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Toward Real-Time Analysis of Synchrotron Micro-Tomography Data: Accelerating Experimental Workflows with AI and HPC

Conference ·
 [1];  [2];  [3];  [2];  [2];  [4];  [3];  [2];  [5]
  1. Virginia Tech, Blacksburg, VA
  2. ORNL
  3. University of New South Wales, Australia
  4. Oak Ridge National Laboratory (ORNL)
  5. University of Chicago
+ Show Author Affiliations

ynchrotron light sources are routinely used to perform imaging experiments. In this paper, we review the relevant computational stages, identify bottlenecks, and highlight future opportunities to streamline data acquisition for experimental microscopy workflows. We demonstrate our preliminary exploration with an end-to-end scientific workflow on Summit based on micro-computed tomography data. Computational elements include: 1) reconstruction of volumetric image data; 2) denoising with deep neural networks; and 3) non-local means based segmentation and quantitative analysis.

Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE
DOE Contract Number:
AC05-00OR22725
OSTI ID:
1855697
Country of Publication:
United States
Language:
English

References (33)

Real-Time Data Analysis and Autonomous Steering of Synchrotron Light Source Experiments conference October 2017
Design of an image edge detection filter using the Sobel operator journal April 1988
U-Net: Convolutional Networks for Biomedical Image Segmentation
  • Ronneberger, Olaf; Fischer, Philipp; Brox, Thomas
  • Medical Image Computing and Computer-Assisted Intervention – MICCAI 2015: 18th International Conference, Munich, Germany, October 5-9, 2015, Proceedings, Part III https://doi.org/10.1007/978-3-319-24574-4_28
book November 2015
Image analysis algorithms for estimating porous media multiphase flow variables from computed microtomography data: a validation study journal February 2009
Synchrotron Big Data Science journal September 2018
Laboratory x-ray micro-computed tomography: a user guideline for biological samples journal April 2017
Critical capillary number: Desaturation studied with fast X-ray computed microtomography: MICROTOMOGRAPHY IMAGED DESATURATION journal January 2014
DAGAN: Deep De-Aliasing Generative Adversarial Networks for Fast Compressed Sensing MRI Reconstruction journal June 2018
tomoRecon: High-speed tomography reconstruction on workstations using multi-threading conference October 2012
Artifact Removal using Improved GoogLeNet for Sparse-view CT Reconstruction journal April 2018
Statistical segmentation and porosity quantification of 3D x-ray microtomography conference September 2011
Artifacts in CT: Recognition and Avoidance journal November 2004
TomoGAN: low-dose synchrotron x-ray tomography with generative adversarial networks: discussion journal January 2020
Marching cubes: A high resolution 3D surface construction algorithm journal August 1987
Fast Non-Local algorithm for image denoising conference November 2009
Evaluation of noise removal algorithms for imaging and reconstruction of vascular networks using micro-CT journal August 2016
The Watershed Transform: Definitions, Algorithms and Parallelization Strategies journal January 2000
Segmentation of microscope images of living cells journal April 2007
Insight into 3D micro-CT data: exploring segmentation algorithms through performance metrics journal August 2017
Deep Learning Accelerated Light Source Experiments conference November 2019
Segmentation of X-ray microtomography images of soil using gradient masks journal October 2010
Globus: Recent Enhancements and Future Plans conference January 2016
Segmentation of X-ray computed tomography images of porous materials: A crucial step for characterization and quantitative analysis of pore structures: X-RAY CT IMAGE SEGMENTATION journal September 2009
Data automation at light sources conference January 2019
X-ray imaging and analysis techniques for quantifying pore-scale structure and processes in subsurface porous medium systems journal January 2013
Real-time 3D imaging of Haines jumps in porous media flow journal February 2013
Developments in synchrotron x-ray computed microtomography at the National Synchrotron Light Source
  • Dowd, Betsy A.; Campbell, Graham H.; Marr, Robert B.
  • SPIE's International Symposium on Optical Science, Engineering, and Instrumentation, SPIE Proceedings https://doi.org/10.1117/12.363725
conference September 1999
Relative Permeability Calculations from Two-Phase Flow Simulations Directly on Digital Images of Porous Rocks journal September 2011
A Computational Approach to Edge Detection journal November 1986
A fast two-dimensional median filtering algorithm journal February 1979
Beyond Darcy's law: The role of phase topology and ganglion dynamics for two-fluid flow journal October 2016
Regridding reconstruction algorithm for real-time tomographic imaging journal September 2012
Image processing of multiphase images obtained via X-ray microtomography: A review journal April 2014

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