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Bibliography

The methods and software behind PoreStore's operations. If you publish results computed with PoreStore, please cite the software that produced them, as well as PoreStore.

Software

Software Used for Reference
PoreSpy pore size distribution, mercury porosimetry, chord length, radial density, porosity profile, REV porosity, SEM View and X-Ray View, Image Cleaning, STL export, connectivity analysis, interfacial area meshing, network extraction J. T. Gostick et al., J. Open Source Softw. 4 (2019) 1296. doi:10.21105/joss.01296
OpenPNM beta network validation J. Gostick et al., Comput. Sci. Eng. 18 (2016) 60–74. doi:10.1109/MCSE.2016.49
waLBerla permeability (default) M. Bauer et al., Comput. Math. Appl. 81 (2021) 478–501. doi:10.1016/j.camwa.2020.01.007
lbmpy waLBerla's LBM kernels M. Bauer, H. Köstler, U. Rüde, J. Comput. Sci. 49 (2021) 101269. doi:10.1016/j.jocs.2020.101269
Kabs permeability (Kabs Taichi) github.com/PMEAL/kabs
Taichi-LBM3D the LBM Kabs Taichi is adapted from J. Yang, Y. Xu, L. Yang, Fluids 7 (2022) 270. doi:10.3390/fluids7080270
Taichi GPU kernels for Kabs Y. Hu et al., ACM Trans. Graph. 38 (2019) 201. doi:10.1145/3355089.3356506
Palabos beta permeability (CPU, beta) J. Latt et al., Comput. Math. Appl. 81 (2021) 334–350. doi:10.1016/j.camwa.2020.03.022
LattEasy beta the Palabos set-up PoreStore's is adapted from github.com/lanl/LattEasy
XLB beta permeability (qualification only) M. Ataei, H. Salehipour, Comput. Phys. Commun. 300 (2024) 109187. doi:10.1016/j.cpc.2024.109187
Tortuosity.jl diffusivity and conductivity (default) github.com/poromics/Tortuosity.jl
TauFactor diffusivity and conductivity S. J. Cooper et al., SoftwareX 5 (2016) 203–210, doi:10.1016/j.softx.2016.09.002; S. Kench, I. Squires, S. J. Cooper, J. Open Source Softw. 8 (2023) 5358, doi:10.21105/joss.05358
ParaView ParaView Server paraview.org
PyVista, trame 3D Visualization C. B. Sullivan, A. A. Kaszynski, J. Open Source Softw. 4 (2019) 1450, doi:10.21105/joss.01450; kitware.github.io/trame
trimesh interfacial area smoothing, STL import trimesh.org
scikit-image thresholds, denoising filters, segmentation features S. van der Walt et al., PeerJ 2 (2014) e453. doi:10.7717/peerj.453
scikit-learn interactive segmentation's random forest F. Pedregosa et al., J. Mach. Learn. Res. 12 (2011) 2825–2830. jmlr.org/papers/v12/pedregosa11a
SciPy beta resizing's anti-aliasing filter and interpolation P. Virtanen et al., Nat. Methods 17 (2020) 261–272. doi:10.1038/s41592-019-0686-2

Methods

  • Archie 1942. G. E. Archie, "The electrical resistivity log as an aid in determining some reservoir characteristics," Trans. AIME 146 (1942) 54–62. doi:10.2118/942054-G. The formation factor.
  • Bear 1972. J. Bear, Dynamics of Fluids in Porous Media, American Elsevier (1972). The REV concept.
  • Berg et al. 2019. "ilastik: interactive machine learning for (bio)image analysis," Nat. Methods 16 (2019) 1226–1232. doi:10.1038/s41592-019-0582-9. The approach interactive segmentation follows.
  • Breiman 2001. "Random forests," Mach. Learn. 45 (2001) 5–32. doi:10.1023/A:1010933404324
  • Buades, Coll & Morel 2005. "A non-local algorithm for image denoising," Proc. IEEE CVPR 2005, vol. 2, 60–65. doi:10.1109/CVPR.2005.38. Non-local means. beta
  • Chambolle 2004. A. Chambolle, "An algorithm for total variation minimization and applications," J. Math. Imaging Vis. 20 (2004) 89–97. doi:10.1023/B:JMIV.0000011325.36760.1e beta
  • Epstein 1989. N. Epstein, "On tortuosity and the tortuosity factor in flow and diffusion through porous media," Chem. Eng. Sci. 44 (1989) 777–779. doi:10.1016/0009-2509(89)85053-5
  • Gostick 2017. J. T. Gostick, "Versatile and efficient pore network extraction method using marker-based watershed segmentation," Phys. Rev. E 96 (2017) 023307. doi:10.1103/PhysRevE.96.023307. SNOW. beta
  • Hildebrand & Rüegsegger 1997. "A new method for the model-independent assessment of thickness in three-dimensional images," J. Microsc. 185 (1997) 67–75. doi:10.1046/j.1365-2818.1997.1340694.x. Local thickness.
  • Hilpert & Miller 2001. "Pore-morphology-based simulation of drainage in totally wetting porous media," Adv. Water Resour. 24 (2001) 243–255. doi:10.1016/S0309-1708(00)00056-7. Morphological porosimetry.
  • Li & Lee 1993. "Minimum cross entropy thresholding," Pattern Recognit. 26 (1993) 617–625. doi:10.1016/0031-3203(93)90115-D
  • Lindblad 2005. "Surface area estimation of digitized 3D objects using weighted local configurations," Image Vis. Comput. 23 (2005) 111–122. doi:10.1016/j.imavis.2004.06.012 beta
  • McKague et al. 2025. "MAGNET: Medial Axis Guided Network Extraction Tool," InterPore J. 2 (2025) IPJ011225-7. doi:10.69631/g47x8w91 beta
  • Münch & Holzer 2008. "Contradicting geometrical concepts in pore size analysis attained with electron microscopy and mercury intrusion," J. Am. Ceram. Soc. 91 (2008) 4059–4067. doi:10.1111/j.1551-2916.2008.02736.x
  • Otsu 1979. "A threshold selection method from gray-level histograms," IEEE Trans. Syst. Man Cybern. 9 (1979) 62–66. doi:10.1109/TSMC.1979.4310076
  • Pan, Luo & Miller 2006. "An evaluation of lattice Boltzmann schemes for porous medium flow simulation," Comput. Fluids 35 (2006) 898–909. doi:10.1016/j.compfluid.2005.03.008
  • Taubin 1995. "A signal processing approach to fair surface design," Proc. SIGGRAPH '95 (1995) 351–358. doi:10.1145/218380.218473 beta
  • Tjaden, Brett & Shearing 2018. "Tortuosity in electrochemical devices: a review of calculation approaches," Int. Mater. Rev. 63 (2018) 47–67. doi:10.1080/09506608.2016.1249995
  • Torquato & Lu 1993. "Chord-length distribution function for two-phase random media," Phys. Rev. E 47 (1993) 2950–2953. doi:10.1103/PhysRevE.47.2950
  • Torquato 2002. Random Heterogeneous Materials: Microstructure and Macroscopic Properties, Springer (2002). doi:10.1007/978-1-4757-6355-3
  • Zou & He 1997. "On pressure and velocity boundary conditions for the lattice Boltzmann BGK model," Phys. Fluids 9 (1997) 1591–1598. doi:10.1063/1.869307 beta