GPU Accelerated 3D Tomographic Reconstruction and Visualization from Noisy Electron Microscopy Tilt-Series

Research output: Contribution to journalArticlepeer-review

Abstract

We present a novel framework for 3D tomographic reconstruction and visualization of tomograms from noisy electron microscopy tilt-series. Our technique takes as an input aligned tilt-series from cryogenic electron microscopy and creates denoised 3D tomograms using a proximal jointly-optimized approach that iteratively performs reconstruction and denoising, relieving the users of the need to select appropriate denoising algorithms in the pre-reconstruction or post-reconstruction steps. The whole process is accelerated by exploiting parallelism on modern GPUs, and the results can be visualized immediately after the reconstruction using volume rendering tools incorporated in the framework. We show that our technique can be used with multiple combinations of reconstruction algorithms and regularizers, thanks to the flexibility provided by proximal algorithms. Additionally, the reconstruction framework is open-source and can be easily extended with additional reconstruction and denoising methods. Furthermore, our approach enables visualization of reconstruction error throughout the iterative process within the reconstructed tomogram and on projection planes of the input tilt-series. We evaluate our approach in comparison with state-of-the-art approaches and additionally show how our error visualization can be used for reconstruction evaluation.

Original languageEnglish (US)
Pages (from-to)1-15
Number of pages15
JournalIEEE Transactions on Visualization and Computer Graphics
DOIs
StateAccepted/In press - 2022

Bibliographical note

Publisher Copyright:
Author

Keywords

  • cryo-ET
  • Electron microscopy
  • electron tomography
  • GPU acceleration
  • Image reconstruction
  • Iterative methods
  • Noise reduction
  • Three-dimensional displays
  • tilt-series
  • tomographic reconstruction
  • Uncertainty
  • Visualization
  • visualization

ASJC Scopus subject areas

  • Software
  • Signal Processing
  • Computer Vision and Pattern Recognition
  • Computer Graphics and Computer-Aided Design

Fingerprint

Dive into the research topics of 'GPU Accelerated 3D Tomographic Reconstruction and Visualization from Noisy Electron Microscopy Tilt-Series'. Together they form a unique fingerprint.

Cite this