Tomographic collection of block-based sparse STEM images: Practical implementation and impact on the quality of the 3D reconstructed volume

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The reduction of the electron dose in electron tomography of biological samples is of high significance to diminish radiation damages. Simulations have shown that sparse data collection can perform efficient electron dose reduction. Frameworks based on compressive-sensing or inpainting algorithms have been proposed to accurately reconstruct missing information in sparse data. The present work proposes a practical implementation to perform tomographic collection of block-based sparse images in scanning transmission electron microscopy. The method has been applied on sections of chemically-fixed and resin-embedded Trypanosoma brucei cells. There are 3D reconstructions obtained from various amounts of downsampling, which are compared and eventually the limits of electron dose reduction using this method are explored.

Original languageEnglish
Article number2281
Number of pages14
Issue number14
Publication statusPublished - 2 Jul 2019
Externally publishedYes


  • Biological samples
  • Electron tomography (ET)
  • Inpainting reconstruction
  • Scanning transmission electron microscopy (STEM)
  • Sparse imaging
  • Trypanosoma brucei

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