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Random-Beam STEM Acquisition Method for Tomographic Reconstruction Based on Compressive Sensing

S. Trépout, L. Donati, M. Nilchian, M. Unser, S. Marco

Thirteenth International Conference on x-Ray Microscopy (XRM'16), Oxford, United Kingdom, August 15-19, 2016.

Scanning transmission electron microscopy (STEM) is nowadays becoming a powerful tool for electron tomography in biology. It allows the observation of thick (more than 700 nm) resin embedded samples [1] and is also valuable for cryo-electron tomography [2]. STEM is based on dot acquisition during a scanning process, which is well adapted to perform projection measurements by randomly scanning pixel subsets at every tilt view for tomography. This acquisition procedure, call random-beam STEM (RB-STEM) allows to reduce the electron radiation dosage required for accurate imaging of frozen-hydrated biological nano-structures and it is compatible with compressive sensing approaches [3]. Here we present a tomographic acquisition and reconstruction pipeline based on RB-STEM, fully exploiting compressive sensing principles. This pipeline opens the path for the development of optimized low-dose cryo-STEM tomography adapted for thick biological samples.


  1. S. Trepout, C. Messaoudi, S. Perrot, P. Bastin, S. Marco, "Scanning Transmission Electron Microscopy Through-Focal Tilt-Series on Biological Specimens," Micron, vol. 77, pp. 9-15, October 2015.

  2. S.G. Wolf, L. Houben, M. Elbaum, "Cryo-Scanning Transmission Electron Tomography Of Vitrified Cells," Nature Methods, vol. 11, no. 4, pp. 423-429, April 2014.

  3. L. Donati, M. Nilchian, S. Trépout, C. Messaoudi, S. Marco, M. Unser, "Compressed Sensing for STEM Tomography," Ultramicroscopy, vol. 179, pp. 47-56, August 2017.

AUTHOR="Tr{\'{e}}pout, S. and Donati, L. and Nilchian, M. and Unser, M.
        and Marco, S.",
TITLE="Random-Beam {STEM} Acquisition Method for Tomographic
        Reconstruction Based on Compressive Sensing",
BOOKTITLE="Thirteenth International Conference on x-Ray Microscopy
address="Oxford, United Kingdom",
month="August 15-19,",

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