Computers & Geosciences 156 (2021) 104895

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Computers and Geosciences

journal homepage: www.elsevier.com/locate/cageo

Characterization of pore and grain size distributions in porous geological

samples – An image processing workflow
Hossein Safari a, Bruce J. Balcom b, Armin Afrough c, *
a
Reservoir Studies Division, Pars Petro Zagros Engineering & Services Company, 42 38th St, JahanAra Ave, Tehran, Iran
b
MRI Research Centre, University of New Brunswick, 8 Bailey Dr, Fredericton, E3B 9K6 NB, Canada
c
The Danish Hydrocarbon Research and Technology Centre, Technical University of Denmark, Kongens Lyngby 2800, Denmark

A R T I C L E I N F O A B S T R A C T

Keywords: An image processing workflow is presented for the characterization of pore and grain size distributions in porous
X-ray microcomputed tomography (μCT) geological samples from X-ray microcomputed tomography (μCT) and scanning electron microscopy (SEM)
Scanning electron microscopy (SEM) images. The pore and grain size distributions of five sandstone samples including Berea, Buff Berea, Nugget,
Pore size distribution
Castlegate, and Bentheimer, and one carbonate sample, Indiana limestone, are extracted using the proposed
Grain size distribution
Image processing
workflow. Two-dimensional size distributions acquired from SEM images were found to be biased toward smaller
Rocks sizes misrepresenting the actual 3D distributions. Stereological techniques unfolded the measured 2D size dis­
Porous materials tributions from SEM images to 3D distributions comparable with μCT results. While larger pores and grains can
easily be detected from μCT and SEM images, the quantification of small-scale heterogeneities is severely
influenced by their limits of resolution. We show that microstructural details resolved by SEM can significantly
impact the pore and grain size distributions in sandstone and carbonate rock samples. For example, SEM-resolved
microporosities in Indiana limestone result in bimodal distributions of pore and grain sizes, whereas μCT ob­
servations exhibit unimodal distributions. The acquired images and processed results are openly available and
may be used by researchers investigating image processing, magnetic resonance relaxation or fluid flow simu­
lations in natural rocks. The proposed methodology can be implemented to process μCT and SEM images of
natural rocks as well as other types of porous materials.

1. Introduction on macroscopic properties has been studied in a broad range of physical

The characterization of pore and particle/crystal/grain size distri­
butions in porous materials has a broad spectrum of applications in
geosciences (Berger et al., 2011; Ghasemi et al., 2018; Roostaei et al.,
2020; Srisutthiyakorn and Mavko, 2019), sedimentology (Gaafar et al.,
2014; Palavecino et al., 2018), petroleum engineering (Burdine, 1953;
Luo et al., 2019; Song et al., 2019, 2019b; Tian et al., 2019), chemical
engineering (Bardestani et al., 2019; Kenvin et al., 2015; Occelli et al.,
2003), and biomedical sciences (Bagherzadeh et al., 2013; Bartoš et al.,
2018; Udenni Gunathilake et al., 2017). In the context of rock physics,
the transport and mechanical properties of rocks are strongly influenced
by the size and arrangement of their pores and grains, respectively. Most
naturally occurring geological materials are composed of heterogeneous
and complex pore and grain structures. The pore size distribution is used
as a key measure in many engineering calculations to quantify the
complex geometry of the pore space. The impact of pore size distribution
processes, for example in the multiphase flow in porous media (Yang
et al., 2016), permeability estimation in hydrate-bearing sediments
(Minagawa et al., 2009), phase transition in nanoconfined fluids (Luo
et al., 2019), propagation of wormholes in reactive fluid transport
(Dubetz et al., 2016), compressive strength of cementitious materials
(Jin et al., 2021), and particle diffusion in filamentous biopolymer
networks (Mickel et al., 2008).
The description of particle, crystal, and grain size distributions is of
significant practical importance in various fields aiming to understand
and characterize components of microstructures (Berger et al., 2011;
Higgins, 2000; Roostaei et al., 2020). The particle size distribution is
used amongst others in soil sciences for soil classification, the estimation
of soil hydraulic properties, and evaluation of depositional history of
transported soils (Roostaei et al., 2020). Crystal and grain size distri­
butions are used to quantify the texture of solid rocks, characterize
sediments based on their depositional environments, and control sand

* Corresponding author.
E-mail address: armafr@dtu.dk (A. Afrough).

https://doi.org/10.1016/j.cageo.2021.104895
Received 23 March 2021; Received in revised form 28 June 2021; Accepted 20 July 2021
Available online 26 July 2021
0098-3004/© 2021 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
H. Safari et al.
production in wellbores drilled in unconsolidated and consolidated
sandstone rocks (Ghasemi et al., 2018; Higgins, 2000; Srisutthiyakorn
and Mavko, 2019).
Various experimental methods have been developed for analyzing
the pore and grain size distributions in porous rocks over the years.
Practical methods for determining the grain size distribution include
sieve analysis, laser diffraction, point-count method, and more recently
the dynamic image analysis method (Roostaei et al., 2020; Srisutthiya­
korn and Mavko, 2019). Although these methods are widely used for
determining the particle size and shape in unconsolidated materials,
they cannot be applied to consolidated porous media (Ghasemi et al.,
2018). Experimental methods for measuring the pore size distribution
include mercury injection porosimetry (MIP) for the pore throat size
distribution, nitrogen adsorption isotherms for the pore body size dis­
tribution of micropores, and nuclear magnetic resonance (NMR) for the
pore body size distribution (Afrough et al., 2019; Arns, 2004; Kruschwitz
et al., 2020; Shuaibing Song et al., 2019). These methods normally
require the injection of a fluid phase into porous samples and mostly
describe the spatial distribution of connected pore space. As a result,
disconnected pore structures which might become reconnected in pro­
cesses such as reactive fluid transport still remain undetected (Al-Khu­
laifi, 2018).
The emergence of X-ray microcomputed tomography (μCT) as a non-
invasive and non-destructive method along with recent improvements in
the computational power has made it possible to visualize the internal
structure of porous materials. The μCT scanning techniques have been
broadly used to characterize the geometrical structure of pore, grain,
and mineral phases in rock samples (Arns, 2004; Elkhoury et al., 2019;
Ghasemi et al., 2018; Lai et al., 2015; Schmitt et al., 2015; Srisutthiya­
korn and Mavko, 2019; Zhang et al., 2018). The resolution of 3D scans is
directly proportional to the sample size, beam quality, and specifications
of the detector (Blunt et al., 2013). The true resolution of μCT systems is
limited to approximately 0.3 μm in projection imaging, in comparison
with a sub-50 nm imaging resolution in lens-based X-ray CT systems
(Withers, 2007). High-resolution scans can reveal submicron textures
and heterogeneities in porous materials at the cost of significant sample
size reduction (Bai et al., 2013; Blunt et al., 2013). Scanning electron
microscopy (SEM) is another method widely employed in describing the
submicron structure of porous materials. SEM offers high-resolution
images with limited field of views (FOVs) that could be used in the
characterization of small-scale heterogeneities in natural rocks. SEM, in
the backscattered electron detection mode, can observe compositional
variations with a lateral spatial resolution of approximately 10–100 nm
depending on the specimen composition and the beam energy selected
(Goldstein et al., 2018). Two-dimensional SEM images have been mostly
considered as a qualitative tool and their quantitative analysis to obtain
pore and grain size distributions have been limited (Song et al., 2019; S.
Song et al., 2019b; Zhang et al., 2015).
Two-dimensional size distributions obtained from SEM images do
not represent the actual 3D distributions because of the sectioning bias
(Liu et al., 2020; Reppel and Weinberg, 2019; Song et al., 2019b). Sri­
sutthiyakorn and Mavko (2019) presented a general approach for con­
verting 2D grain size distributions acquired from thin section images to
3D distributions by providing a forward solution to the Wicksell’s
corpuscle problem. They obtained transformation matrices relating 2D
(from CT slices) to 3D grain size distributions using μCT images of
natural rocks. We show in this study how their method could fail when
inherent microstructures in porous rocks are not properly resolved in
μCT images. A variety of methods have been presented in the literature
for the characterization of pore and grain size distribution in porous
geological samples. However, proposed methodologies are limited from
one image processing environment to another and are not checked
against several other methods and several samples. Therefore, a general
image processing workflow that could be applied to both 2D and 3D
images of rock samples for quantitative analysis of pore and grain size
distributions is still lacking.
2
Computers and Geosciences 156 (2021) 104895
In this work, we propose an image processing workflow for
extracting pore and grain size distributions of natural rocks from X-ray
microcomputed tomography and scanning electron microscopy images.
We employ stereological techniques to convert 2D distributions ob­
tained from SEM images to 3D distributions comparable with μCT re­
sults. While most commercial image processing software do not offer
stereological algorithms, this study emphasizes the role of stereology in
obtaining representative pore and grain size distributions from 2D SEM
images. Pore and grain size distributions are presented in terms of
volumetric probabilities as opposed to frequency- and count-based
methods. Volume fractions are of significant importance in engineer­
ing and theoretical calculations concerning aquifer capacity, distribu­
tion of fluid saturations in oil reservoirs, and geo-mechanical properties
of rocks. The pore and grain size distribution of six common
commercially-accessible rock samples, including five sandstones and
one carbonate, are investigated. The rock samples span a variety of rock
types with different and similar pore and grain size distributions and are
used by researchers worldwide in their verifying of measurement
methods, such as in magnetic resonance relaxation (Afrough et al., 2019;
Arns, 2004). The algorithms presented in this study could directly be
applied or easily extended to other porous materials. The acquired im­
ages and obtained results can also be used by those processing μCT and
SEM images, analyzing magnetic resonance relaxation, or those per­
forming fluid flow simulation in rocks.
2. Material and methods
2.1. Description of rock samples
Five different sandstone samples including Berea (BA), Nugget (NU),
Buff Berea (BB), Castlegate (CG), and Bentheimer (BT), and one car­
bonate sample, Indiana Limestone (IL), were acquired from Kocurek
Industries (Caldwell, TX, USA). The selected rock samples present a wide
range of pore and grain size distributions.
Berea and Buff Berea samples are Upper Devonian grain-supported
sandstones from the Kipton formation. Porosity of the Berea sample
ranges from 18 to 21 percent, while Buff Berea has slightly higher po­
rosities ranging from 20 to 22 percent. Castlegate is a Late Cretaceous
sandstone sample from the Price River formation of Mesaverde group
which has a porosity ranging from 26 to 29 percent. Nugget is a Late
Triassic heterogeneous sandstone sample from the Utah formation
which compared to other samples has a lower porosity ranging from 10
to 15 percent. Bentheimer is a well-sorted Valaginian sandstone from the
Germany formation and has a porosity ranging between 21 and 26
percent. The sandstone samples are composed dominantly of quartz,
with other present minerals being feldspar, clays, and sometimes calcite
(Afrough et al., 2017; Dalton et al., 2020).
Indiana limestone is a Mississippian fossiliferous limestone from the
Salem limestone formation in the Bedford-Bloomington area which is
mainly composed of calcite (more than 97 %) with minor amounts of
other minerals, such as alumina, iron oxide, silica, and magnesite pre­
sent (Ji et al., 2012). Its porosity with a bimodal pore size distribution is
characterized by intergranular micro-connected macropores and ranges
between 12 and 19 percent.
2.2. X-ray microcomputed tomography
Standard 1.5 inch core plugs were cut into 2–3 mm thick slabs. Small
samples were chipped from these slabs and installed on stubs by glue.
These samples had varying dimensions approximately close to 2 × 2 × 4
mm3, but were not perfectly shaped. High-resolution μCT images were
acquired using a Skyscan 1072 system at the Microscopy and Micro­
analysis Facility of the University of New Brunswick in Fredericton,
Canada. Some of the samples were slightly larger than the field of view
and were imaged in the region of interest imaging mode. Imaging was
performed with a tube voltage of 91 kV and a source current of 110 μA
H. Safari et al. Computers and Geosciences 156 (2021) 104895

with a 1-mm aluminum filter. Source-to-object distance (SOD) was set to

29.73 mm. Samples were rotated one step at a time (0.9◦ ) through 360◦
and 16-bit images were recorded at each rotation step with a 1024 ×
1024 detector. The 3D reconstruction of X-ray radiographs was per­
formed with the Skyscan volumetric reconstruction program “NRecon”
(Version: 1.6.4.8) with a voxel size of 2.7 μm/pixel.

2.3. Scanning electron microscopy

For SEM observations, resin-impregnated samples were cut, grinded,

and polished to prepare thin sections. Imaging was performed by a JEOL
6400 scanning electron microscope operating at a voltage of 15 kV. All
SEM micrographs were acquired in the backscattered electron mode.
Prepared thin sections were scanned at different FOVs and between
twelve to nineteen 4096 × 4096 16-bit images were acquired for each
sample. Table 1 summarizes the typical resolution of the SEM images
captured for each sample. The resolution scales are fixed for all the
images acquired from each thin section sample except for Berea sand­
stone which has a few images captured at different magnifications.

3. Image processing workflow

The Avizo image processing software (Thermo Fisher Scientific, V.

2019.1) was employed in analyzing the 3D reconstructed μCT images of
the rock samples. For SEM images, a similar procedure was followed by
developing a computer program in the Python programming language.

3.1. X-ray microcomputed tomography

The acquired 16-bit images were first converted into 8-bit images
and their beam hardening and region of interest imaging artifacts were
corrected. The maximum possible rectangular sub-volumes were
extracted from each image for the quantification of the samples’ pore
and grain size distributions (see Appendix). Fig. 1 shows the general
workflow employed in this study for analyzing the μCT images. To
improve the signal-to-noise ratio, a 2D edge-preserving non-local means
filter was applied on every slice in the xy-plane. Two-dimensional,
instead of 3D, non-local means filtering was employed because of the
poor computational performance of the 3D filter in Avizo, even in the
GPU-processing mode. Table 2 summarizes the non-local means filter
settings along with other image parameters including image resolution,
and dimensions of the extracted sub-volumes. The pore size distribution
was not very sensitive to the variation of the search window size in the
non-local means filtering.
In the next step, we applied image segmentation techniques to
segment each gray-scale image into two binary images representing the
pores and grains of the rock samples. This is the most crucial step as it
affects all the subsequent quantitative analysis. Although a variety of
segmentation algorithms have been proposed in the literature, global
thresholding technique is still the most commonly applied approach in
porous media research (Iassonov et al., 2009). Automatic thresholding
algorithms such as Otsu’s method (Otsu, 1979) tended to over-segment
the gray-scale images in almost all the samples. This could be attributed
to their sensitivity to partial volume effects arising from the unresolved
sub-resolution features and limited contrast-to-noise ratio in μCT images
(Sheppard et al., 2014). An interactive thresholding procedure with
immediate visual feedback was found to provide more accurate and
consistent segmentation results. However, manual thresholding still
remains labor intensive and might introduce some operator bias.
Having performed image segmentation, a Euclidean distance
Table 1
Typical resolution scales of the captured SEM images for each sample.
Samples NU CG BT BB BA IL
Fig. 1. The general workflow employed in the extraction of pore and grain size
distributions from μCT images. An edge-preserving non-local means filter is
applied for denoising purposes and the filtered images are segmented into two
binary images representing pores and grains. A Euclidean distance transform is
applied on the binary images which is then masked by a medial axis transform.
An H-maxima filter is applied on the masked distance map to obtain markers for
watershed segmentation. The labeled images from the watershed algorithm are
used to obtain volumetric pore and grain size distributions. Each side of a cube
is 675 μm.
transform was applied to the segmented images of pores and grains. A
medial axis transform was applied to binary images to extract connected
voxel skeletons which was then used to mask the calculated distance
maps. An H-Maxima filter was applied on the new distance map to find
the peaks in every region. The calculated peaks were passed as seeds to a
marker-based watershed segmentation algorithm to provide labeled
images for pore and grain volumes. Segmented regions were analyzed
and equivalent diameters, defined as the diameter of a sphere of the
same volume as that of a segmented region, were calculated. Therefore,
the term diameter in the context of pore and grain diameters is referring
to the equivalent diameter throughout this paper. These spheres with
varying equivalent diameters are represented as nodes in the generated
pore and grain network models. Volumetric probability functions for
pore and grain size distributions were calculated using the regional
volumes and their respective equivalent diameters.

Resolution (μm) 0.406 0.406 0.338 0.406 0.239 0.406

3
H. Safari et al. Computers and Geosciences 156 (2021) 104895

Table 2
Parameters of the μCT images including their resolution, the dimensions of extracted sub-volumes, and the non-local means filter settings for each sample.
Parameters NU CG BT BB BA IL

Resolution (μm) 2.7 2.7 2.7 2.7 2.7 2.7

Size (voxels) 528 × 281 × 433 × 603 × 378 × 406 × 584 × 584 × 664 × 400 × 628 × 320 ×
700 794 520 600 700 519
Non-Local Means Filter Search Window (pixels) 10 10 10 5 5 10
(2D) Local Neighbourhood 3 3 3 3 3 3
(pixels)
Similarity Value 0.6 0.6 0.6 0.6 0.6 0.6

3.2. Scanning electron microscopy

A computer program was developed in Python for quantitative

analysis and processing of all the 2D SEM images captured at different
FOVs from the prepared thin section samples. This program integrates
pore and grain size distributions from several fields of view and unfolds
the resulting 2D size distribution to a 3D size distribution for each
sample.
The “ncempy” module was first imported to load the metadata from
DM4 files into Python. Image data and magnification scales were then
extracted from all the captured views. Next, a nonlocal-means filter from
the skimage library was employed with a patch size and patch distance
of 3 to denoise all the SEM images. Backscattered SEM images provided
sufficient contrast to observe the mineral phases present in the rock
samples. Quartz, feldspar, and clays were the dominant minerals present
in sandstone samples, while for Indiana limestone, calcite was the only
mineral phase. A multiphase automatic segmentation was performed on
SEM images employing a fast multi-Otsu thresholding algorithm
developed by Liao et al. (2001). The method provides universal
threshold values by maximizing the inter-class variances. Unlike μCT
images, automatic segmentation algorithms provide fairly accurate re­
sults in SEM images due to limited partial volume effects and good
contrast-to-noise ratio. Sandstone samples were segmented into four
different phases consisting of pores and three main minerals namely
quartz, feldspar, and clays. Indiana limestone was segmented into two
phases representing pores and solids (dominated by calcite). Fig. 2
shows the general workflow employed for the extraction of pore and
grain size distributions from SEM images.
Similar to the μCT workflow, an H-Maxima filter was applied to the
masked distance maps of pores and grains to find markers for watershed
segmentation. However, resolved microstructural details in SEM images
resulted in homogeneous distance maps with spurious local maxima,
with ridges and plateaus, leading to an over-segmented watershed. To
solve this problem, the methodology proposed by Gostick (2017) was
used to dilate the distance maps by trimming the saddle points and
nearby peaks with a cubic structuring element. The new markers were
passed into the watershed algorithm to generate labeled images for
pores and grains. Although dilation of distance maps resulted in lesser
bisection of larger regions, several pores and grains appear to have been Fig. 2. The general workflow used for the extraction of pore and grain size
labeled incorrectly as shown in Fig. 2 (e, f). Despite the improved image distributions from SEM images, (a) backscattered SEM images of resin-
processing procedures employed in this study, automatic segmentation impregnated sandstones. The pore space is black, quartz is medium gray,
still remains challenging and a few segmentation errors are inevitable feldspar is white, and clays are dark gray, (b) multiphase segmentation of
minerals and the pore space, (c), (d) a distance transform performed on the pore
(Sheppard et al., 2014). The “regionprops” method from the “measure”
and grain space, respectively (e), (f) the watershed segmentation of pores and
module of the “skimage” library was then used to analyze the regions
grains, respectively, using markers obtained from dilated distance maps. The
labeled by the watershed algorithm. The areas of regions were obtained
scale bar is equivalent to 500 μm.
by summing the pixels in each region and equivalent diameters of circles
with the same area as the regions were calculated afterwards. Using
sectioning bias. Stereological solutions to this problem are categorized
regional areas and their respective equivalent diameters, area-weighted
into two classes of (1) direct methods, for which no shape and size
probability functions were obtained for the pore and grain size
distributions are assumed, and (2) indirect methods, in which a few
distributions.
assumptions are necessary (Higgins, 2015). Although direct methods
provide more precise size distributions, they are rarely employed mainly
3.3. Stereological unfolding of 2D distributions to 3D
due to their requirements of many closely obtained serial sections from
the 3D object. In most cases, only a few slices are available or could be
The pore and grain size distributions obtained from 2D SEM images
obtained from the 3D structure, hence leaving the indirect methods as
do not represent the actual 3D distributions, mainly because of the

4
H. Safari et al.
the only viable solution (Higgins, 2015).
Stereological techniques have been widely used to obtain volume
fractions and 3D particle size distributions from measurements per­
formed on 2D cross-sections (Berger et al., 2011; Jutzeler et al., 2012;
Reppel et al., 2019). A classical problem in stereology which addresses
the unfolding of size distributions from 2D to 3D is the well-known
Wicksell’s corpuscle problem in which Wicksell investigated the size
distribution of spherical corpuscles in the human spleen (Reppel and
Weinberg, 2019; Srisutthiyakorn and Mavko, 2019; Wicksell, 1925). In
this study, we employed the methodology proposed by Sahagian and
Proussevitch (1998) for poly-dispersed spherical particles to unfold the
population of 2D diameters obtained from processing SEM images into
3D size distributions. Their technique is applicable to any particle size or
size distribution regardless of the lognormality of distribution. Fig. 3
provides a simplified representation of the stereological unfolding
process.
In Fig. 3, the occurrence frequency ϕ, for spherical particles with
radius R intersecting with circles of radius r is:
Fig. 3. Stereological unfolding of 2D size distributions from SEM images to 3D
distributions, (a) typical backscattered SEM images of resin-impregnated
sandstone thin sections, (b) binary segmentation of the rock matrix and the
pore space. The pore space is filled with inscribed circles of various radii, (c) a
representation of the Wicksell’s corpuscle problem indicating the likelihood of a
certain circular region of radius r intersecting with a sphere of radius R, (d)
stereological conversion of 2D size distributions (NA) obtained from 2D cross-
sections to 3D distributions (Nv) comparable with those of μCT images. While
2D size distributions always show large negative skewness toward smaller sizes,
the occurrence probability of most of the small pores almost disappears during
stereological conversion to 3D size distributions. The scale bar is equivalent to
500 μm. The inscribed circles are for demonstration only; an equivalent
diameter definition is employed in the rest of the manuscript.
5
Computers and Geosciences 156 (2021) 104895
r
ϕ(r) = √̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅ (1)
R2 − r 2
Employing the workflow described in section 3.2, 2D pore and grain
size distributions are obtained from the SEM images taken at different
FOVs. Then, for each bin in the 2D size distribution histogram, the
number of particles per unit volume Nvi (or 3D size distribution) is
directly calculated from the number of sections per unit area NAi (or 2D
size distribution) via the following formulations:
(
i−∑
1
)
1
Nvi = ’ α1 NAi − αj+1 NA(i− j) (2)
Hi j=1
( )
1 ∑
i− 2
αi = α1 Pi − αj+1 Pi− (3)
P1 j=1
j
where i = 1, .., n with n being the number of bins in the histogram, Hi is
′
the mean projected height which is equal to 1 for spherical particles, α1
is the conversion coefficient of the first class, and P represents the cross-
section size probabilities. The probability of a particular class in the
cross section with radius r (r1 < r < r2 ) intersecting with a sphere of
radius R is given by:
√̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅ √̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅
1
P(r|R) = ( (R2 − r21 ) − (R2 − r22 )) (4)
R
where r1 and r2 are the lower and upper limits of the classes in 2D his­
togram, respectively. Mathematical details of the above formulations
could be found in the work of Sahagian and Proussevitch (1998).
The “GrainSize Tools” Python scripts developed by Lopez-Sanchez
(2018) for grain size analysis were modified to account for the volu­
metric probabilities and employed in this study to calculate 3D distri­
butions of pore and grain sizes from 2D distributions.
4. Results and discussion
Fig. 4 shows the 3D gray-scale reconstruction of carbonate and
sandstone samples used in this study for the characterization of pore and
grain size distributions along with their segmented pore and grain
spaces. Berea, Buff Berea, and Castlegate sandstone samples have similar
pore and grain structures. Nugget has smaller pore sizes compared to
other samples, while pore and grain sizes in Bentheimer are visibly
larger. The backscattered SEM images and their multiphase segmenta­
tion results shown in Fig. 5 provide a 2D impression of the inherent
structures of pores, grains, and minerals specific to each rock sample.
The relatively low contrast of μCT images and the close gray levels of
clay minerals and pores made it difficult to appropriately segment clays
in sandstone samples imaged by our instrument. Other researchers have
successfully segmented clay minerals from the surrounding pore space
by acquiring high-contrast μCT images (Cnudde et al., 2011; Lai et al.,
2015). However, in most cases the microporosities in clay minerals are
not resolved. In contrast to μCT images, SEM images provided sufficient
contrast to observe various minerals as well as small-scale heterogene­
ities in rock samples.
SEM observations show that sandstone samples are predominantly
composed of moderately well-sorted quartz grains and small amounts of
feldspar and clays. Clay minerals are distributed either as thin layers on
other minerals’ surfaces or as agglomerates filling the pore space. Ben­
theimer featured weathered feldspar grains that were consistently
observed in μCT images and also by light microscopy.
Indiana limestone shows a monomineralic texture predominantly
composed of calcite with allochems such as fossils and ooids constituting
a major fraction of the solid structure. SEM images reveal a high con­
centration of microporosity regions at the boundaries of allochems
which account for the connectivity of larger macropores throughout the
structure. These microporosity details are not resolved in μCT images
H. Safari et al.
Fig. 4. The 2D and 3D gray-scale reconstruction of sandstone and carbonate
samples and their segmented pore and grain space. Berea, Buff Berea, and
Castlegate have similar pore and grain structures. Nugget shows smaller pore
sizes, whereas the pore and grain sizes of Bentheimer are clearly larger. It is
difficult to distinguish clay minerals in sandstone samples due to their gray
level that is similar to that of the pore space. The intermediate gray levels in
Indiana limestone represent unresolved microporosity regions in the recon­
structed μCT image. Each side of the cubes (slices) has a length and size of 250
voxels (pixels) and 675 μm, respectively.
and are represented mostly with intermediate gray levels as a result of
the partial volume effect.
Table 3 compares the experimental porosity of the samples with
those calculated from processing the μCT and SEM images. The experi­
mental porosity was determined by calculating (1) the pore volume from
the saturated weight and dry weight employing the ‘Liquid Saturation
Method’ and (2) the bulk volume employing the ‘Calipering’ technique –
both by largely following the procedures described in the API Recom­
mended Practices for Core Analysis. While volumetric estimates from
μCT are largely consistent with experimental data, SEM observations
appear to underestimate the void fractions in sandstones and provide
slightly higher values for Indiana limestone. The porosity obtained for
the Castlegate sandstone from SEM images is underestimated by more
than 20 % compared to its experimental value. The SEM porosity of
Bentheimer might had been altered by the presence of fine weathered
feldspar particles from sample preparation. Table 4 provides area frac­
tions of the mineral phases present in sandstone samples derived from
backscattered SEM images. Comparing the bulk minerology, all the
6
Computers and Geosciences 156 (2021) 104895
sandstones appear to have similar mineral compositions with quartz
mineral constituting a major part of their grain structures. These mineral
compositions are consistent with other XRD observations in the litera­
ture (Afrough et al., 2017; Churcher et al., 1991; Peksa et al., 2015;
Shehata and Nasr-El-Din, 2015).
4.1. Pore size distribution
Fig. 6 compares the pore size distribution of rock samples derived
from SEM and μCT images in terms of their volumetric probabilities. The
red histograms represent the 3D pore size distributions obtained from
the stereological unfolding process. Pore size distributions obtained
from processing μCT images for all sandstone samples are approximately
lognormal, while 3D unfolded SEM distributions indicate skewness to­
ward smaller pore diameters. This skewness is attributed to the SEM-
resolved microporosity in clay minerals. For Indiana limestone, the
distribution of pore diameters from μCT shows negative skewness to­
ward smaller pores, whereas SEM observations present a clear bimodal
pore size distribution which is attributed to the well-resolved micropo­
rosity regions in SEM images. The methodology proposed by Sri­
sutthiyakorn and Mavko (2019) overlooks the effect of these
microstructural heterogeneities in converting size distributions from 2D
to 3D.
Table 5 summarizes the statistical descriptions of pore diameters
obtained from μCT, 2D SEM, and the stereologically unfolded 3D SEM
distributions for all rock samples. The skewness in this table describes
the lack of symmetry in lognormal distributions whereas kurtosis mea­
sures the weight of distribution’s tail relative to its center. The original
pore sizes obtained from 2D SEM analysis prior to 3D unfolding present
very large values of kurtosis and skewness for all the rock samples
indicating that their size distributions are heavily tailed toward smaller
pore diameters. This is due to the sectioning bias originating from the
fact that the majority of pores and grains are not necessarily sectioned
through their maximum possible dimensions. As a result, 2D size dis­
tributions of the cross-sections are always biased toward smaller di­
ameters and do not represent the actual 3D distributions.
For Berea sandstone, the mean pore diameter from μCT and 3D SEM
analysis are 22 and 26 μm, respectively. For Indiana limestone, the
average pore size from μCT is 36 μm, while the mean pore diameters
from processed SEM images are 9.5 and 50 μm for small and large pores,
respectively. These results are in close agreement with the absolute pore
sizes measured by Afrough et al. (2019) using non-ground eigenvalues of
magnetic resonance relaxations.
The average pore sizes and pore size distributions obtained from μCT
and SEM images for Berea and Buff Berea are relatively close as expected
from their similar pore structures. Mean pore diameters of Castlegate
and Nugget sandstones are almost identical with Castlegate exhibiting a
wider range of pore sizes. Among sandstone samples, Bentheimer has
the highest mean pore diameter consistent with its relatively large and
well connected pore space. The small pore size measured from SEM
images of Bentheimer is ascribed to the presence of fine weathered
feldspar particles and possible smearing of clay minerals that might have
had been introduced to the sample surface in the sample preparation
stage. This is the likely reason behind deviation between the μCT and
SEM mean pore size for Bentheimer.
4.2. Grain size distribution
Fig. 7 shows the grain size distribution of minerals present in rock
samples from 3D unfolded SEM observations. The predominant minerals
are quartz, feldspar, and clay minerals in sandstones and calcite in
Indiana limestone.
Table 6 summarizes the statistical description of mineral grain sizes
in sandstone samples. Clay exhibits a wide range of grain sizes with the
majority of grains occurring in the range of 1–40 μm. The appearance of
large clay grains is attributed to the agglomeration of clays within the
H. Safari et al. Computers and Geosciences 156 (2021) 104895

Fig. 5. Typical SEM images of sandstone and carbonate samples and their multiphase segmentation results. Sandstone samples are mainly composed of quartz grains
and small amounts of feldspar and clays. Clay minerals are observed either as thin layers or as agglomerates filling the pore space. Indiana limestone features a
monomineralic texture predominantly composed of calcite mineral. Well-resolved SEM images reveal microporosity regions in sandstones and Indiana limestone. The
scale bars are equivalent to 500 μm except for Berea sandstone which has a scale bar equivalent to 200 μm.

Table 3 Table 4
Comparison of the experimental porosities obtained from gravimetry with those Area fractions of the minerals present in sandstone samples derived from SEM
calculated from μCT and SEM images. observations.
Porosity (%) NU CG BT BB BA IL Minerals NU CG BT BB BA

μCT 15 27 22 22 21 14 Clays 0.057 0.074 0.052 0.060 0.074

SEM 13 19 12 18 19 16 Feldspar 0.051 0.040 0.050 0.054 0.065
Exp. 15 26 21 22 21 14 Quartz 0.76 0.69 0.78 0.71 0.67

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H. Safari et al. Computers and Geosciences 156 (2021) 104895

Fig. 6. The volumetric probability of pore diameters from μCT (blue) and unfolded SEM (red) for Bentheimer (BT), Berea (BA), and Indiana limestone (IL) (Top), and
for Castlegate (CG), Buff Berea (BB), and Nugget (NU) (Bottom). SEM-resolved microporosity regions in clay minerals has shifted pore size distributions of sandstone
samples toward smaller sizes. The bimodal pore size distribution obtained from SEM images of Indiana limestone is also attributed to highly resolved microporosity
regions at the grain boundaries. The pore size distributions from μCT and SEM images are consistent. (For interpretation of the references to colour in this figure
legend, the reader is referred to the Web version of this article.)

Table 5
The statistical description of pore diameters from μCT, 2D SEM, and the unfolded 3D SEM distributions for all rock samples. All pore diameters are in μm.
Statistical Parameters NU IL CG

μCT SEM (2D) SEM (3D) μCT SEM (2D) SEM (3D) μCT SEM (2D) SEM (3D)

mean 42 8.3 42 36 4.8 39 40 8.0 39

std 25 8.8 29 27 4.3 42 24 8.3 29
min 3.3 0.6 10 3.3 0.5 2.9 3.3 0.5 8.3
25 % 23 3.2 18 15 2.4 8.4 22 3.2 16
50 % 40 5.4 33 30 3.5 22 38 5.3 30
75 % 59 9.9 60 49 5.6 56 56 9.4 56
max 151 113 108 170 166 158 193 111 106
kurtosis 0.3 17 0.1 2.8 36 1.3 0.1 25.1 0.1
skewness 1.5 3.7 0.9 1.6 3.8 1.4 1.5 4.4 0.9

Statistical Parameters BT BB BA
μCT SEM (2D) SEM (3D) μCT SEM (2D) SEM (3D) μCT SEM (2D) SEM (3D)

mean 53 5.3 28 36 7.9 44 22 4.6 26

std 34 4.7 23 27 8.0 36 22 4.8 21
min 3.3 0.4 4.9 3.3 0.5 8.7 3.3 0.3 4.7
25 % 27 2.6 9.6 13 3.2 17 4.8 1.9 9.4
50 % 48 4.0 19 31 5.3 32 11 3.2 19
75 % 73 6.4 41 52 9.3 63 35 5.5 37
max 212 91 87 252 155 147 163 84 80
kurtosis 0.5 64 0.3 0.5 24 1.3 0.3 35 0.4
skewness 1.4 6.9 1.1 1.5 4.4 1.3 1.4 5.2 1.1

pore space. These agglomerates even resulted in a bimodal grain size
distribution of clays in Berea sandstone (see Fig. 7). Quartz and feldspar
minerals show similar distributions with grain sizes spanning from 1 to
250 μm. These minerals demonstrate a unimodal grain size distribution
in all sandstone samples, except for Castlegate where a bimodal grain
size distribution is observed for feldspar. The calcite mineral in Indiana
limestone also exhibits a bimodal grain size distribution consistent with
its highly resolved microstructural details in SEM images.
To compare the grain size distribution histograms with those ob­
tained from μCT, the mineral phases were merged into a single solid

8
H. Safari et al. Computers and Geosciences 156 (2021) 104895

Fig. 7. The volumetric probability of mineral grain diameters from SEM images for Bentheimer (BT), Berea (BA), and Indiana limestone(IL) (Top), and for Castlegate
(CG), Buff Berea (BB), and Nugget (NU) (Bottom). Clay minerals in sandstones exhibit a wide range of grain sizes ranging from 1 to 40 μm. The appearance of large
grain sizes are due to agglomeration of clays within the pore space resulting in a bimodal grain size distribution in Berea sandstone. The distribution of grain sizes in
quartz and feldspar minerals is unimodal in almost all sandstone samples except for Castlegate sandstone where a bimodal grain size distribution is observed for
Feldspar. Calcite in Indiana limestone also shows a bimodal grain size distribution due to its well-resolved microstructural details from SEM images.

Table 6
Statistical description of the quartz, feldspar, and clay grain diameters from the unfolded 3D SEM distributions for sandstone samples. All grain diameters are in μm.
Statistical Parameters NU CG BT

Quartz Feldspar Clay Quartz Feldspar Clay Quartz Feldspar Clay

mean 126 67 14 55 96 12 47 104 9.1

std 65 55 8.9 61 59 7.4 50 60 5.9
min 48 11 4.0 3.9 13 3.6 1.1 32 1.0
25 % 73 24 6.9 9.0 50 6.0 4.4 56 4.5
50 % 111 52 12 21 82 10 35 90 7.5
75 % 168 93 20 84 134 17 77 143 12
max 256 231 34 217 218 30 173 227 25
kurtosis 0.7 2.3 0.5 0.8 0.6 0.3 0.0 0.6 0.5
skewness 0.7 1.4 0.8 1.3 0.6 0.8 0.9 0.7 1.0

Statistical Parameters BB BA
Quartz Feldspar Clay Quartz Feldspar Clay

mean 96 61 12 44 38 9.6
std 47 51 7.8 35 35 9.5
min 39 11 3.3 1.0 1.1 1.0
25 % 57 22 6.1 17 10 3.3
50 % 85 43 10 34 24 6.4
75 % 127 86 18 65 55 13
max 188 190 30 125 127 46
kurtosis 0.7 0.6 0.5 0.2 0.3 5.6
skewness 0.6 1.2 0.8 0.9 1.1 2.1

phase. Fig. 8 illustrates the volumetric probabilities of grain size dis­
tribution in sandstone and carbonate rock samples. Although the 3D
volumetric grain size distributions obtained from SEM images are
largely consistent with μCT results, the probabilities of small-scale
grains like those of clay minerals have vanished due to merging.
Table 7 provides the statistical description of the grain diameters
derived from μCT and SEM images for all samples. Despite the
agreement between volume-weighted grain sizes, the merging of min­
eral grain components resulted in large arithmetic mean grain diameters
from SEM images, compared to those of μCT results. Similar to pore size
distributions, 2D grain size distributions from SEM images represent
high values of kurtosis and skewness compared to 3D distributions.
Among sandstones, Bentheimer has the largest average grain diam­
eter (82 μm from μCT and 208 μm from SEM), while Berea represents the

9
H. Safari et al. Computers and Geosciences 156 (2021) 104895

Fig. 8. Volumetric probability of grain diameters from μCT (blue) and unfolded SEM (red) for Bentheimer (BT), Berea (BA), and Indiana limestone (IL) (Top), and for
Castlegate (CG), Buff Berea (BB), and Nugget (NU) (Bottom). The merging process resulted in the disappearance of small-scale grains like clays in SEM images and
shifted the mean grain diameters toward larger values. Despite discrepancies in arithmetic means, volume-weighted averages of grain diameters from SEM images are
largely consistent with μCT results. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Table 7
Statistical description of the grain diameters from μCT, 2D SEM, and the unfolded 3D SEM distributions for all rock samples. All grain diameters are in μm.
Statistical Parameters NU IL CG

μCT SEM (2D) SEM (3D) μCT SEM (2D) SEM (3D) μCT SEM (2D) SEM (3D)

mean 58 16 161 71 10 73 64 13 153

std 46 28 71 55 8.2 66 41 20 67
min 3.3 0.5 74 4.2 0.5 9.6 3.3 0.5 71
25 % 21 3.9 104 31 4.9 22 32 4.2 100
50 % 43 6.7 147 56 8.2 48 56 7.2 140
75 % 86 12 207 96 13 107 90 12 197
max 261 310 292 392 251 238 263 294 278
kurtosis 0.1 16 0.1 2.0 95 0.3 0.5 18.5 0.1
skewness 0.6 3.3 0.6 1.3 6.4 1.1 0.7 3.5 0.6

Statistical Parameters BT BB BA
μCT SEM (2D) SEM (3D) μCT SEM (2D) SEM (3D) μCT SEM (2D) SEM (3D)

mean 82 9.3 208 63 13 150 51 7.5 95

std 64 17 97 41 21 55 35 12 40
min 3.3 0.5 81 3.3 0.6 81 3.3 0.4 44
25 % 27 3.2 132 31 3.9 107 23 2.4 62
50 % 66 5.4 189 54 6.7 142 42 4.1 87
75 % 125 9.1 271 88 12 187 73 7.1 122
max 350 414 390 299 261 247 246 180 171
kurtosis 0.8 40 0.1 1.1 20 0.1 1.3 31 0.1
skewness 0.8 4.7 0.6 1.0 3.6 0.5 1.3 4.3 0.5

smallest (51 μm from μCT and 95 μm from SEM). Castlegate, Buff Berea,
and Nugget represent relatively similar mean grain diameters. For
Indiana limestone, the average grain diameter from μCT is 71, whereas
the mean grain sizes from SEM observations are 12 and 88 for small and
large grains, respectively. The grain size distribution of Indiana lime­
stone obtained from μCT exhibits a left-tailed unimodal distribution
skewed toward smaller grain diameters.
4.3. Representativeness
All the rock samples used in this study showed homogeneous char­
acteristics. The agreements between the pore and grain size distributions
obtained from μCT and SEM images confirm this homogeneity and
indicate that the selected volumes for μCT imaging are fairly represen­
tative. Yet, discrepancies exist between the amount of microstructural
details, such as small pores and grains, resolved in μCT and SEM images

10
H. Safari et al.
which is attributed to their limits of resolution. High resolution μCT
imaging requires even smaller sample sizes which might result in their
loss of representativeness as compared to other characterization meth­
odologies. For the rock samples considered in this study, the pore vol­
ume fractions from μCT images were quite consistent with experimental
porosities obtained by gravimetry, whereas void fractions derived from
SEM observations presented noticeable discrepancies. The mean pore
sizes obtained from μCT and SEM images, however, were found to be in
close agreement with each other as well as with the absolute pore sizes
measured using magnetic resonance relaxation. Unlike μCT and SEM
imaging techniques, experimental methods such as NMR and MIP, only
provide information about the connected pore space.
5. Conclusions
We have shown the application of a proposed image processing
workflow for the extraction of pore and grain size distributions from X-
ray microcomputed tomography and scanning electron microscopy im­
ages in five different sandstones and one carbonate sample. While it was
difficult to distinguish between the mineral phases in rock samples from
μCT images, particularly clay minerals in sandstones, SEM images pro­
vided a sufficient contrast to observe different minerals from 2D cross-
sections. The predominant minerals in sandstone rocks were quartz,
feldspar, and clays, whereas Indiana limestone exhibited a mono­
mineralic texture of calcite mineral. Two-dimensional pore and grain
size distributions from SEM images were found to be misrepresenting
the actual 3D distributions due to the sectioning bias. Stereological
methods converted the 2D size distributions obtained from SEM images
to 3D distributions and the results were compared with μCT observa­
tions. The distribution histograms derived from processing μCT and SEM
images presented noticeable differences with regard to their limits of
resolution. We observed that microstructural details resolved in SEM
images can significantly affect the distribution of pore and grain sizes in
both sandstone and carbonate samples. The agglomeration of clay
Appendix
Figure A.1 illustrates an example of the artifact correction, sub-volume extraction, and nonlocal means filtering for X-ray CT images.
11
Computers and Geosciences 156 (2021) 104895
minerals within the pore space resulted in a bimodal grain size distri­
bution in Berea sandstone. The clay microporosities were also observed
to influence the pore size distributions in sandstone samples. In Indiana
limestone, the SEM-resolved microporosity regions led to bimodal pore
and grain size distributions as opposed to unimodal distributions ob­
tained from μCT images.
We showed that our workflow can be successfully employed to
process and extract quantitative information from μCT and SEM images
of natural rocks. We addressed the impact of sectioning bias in SEM
images and highlighted the role of stereology in obtaining representa­
tive 3D size distributions. The rock materials implemented in this study
span a variety of rock types with different and similar pore and grain size
distributions. These rock samples are widely used by researchers
worldwide for analyzing magnetic resonance relaxation or performing
pore-scale fluid flow simulations.
Declaration of competing interest
The authors declare that they have no known competing financial
interests or personal relationships that could have appeared to influence
the work reported in this paper.
Acknowledgements
Authors thank Steven R. Cogswell from Microscopy and Microanal­
ysis for microscopy, Stephen Delahunty from the Earth Sciences
Department for sample preparation, Tatiana Zaraiskaya from UNB Li­
braries for data management, and Florea Marica from UNB MRI
Research Center for assistance, all from the University of New Bruns­
wick. Armin Afrough acknowledges the Danish Hydrocarbon Research
and Technology Centre for funding. Bruce J. Balcom acknowledges
NSERC of Canada for a Discovery Grant and the Canada Chairs Program
for a Chair in Material Science MRI.
H. Safari et al. Computers and Geosciences 156 (2021) 104895

Fig. A.1. Illustration of the image processing steps performed on μCT images, (a) original image (b) artifact correction. There are two different artifacts in the
original image including (1) the region of interest imaging artifact and (2) the beam hardening artifact. We applied the beam hardening module in Avizo software to
correct for the intensity variations caused by both artifacts, (c) maximum possible rectangular sub-volume extraction from the image, (d) cropping of the selected
rectangular sub-volume, and (e) denoising the extracted sub-volume via applying a nonlocal means filter.

Author contributions

All authors contributed to this paper.

Data and code availability

The data and code/procedures of this manuscript are available from a data repository.

Data and computer code availability

Data, Python codes, and Avizo procedures associated with this manuscript are available in the UNB institutional repository Dataverse at DOI htt
ps://doi.org/10.25545/A19OPN. The Python code is available as a Jupyter Notebook SEM_Analyzer.ipynb, version 1.0, and the Avizo 2019.1 pro­
cedure, including all parameters for all samples, is available in Avizo_Worflow.csv. The data and codes are available as CC0 – Public Domain
Dedication.

12
H. Safari et al. Computers and Geosciences 156 (2021) 104895

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