Skip to main content
U.S. flag

An official website of the United States government

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

3D Imaging of Diatoms with Ion-abrasion Scanning Electron Microscopy



Keana C. Scott, Mark Hildebrand, Sang Kim, Dan Shi, Sriram Subramaniam


Ion-abrasion scanning electron microscopy (IASEM) takes advantage of focused ion beams to abrade thin sections from the surface of bulk specimens, coupled with SEM to image the surface of each section, enabling 3D reconstructions of subcellular architecture at ~ 30 nm resolution. Here, we report the first application of IASEM for imaging a biomineralizing organism, the marine diatom Thalassiosira pseudonana. Diatoms have highly patterned silica-based cell wall structures that are unique models for the study and application of directed nanomaterials synthesis by biological systems. Our study provides new insights into the architecture and assembly principles of both the hard (siliceous) and soft (organic) components of the cell. From 3D reconstructions of developmentally synchronized diatoms captured at different stages, we show that both micro- and nanoscale siliceous structures can be visualized at specific stages in their formation. We show that not only are structures visualized in a whole-cell context, but demonstrate that fragile, early-stage structures are visible, and that this can be combined with elemental mapping in the exposed slice. We demonstrate that the 3D architectures of silica structures, and the cellular components that mediate their creation and positioning can be visualized simultaneously, providing new opportunities to study and manipulate mineral nanostructures in a genetically tractable system.
Journal of Structural Biology


"Diatom", "Ion-abrasion SEM", "Biomineral structure formation", "Biosilicification", "3D tomography"


Scott, K. , Hildebrand, M. , Kim, S. , Shi, D. and Subramaniam, S. (2009), 3D Imaging of Diatoms with Ion-abrasion Scanning Electron Microscopy, Journal of Structural Biology, [online], (Accessed July 13, 2024)


If you have any questions about this publication or are having problems accessing it, please contact

Created June 9, 2009, Updated February 19, 2017