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Electron Microscope Tomography and Single-particle Reconstruction01:07

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Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
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Dynamic Pore-scale Reservoir-condition Imaging of Reaction in Carbonates Using Synchrotron Fast Tomography
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Deep learning based classification of dynamic processes in time-resolved X-ray tomographic microscopy.

Minna Bührer1,2, Hong Xu3, Allard A Hendriksen4

  • 1Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen, Aargau, Switzerland.

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|December 18, 2021
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Summary
This summary is machine-generated.

This study introduces a fast pipeline for analyzing dynamic 3D X-ray tomographic microscopy data. The method uses machine learning to automatically extract features from low signal-to-noise images, speeding up analysis significantly.

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Area of Science:

  • Materials Science
  • Imaging Science
  • Computational Science

Background:

  • Time-resolved X-ray tomographic microscopy enables 3D dynamic process investigation.
  • Limited signal-to-noise ratio and computational costs hinder quantitative analysis and data processing.
  • Current automatic reconstruction methods are computationally intensive.

Purpose of the Study:

  • To develop a computationally efficient pipeline for reconstructing and classifying dynamic features from X-ray tomographic microscopy data.
  • To overcome the limitations of low signal-to-noise ratios and manual post-processing.
  • To enable high-throughput analysis of dynamic processes.

Main Methods:

  • A novel pipeline (SIRT-FBP-MS-D-DIFF) combining algebraic filter approximation and machine learning.
  • Reconstruction using filtered back-projection with an algebraic filter for efficiency.
  • Post-processing with a trained convolutional neural network for automatic feature extraction.

Main Results:

  • The pipeline significantly reduces computational time for reconstruction and classification.
  • Successfully demonstrated on dynamic fuel cell datasets for training and testing.
  • Enables automatic processing of hundreds of datasets on a single GPU in one day.

Conclusions:

  • The proposed pipeline offers a highly efficient and automatic solution for analyzing time-resolved X-ray tomographic microscopy data.
  • It overcomes previous limitations related to data quality and computational demands.
  • Facilitates broader application and exploration of dynamic processes in various scientific fields.