Spectroscopy) using a Jeol JEM-ARM200.
  • Dragonfly used for SEM image de-striping and image registration, as well as for deep learning segmentation and visualization.

According to lead author Elena Macías-Sánchez: "Dragonfly was really useful in segmenting the complex topography of the mineral spherulites. The intricacies of these structures make them almost impossible to segment manually, and the deep learning toolset made a difference with respect to other software."


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Macías‐Sánchez, E., Tarakina, N.V., Ivanov, D., Blouin, S., Berzlanovich, A.M. and Fratzl, P. Spherulitic Crystal Growth Drives Mineral Deposition Patterns in Collagen‐Based Materials. Advanced Functional Materials2022 (

Research Center

Max Planck Institute of Colloids and Interfaces - Biomaterials

Keywords: Bone Mineralization, Collagen Mineralization, Ultrastructure, 3D Electron Microscopy, Transmission Electrin Microscopy


FIB-SEM reconstruction showing how the mineral spherulite (yellow) permeates several collagen fibrils (multicolored).