DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Deep-learning-based workflow for boundary and small target segmentation in digital rock images using UNet++ and IK-EBM

Abstract

We report three-dimensional (3D) X-ray micro-computed tomography (μCT) has been widely used in petroleum engineering because it can provide detailed pore structural information for a reservoir rock, which can be imported into a pore-scale numerical model to simulate the transport and distribution of multiple fluids in the pore space. The partial volume blurring (PVB) problem is a major challenge in segmenting raw μCT images of rock samples, which impacts boundaries and small targets near the resolution limit. We developed a deep-learning (DL)-based workflow for accurate and fast partial volume segmentation. The DL model's performance depends primarily on the training data quality and model architecture. This study employed the entropy-based-masking indicator kriging (IK-EBM) to segment 3D Berea sandstone images as training datasets. The comparison between IK-EBM and manual segmentation using a 3D synthetic sphere pack, which had a known ground truth, showed that IK-EBM had higher accuracy on partial volume segmentation. We then trained and tested the UNet++ model, a state-of-the-art supervised encoder-decoder model, for binary (i.e., void and solid) and four-class segmentation. We compared the UNet++ with the commonly used U-Net and wide U-Net models and showed that the UNet++ had the best performance in terms of pixel-wise and physics-basedmore » evaluation metrics. Specifically, boundary-scaled accuracy demonstrated that the UNet++ architecture outperformed the regular U-Net architecture in the segmentation of pixels near boundaries and small targets, which were subjected to the PVB effect. Feature map visualization illustrated that the UNet++ bridged the semantic gaps between the feature maps extracted at different depths of the network, thereby enabling faster convergence and more accurate extraction of fine-scale features. The developed workflow significantly enhances the performance of supervised encoder-decoder models in partial volume segmentation, which has extensive applications in fundamental studies of subsurface energy, water, and environmental systems.« less

Authors:
 [1]; ORCiD logo [2]; ORCiD logo [3];  [1];  [1];  [4]; ORCiD logo [5]
  1. Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States)
  2. North Carolina State Univ., Raleigh, NC (United States)
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  4. National Energy Technology Lab. (NETL), Morgantown, WV (United States)
  5. Environmental and Ocean Engineering, Hoboken, NJ (United States)
Publication Date:
Research Org.:
National Energy Technology Laboratory (NETL), Pittsburgh, PA, Morgantown, WV, and Albany, OR (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Fossil Energy (FE)
OSTI Identifier:
1875462
Alternate Identifier(s):
OSTI ID: 1870206
Grant/Contract Number:  
FE0004000; FE0026825; AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Petroleum Science and Engineering
Additional Journal Information:
Journal Volume: 215; Journal Issue: A; Journal ID: ISSN 0920-4105
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
02 PETROLEUM; digital rock physics; partial volume blurring; image segmentation; boundary and small targets; IK-EBM; supervised deep learning; UNet++

Citation Formats

Wang, Hongsheng, Dalton, Laura, Fan, Ming, Guo, Ruichang, McClure, James E., Crandall, Dustin, and Chen, Cheng. Deep-learning-based workflow for boundary and small target segmentation in digital rock images using UNet++ and IK-EBM. United States: N. p., 2022. Web. doi:10.1016/j.petrol.2022.110596.
Wang, Hongsheng, Dalton, Laura, Fan, Ming, Guo, Ruichang, McClure, James E., Crandall, Dustin, & Chen, Cheng. Deep-learning-based workflow for boundary and small target segmentation in digital rock images using UNet++ and IK-EBM. United States. https://doi.org/10.1016/j.petrol.2022.110596
Wang, Hongsheng, Dalton, Laura, Fan, Ming, Guo, Ruichang, McClure, James E., Crandall, Dustin, and Chen, Cheng. Wed . "Deep-learning-based workflow for boundary and small target segmentation in digital rock images using UNet++ and IK-EBM". United States. https://doi.org/10.1016/j.petrol.2022.110596. https://www.osti.gov/servlets/purl/1875462.
@article{osti_1875462,
title = {Deep-learning-based workflow for boundary and small target segmentation in digital rock images using UNet++ and IK-EBM},
author = {Wang, Hongsheng and Dalton, Laura and Fan, Ming and Guo, Ruichang and McClure, James E. and Crandall, Dustin and Chen, Cheng},
abstractNote = {We report three-dimensional (3D) X-ray micro-computed tomography (μCT) has been widely used in petroleum engineering because it can provide detailed pore structural information for a reservoir rock, which can be imported into a pore-scale numerical model to simulate the transport and distribution of multiple fluids in the pore space. The partial volume blurring (PVB) problem is a major challenge in segmenting raw μCT images of rock samples, which impacts boundaries and small targets near the resolution limit. We developed a deep-learning (DL)-based workflow for accurate and fast partial volume segmentation. The DL model's performance depends primarily on the training data quality and model architecture. This study employed the entropy-based-masking indicator kriging (IK-EBM) to segment 3D Berea sandstone images as training datasets. The comparison between IK-EBM and manual segmentation using a 3D synthetic sphere pack, which had a known ground truth, showed that IK-EBM had higher accuracy on partial volume segmentation. We then trained and tested the UNet++ model, a state-of-the-art supervised encoder-decoder model, for binary (i.e., void and solid) and four-class segmentation. We compared the UNet++ with the commonly used U-Net and wide U-Net models and showed that the UNet++ had the best performance in terms of pixel-wise and physics-based evaluation metrics. Specifically, boundary-scaled accuracy demonstrated that the UNet++ architecture outperformed the regular U-Net architecture in the segmentation of pixels near boundaries and small targets, which were subjected to the PVB effect. Feature map visualization illustrated that the UNet++ bridged the semantic gaps between the feature maps extracted at different depths of the network, thereby enabling faster convergence and more accurate extraction of fine-scale features. The developed workflow significantly enhances the performance of supervised encoder-decoder models in partial volume segmentation, which has extensive applications in fundamental studies of subsurface energy, water, and environmental systems.},
doi = {10.1016/j.petrol.2022.110596},
journal = {Journal of Petroleum Science and Engineering},
number = A,
volume = 215,
place = {United States},
year = {Wed May 04 00:00:00 EDT 2022},
month = {Wed May 04 00:00:00 EDT 2022}
}

Works referenced in this record:

Image thresholding by indicator kriging
journal, July 1999

  • Wonho Oh, ; Lindquist, B.
  • IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 21, Issue 7
  • DOI: 10.1109/34.777370

Temporal evolution of pore geometry, fluid flow, and solute transport resulting from colloid deposition: TEMPORAL EVOLUTION OF PORE GEOMETRY FROM COLLOID DEPOSITION
journal, June 2009

  • Chen, Cheng; Lau, Boris L. T.; Gaillard, Jean-François
  • Water Resources Research, Vol. 45, Issue 6
  • DOI: 10.1029/2008WR007252

Pore scale investigation of hydrogen injection in sandstone via X-ray micro-tomography
journal, October 2021

  • Jha, Nilesh Kumar; Al-Yaseri, Ahmed; Ghasemi, Mohsen
  • International Journal of Hydrogen Energy, Vol. 46, Issue 70
  • DOI: 10.1016/j.ijhydene.2021.08.042

Digital rock physics benchmarks—part II: Computing effective properties
journal, January 2013


Segmentation of digital rock images using deep convolutional autoencoder networks
journal, May 2019


Benchmarking conventional and machine learning segmentation techniques for digital rock physics analysis of fractured rocks
journal, January 2022

  • Reinhardt, Marcel; Jacob, Arne; Sadeghnejad, Saeid
  • Environmental Earth Sciences, Vol. 81, Issue 3
  • DOI: 10.1007/s12665-021-10133-7

Active contours without edges
journal, January 2001

  • Chan, T. F.; Vese, L. A.
  • IEEE Transactions on Image Processing, Vol. 10, Issue 2
  • DOI: 10.1109/83.902291

Unsupervised Learning of Image Segmentation Based on Differentiable Feature Clustering
journal, January 2020

  • Kim, Wonjik; Kanezaki, Asako; Tanaka, Masayuki
  • IEEE Transactions on Image Processing, Vol. 29
  • DOI: 10.1109/TIP.2020.3011269

CNN Explainer: Learning Convolutional Neural Networks with Interactive Visualization
journal, February 2021

  • Wang, Zijie J.; Turko, Robert; Shaikh, Omar
  • IEEE Transactions on Visualization and Computer Graphics, Vol. 27, Issue 2
  • DOI: 10.1109/TVCG.2020.3030418

Digital rock physics benchmarks—Part I: Imaging and segmentation
journal, January 2013


Cell Shape Dynamics: From Waves to Migration
journal, March 2012


Methods to measure contact angles in scCO2-brine-sandstone systems
journal, December 2018


ML-LBM: Predicting and Accelerating Steady State Flow Simulation in Porous Media with Convolutional Neural Networks
journal, April 2021


UNet++: Redesigning Skip Connections to Exploit Multiscale Features in Image Segmentation
journal, June 2020

  • Zhou, Zongwei; Siddiquee, Md Mahfuzur Rahman; Tajbakhsh, Nima
  • IEEE Transactions on Medical Imaging, Vol. 39, Issue 6
  • DOI: 10.1109/TMI.2019.2959609

Three-dimensional measurement of fractures in heterogeneous materials using high-resolution X-ray computed tomography
journal, October 2010

  • Ketcham, Richard A.; Slottke, Donald T.; Sharp, Jack M.
  • Geosphere, Vol. 6, Issue 5
  • DOI: 10.1130/GES00552.1

Adaptive Thresholding using the Integral Image
journal, January 2007


Development of a Digital Rock Physics workflow for the analysis of sandstones and tight rocks
journal, July 2017


Processing of rock core microtomography images: Using seven different machine learning algorithms
journal, January 2016


Prediction of Porosity and Permeability Alteration Based on Machine Learning Algorithms
journal, March 2019


Accurate Measurement of Small Features in X‐Ray CT Data Volumes, Demonstrated Using Gold Grains
journal, April 2019

  • Ketcham, R. A.; Mote, A. S.
  • Journal of Geophysical Research: Solid Earth, Vol. 124, Issue 4
  • DOI: 10.1029/2018JB017083

Enhancement of oil recovery by emulsion injection: A pore scale analysis from X-ray micro-tomography measurements
journal, March 2021

  • Scheffer, Kamila; Méheust, Yves; Carvalho, Marcio S.
  • Journal of Petroleum Science and Engineering, Vol. 198
  • DOI: 10.1016/j.petrol.2020.108134

The Sensitivity of Estimates of Multiphase Fluid and Solid Properties of Porous Rocks to Image Processing
journal, December 2019


The role of the spatial heterogeneity and correlation length of surface wettability on two-phase flow in a CO2-water-rock system
journal, December 2020


A Novel Experimental Study on Density‐Driven Instability and Convective Dissolution in Porous Media
journal, November 2021

  • Guo, Ruichang; Sun, Hanxing; Zhao, Qingqi
  • Geophysical Research Letters, Vol. 48, Issue 23
  • DOI: 10.1029/2021GL095619

SegNet: A Deep Convolutional Encoder-Decoder Architecture for Image Segmentation
journal, December 2017

  • Badrinarayanan, Vijay; Kendall, Alex; Cipolla, Roberto
  • IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 39, Issue 12
  • DOI: 10.1109/TPAMI.2016.2644615

Micro-computed tomography pore-scale study of flow in porous media: Effect of voxel resolution
journal, September 2016


Digital Rock Segmentation for Petrophysical Analysis With Reduced User Bias Using Convolutional Neural Networks
journal, February 2020

  • Niu, Yufu; Mostaghimi, Peyman; Shabaninejad, Mehdi
  • Water Resources Research, Vol. 56, Issue 2
  • DOI: 10.1029/2019WR026597

Linking Morphology of Porous Media to Their Macroscopic Permeability by Deep Learning
journal, October 2019

  • Kamrava, Serveh; Tahmasebi, Pejman; Sahimi, Muhammad
  • Transport in Porous Media, Vol. 131, Issue 2
  • DOI: 10.1007/s11242-019-01352-5

Deep neural networks for improving physical accuracy of 2D and 3D multi-mineral segmentation of rock micro-CT images
journal, June 2021


Pore-scale analysis of permeability reduction resulting from colloid deposition: COLLOID DEPOSITION REDUCES PERMEABILITY
journal, April 2008

  • Chen, Cheng; Packman, Aaron I.; Gaillard, Jean-François
  • Geophysical Research Letters, Vol. 35, Issue 7
  • DOI: 10.1029/2007GL033077

Entropy-assisted image segmentation for nano- and micro-sized networks: ENTROPY-ASSISTED IMAGE SEGMENTATION
journal, December 2015

  • Kim, D.; Choi, J.; Nam, J.
  • Journal of Microscopy, Vol. 262, Issue 3
  • DOI: 10.1111/jmi.12362

Contact Angle Measurements Using Sessile Drop and Micro-CT Data from Six Sandstones
journal, May 2020

  • Dalton, Laura E.; Tapriyal, Deepak; Crandall, Dustin
  • Transport in Porous Media, Vol. 133, Issue 1
  • DOI: 10.1007/s11242-020-01415-y

Deep Convolutional Neural Networks for Computer-Aided Detection: CNN Architectures, Dataset Characteristics and Transfer Learning
journal, May 2016

  • Shin, Hoo-Chang; Roth, Holger R.; Gao, Mingchen
  • IEEE Transactions on Medical Imaging, Vol. 35, Issue 5
  • DOI: 10.1109/TMI.2016.2528162

Application of high resolution X-ray computed tomography to mineral deposit origin, evaluation, and processing
journal, March 2015


PoreFlow-Net: A 3D convolutional neural network to predict fluid flow through porous media
journal, April 2020


3D-visualization and analysis of macro- and meso-porosity of the upper horizons of a sodic, texture-contrast soil
journal, June 2007


Fuzzy c-means clustering with spatial information for image segmentation
journal, January 2006


Acquisition, optimization and interpretation of X-ray computed tomographic imagery: applications to the geosciences
journal, May 2001


Pore-scale characteristics of multiphase flow in porous media: A comparison of air–water and oil–water experiments
journal, February 2006


NIH Image to ImageJ: 25 years of image analysis
journal, June 2012

  • Schneider, Caroline A.; Rasband, Wayne S.; Eliceiri, Kevin W.
  • Nature Methods, Vol. 9, Issue 7
  • DOI: 10.1038/nmeth.2089

Classification and quantification of pore shapes in sandstone reservoir rocks with 3-D X-ray micro-computed tomography
journal, January 2016

  • Schmitt, Mayka; Halisch, Matthias; Müller, Cornelia
  • Solid Earth, Vol. 7, Issue 1
  • DOI: 10.5194/se-7-285-2016

Deep semantic segmentation of natural and medical images: a review
journal, June 2020

  • Asgari Taghanaki, Saeid; Abhishek, Kumar; Cohen, Joseph Paul
  • Artificial Intelligence Review, Vol. 54, Issue 1
  • DOI: 10.1007/s10462-020-09854-1

Deep residual U-net convolution neural networks with autoregressive strategy for fluid flow predictions in large-scale geosystems
journal, April 2021