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  <front>
    <journal-meta />
    <article-meta>
      <title-group>
        <article-title>Unsupervised segmentation of ceramic proppant particles in 3D microCT images</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>E P Serkova</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
          <xref ref-type="aff" rid="aff1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>I V Safonov</string-name>
          <xref ref-type="aff" rid="aff1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>I V Yakimchuk</string-name>
          <xref ref-type="aff" rid="aff1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>V Yu Evstefeeva</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
          <xref ref-type="aff" rid="aff1">1</xref>
        </contrib>
        <aff id="aff0">
          <label>0</label>
          <institution>Moscow State University</institution>
          ,
          <addr-line>Leninskie Gory 1, Moscow, Russia, 119991</addr-line>
        </aff>
        <aff id="aff1">
          <label>1</label>
          <institution>Schlumberger Moscow Research</institution>
          ,
          <addr-line>Pudovkina 13, Moscow, Russia, 119285</addr-line>
        </aff>
      </contrib-group>
      <pub-date>
        <year>2018</year>
      </pub-date>
      <fpage>282</fpage>
      <lpage>290</lpage>
      <abstract>
        <p>Oil and gas industry uses different types of ceramic proppants in millions of kilograms per year. X-ray microtomography (microCT) imaging can be applied for investigation of quality of the material. For analysis, it is necessary to segment spherical contacting particles of proppant. We apply a marker-controlled watershed for segmentation. The method of markers detection has several parameters which have crucial influence on segmentation outcome. To optimize segmentation quality, we propose unsupervised (nonreference) measure based on a compactness of 3D connected regions, where compactness is calculated via central geometric moments of second order. In addition, we demonstrate advantages of our technique for compactness estimation over the method based on ratio of surface area and volume of a region.</p>
      </abstract>
    </article-meta>
  </front>
  <body>
    <sec id="sec-1">
      <title>1. Introduction</title>
      <sec id="sec-1-1">
        <title>Oil and gas industry uses various types of proppants (from phrase “propping agent”) in hydraulic</title>
        <p>fracturing technology. Annually in the world hundreds of thousands of tons of ceramic proppant are
produced, the particles of which are granules of spherical shape with a size of about 1 mm.
Mechanical strength and conductivity are the most important attributes of proppant pack for optimal
fracturing job design. Crush test is one of conventional procedures for measurement of proppant
characteristics. Proppant grains crush test should be performed at axial stress up to 100 MPa. Some
particles are crushed during the test. The fraction of the crushed particles depends on stress and quality
of the proppant. For some proppants the crush-rate is only a few percent. X-ray micro-tomography
(microCT) makes capable measurement of morphometric characteristics of each particle as well as
their fragments in initial state and after stress.</p>
        <p>Figure 1 shows example of real reconstructed 3D microCT image of proppant pack before stress.</p>
      </sec>
      <sec id="sec-1-2">
        <title>The grayscale image has size 4000х4000х2000 voxels and 8 bit-depth. The image was obtained with</title>
      </sec>
      <sec id="sec-1-3">
        <title>SkyScan 1172 microCT system (Bruker MicroCT, Belgium). One can see proppant particles in the</title>
        <p>image. Also fragments of crushed particles can be found in images scanned after loading. The usual
image of proppant pack contains several hundreds of particles. Intensities of particle regions are much
lighter than dark background. However, there is many contacting regions of granules and their
fragments. Separation of the contacting regions is a challenging task.</p>
      </sec>
      <sec id="sec-1-4">
        <title>Marker-controlled watershed for distance map is a traditional method for segmentation of touching</title>
        <p>regions. An algorithm for detection of markers has several parameters, which influence to
segmentation quality considerably. Since the fraction of broken particles can be equal to several
percent, even single segmentation errors leads to bias of an assessment of quality of the material.</p>
      </sec>
      <sec id="sec-1-5">
        <title>Selecting the segmentation parameters manually by the operator is a long and unobvious process.</title>
      </sec>
      <sec id="sec-1-6">
        <title>In addition, it is quite difficult to detect segmentation errors in a 3D image visually. Our</title>
        <p>preliminary experiments have shown the optimal segmentation parameters vary from image to image;
it is impossible to set parameters once based on a previously processed sample. Therefore, it is
important to develop an unsupervised (non-reference) quality metrics that allow selection of the
parameters automatically with aim to minimize the number of errors of segmentation of proppant
particles.</p>
      </sec>
      <sec id="sec-1-7">
        <title>The main contribution of the paper is proposed unsupervised metrics of segmentation of 3D spherical particles by means of maximization of average compactness of segmented regions, where compactness is calculated via second order central geometrical moments.</title>
      </sec>
    </sec>
    <sec id="sec-2">
      <title>2. Segmentation of particles</title>
      <p>
        Figure 2 demonstrates flow-chart of segmentation algorithm. Reconstructed grayscale 3D image is
downsampled to image G having size 1000x1000x500 voxels and 8-bits depth. It is necessary to
reduce requirements to memory space and decrease processing time. Lighter voxels of ceramic
particles differ from dark voxels of background and holder. Histogram of intensities of the image is
bimodal. For images with such histograms thresholding by Otsu algorithm [
        <xref ref-type="bibr" rid="ref1">1</xref>
        ] is a good solution to
distinguish voxels of particles from background. After thresholding we obtain binary image T, where
voxels of solid are designated by 1 and voxels of voids are designated by 0. It is required to split
regions formed by touching particles in T image.
      </p>
      <p>
        Conventional way for separation of overlapping or contacting convex regions without holes is an
application of watershed algorithm to the inverted outcome of the geodesic distance transform [
        <xref ref-type="bibr" rid="ref2">2</xref>
        ]. The
general idea of watershed algorithm is the following: image is considered as a geological relief; a
water source is placed in each regional minimum in the relief, to flood the entire relief from sources,
and build barriers in the place where different water sources meet; the resulting set of barriers
constitutes a watershed by flooding [
        <xref ref-type="bibr" rid="ref3">3</xref>
        ]. For volumetric images watershed algorithm operates
identically to 2D one.
      </p>
      <sec id="sec-2-1">
        <title>Before application of distance transform we need to fill holes, which are pores in particles. Several</title>
        <p>pores are open, they connect with background voids. That is why filling of holes in 3D keeps these
pores unchanged. It is required to perform filling of holes for 2D slices. Theoretically, the filling of
holes should be done for slices in all three mutually perpendicular directions. Such approach ensures
that the open pores, which are penetrate a particle and are parallel to image axes, are filled. However,
in practice open pores are tortuous, so, it is enough to fill the holes for 2D slices in only one direction.
Binary image Tf is outcome of slice-by-slice filling of holes for T image. It is worth to note, filling of
holes in 2D can lead to filling of space between touching particles. Fortunately, it happens seldom and
it has no negative impact on the next processing steps.</p>
      </sec>
      <sec id="sec-2-2">
        <title>On the next stage, geodesic distance transform builds the distance map D by calculation for each</title>
        <p>
          voxel of Tf image Euclidean distance to the nearest voxel equal to zero. Inverted D plays the role of
relief for watershed algorithm. Local minima on (-D) are basins origins. Frequently there are several
local minima inside a connected region because even survived particles have non-ideal convex shape,
a lot of fragments of crushed particles are concave. It leads to over-segmentation. To avoid
oversegmentation due to the huge number of local minima the marker-controlled watershed is used, where
markers play role of water sources [
          <xref ref-type="bibr" rid="ref4">4</xref>
          ].
        </p>
        <sec id="sec-2-2-1">
          <title>Thresholding by Otsu</title>
        </sec>
        <sec id="sec-2-2-2">
          <title>Filling of holes for 2D slices</title>
          <p>T
f</p>
        </sec>
        <sec id="sec-2-2-3">
          <title>Geodesic distance transform</title>
        </sec>
        <sec id="sec-2-2-4">
          <title>Maximal filter</title>
          <p>R
f
Markers detection: R = = Rf
G
T
D
R
M
L</p>
        </sec>
        <sec id="sec-2-2-5">
          <title>Grayscale morphological reconstruction by dilation</title>
        </sec>
        <sec id="sec-2-2-6">
          <title>Marker-controlled watershed for inverted D</title>
          <p>L
w</p>
        </sec>
        <sec id="sec-2-2-7">
          <title>Masking of labels by T</title>
          <p>max_filter_size
delta_h
(b)
delta_h
max_filter_size
delta_h</p>
          <p>K</p>
        </sec>
      </sec>
    </sec>
    <sec id="sec-3">
      <title>3. Unsupervised segmentation quality metrics</title>
      <p>
        Segmentation outcome depends on parameters delta_h and max_filter_size. Decrease of both leads to
over-segmentation, because regions of granules split in fragments. Increase of both leads to
undersegmentation, because neighbouring particles and fragments
merge. How to set the parameters
properly? Subjective choice based on visual analysis of segmentation result is a troublesome due to 3D
nature of data. It is hard to find optimal parameters visually. Paper [
        <xref ref-type="bibr" rid="ref6">6</xref>
        ] analyses supervised quality
measures for segmentation such as Global Consistency Error and Rand Index. However, we have no
ground truth to be able to apply supervised metrics. How to automatically choose the optimal
parameter values, based only on the analysed image? Survey [
        <xref ref-type="bibr" rid="ref7">7</xref>
        ] describes a few dozen of
unsupervised metrics for estimation of segmentation quality of 2D images. All of them are not
universal, but depend on the task being solved. When segmenting regions have more or less the same
shape, the shape factor can be used as metrics.
      </p>
      <p>We know a-priori that studied particles have a rounded shape. We use the fact for formulation of
criterion of unsupervised segmentation. A sphere is the most compact body in three-dimensional
space. In the next section, we describe a compactness for characterizing the closeness of a region
shape to a sphere. Maximal average compactness of segmented regions corresponds to the best
segmentation:

1



=
∑   ,
where N is the number of segmented regions having volume greater then Vt; Ci is compactness of i-th
region. The threshold Vt is introduced to exclude from consideration too small fragments. In addition,
it is hard issue: what is compactness for regions consisting of only a few voxels?</p>
      <sec id="sec-3-1">
        <title>Let’s consider how</title>
      </sec>
      <sec id="sec-3-2">
        <title>Q changes in the case of improper segmentation.</title>
      </sec>
      <sec id="sec-3-3">
        <title>Over-segmentation is splitting of spherical regions. It leads to decreasing of average compactness Q. Under-segmentation is merging of spherical regions. As rule, it leads to decreasing of average compactness too. It is worth to</title>
        <p>note, proposed segmentation criterion is correct in assumption of existing of at least several tens of
survived spherical particles in image after loading. If almost all particles are crushed then the metrics
is ineffective.</p>
      </sec>
    </sec>
    <sec id="sec-4">
      <title>4. Compactness</title>
      <sec id="sec-4-1">
        <title>Many 3D shape factors are a natural extension of corresponding measures for 2D images.</title>
      </sec>
      <sec id="sec-4-2">
        <title>Compactness in 2D is sometimes called the circularity or the roundness. Shape compactness in 2D is</title>
        <p>
          generally understood as the degree to which a given shape differs from a region bounded by a circle.
There are plenty publications, which describe compactness as ratio of area of region to squared
perimeter. Analogous definition of compactness for 3D regions is ratio of squared volume to area of
surface of a region in cubic power [
          <xref ref-type="bibr" rid="ref9">9</xref>
          ]:
  =
36  2
 3
,
is preferable?
geometric
calculation:
where V is volume of 3D region, S is area of surface.
        </p>
      </sec>
      <sec id="sec-4-3">
        <title>Paper [8] performs detailed analysis of drawbacks of approaches, which use perimeter and surface</title>
        <p>area for calculation of compactness for 2D and 3D images correspondingly. First, a perimeter and a
surface area are difficult to calculate invariantly to rotation and quite precisely due to the digital nature
of images. Second, the surface of the regions is not ideal, there are various types of noises that arise
during the registration and segmentation of regions. Third, the evaluation of compactness is seriously
affected by holes in regions.</p>
        <p>
          Bribiesca [
          <xref ref-type="bibr" rid="ref11">11</xref>
          ] describes compactness for 3D regions that differs from   , but it is based on volume
and area of surface also. The paper [
          <xref ref-type="bibr" rid="ref11">11</xref>
          ] demonstrates Bribiesca’s is less sensitive to small distortions
of surface in comparison with   .
        </p>
      </sec>
      <sec id="sec-4-4">
        <title>There are several approaches for calculation of surface area. For example, the paper [9] considers</title>
        <p>
          marching cubes algorithm [
          <xref ref-type="bibr" rid="ref10">10</xref>
          ] for estimation of outer surface area. A surface area can be estimated as
the number of voxels of the outer shell, where the shell is the difference in the region and the result of
its erosion with a 3x3x3 structural element in the form of a cube (26-connectivity), or a ball
(18connectivity), or a cross (6-connectivity). Surely, all pores should be filled in advance. Which method
Zunic et al. [
          <xref ref-type="bibr" rid="ref12">12</xref>
          ] proves properties of 3D shapes compactness based on second order central
moments and demonstrates its advantages over other algorithms for compactness
where central geometric moments are:
 
=
35/3
        </p>
        <p>∑  ( ,  ,  )( −  100) ( −  010) ( −  001) ,
where geometric moments are:</p>
        <p>= ∑
∑</p>
        <p>∑  ( ,  ,  )      ,</p>
        <p>where  ( ,  ,  ) is indicator function of particle region, I equals one for voxels belonging the region,
 000 =  . First order geometric moments are centroids. Compactness lies in the range from 0 to 1.</p>
      </sec>
      <sec id="sec-4-5">
        <title>Compactness of ideal sphere equals 1.</title>
        <p>0005/3</p>
        <p>
          Paper [
          <xref ref-type="bibr" rid="ref12">12</xref>
          ] is based on outcomes from Mamistvalov‘s theory. Mamistvalov published in English
mathematical theory for recognition of n-dimensional solids via geometric moment invariants in 1998
[
          <xref ref-type="bibr" rid="ref13">13</xref>
          ]. In Russian, it was done in 1974. Unfortunately, those papers are not widely known. Ratio
 200+ 020+ 002 is so-called first 3D moment invariant based on second order central geometric
moments. The invariant is constant or slightly changes for origin translation, uniform scaling and
rotation.   is the inverted first 3D moment invariant multiplied by the constant, so, it is an invariant
for translation, rotation and scaling as well. In general, geometric moments have been widely used in
statistics for description of the form of a probability density function and in classic rigid-body
mechanics to measure the mass distribution of a body. Usage of moment invariants is a prospective
direction in an image processing for creation of shape factors as well as for development of algorithms
for shapes analysis and recognition. According to monography [
          <xref ref-type="bibr" rid="ref14">14</xref>
          ], last decade an interest to shape
analysis and classification via moment invariants grows. Not only geometric invariants are applied,
but orthogonal moments such as Gaussian-Hermite, Zernike, Chebyshev, Legendre and
Fourier
        </p>
      </sec>
      <sec id="sec-4-6">
        <title>Mellin.</title>
      </sec>
      <sec id="sec-4-7">
        <title>Let’s consider which method of computing the compactness is better suited for our problem. We</title>
        <p>calculate the compactness coefficients for spheres of different radii with different random noises such
as protuberances and cavities on a surface. Figure 4 shows a slice of the sphere with typical noise on
the surface. In the next experiment, we determine which method for compactness calculation allows us
to distinguish sphere from regions formed by cutting off segments of different sizes from the sphere
better.</p>
        <p>Plots in figure 5 show various compactnesses depending on radius of sphere:   ;   , where
surface area is calculated by marching cubes algorithm;   , where surface area is calculated by means
of erosion, Bribiesca’s compactness; theoretical ideal case, where compactness equals 1.   for both
considered approaches are very different from 1 and have significant fluctuations.   is close to 1
except for spheres having radius less than 10. Bribiesca’s compactness is almost 1 for all range of
considered radiuses.</p>
        <p>Plots in figure 6 show compactnesses for bodies from hemisphere (L=60) to sphere (L=0). Figure 7
illustrates meaning of L parameter.   and   allow to distinguish sphere and sphere with clipped
segment. Bribiesca’s compactness is too similar even for sphere and hemisphere.</p>
        <p>We conclude, application of compactness   calculated via second order central geometrical
moments has obvious advantages in comparison with well-known approaches based on surface area
and volume of 3D region. In addition, in contrast to  а,  
number of open and close pores.
has robustness to presence of the modest</p>
      </sec>
    </sec>
    <sec id="sec-5">
      <title>5. Results and discussion</title>
      <sec id="sec-5-1">
        <title>For estimation of benefits of proposed unsupervised segmentation technique, we processed five 3D</title>
        <p>images with fixed parameters delta_h and max_filter_size as well as with parameters obtained by
maximization of  metrics. It is worth to note, those fixed parameters were optimal according to 
criterion for two images segmented previously. We apply gradient descent algorithm for looking for
maximal  . Figure 8 shows  metrics depending on parameters delta_h and max_filter_size.</p>
      </sec>
      <sec id="sec-5-2">
        <title>Image</title>
        <p>Table 1 contains for each tested image the number of erroneously segmented particles by
segmentation with fixed parameters and by proposed unsupervised segmentation. Total number of
particles in each image is 615. Segmentation with fixed parameters leads to 30-50 errors. Figure 9
shows slice of segmented and labeled image by segmentation with fixed parameters. One can see, one
ellipsoidal particle was segmented as two regions, ten pairs of neighboring particles were pairwise
combined into one region. Unsupervised segmentation had no errors, or just one or two errors in the
worst case. Figure 10 demonstrates the slice of 3D image, where unsupervised segmentation was
applied. Segmentation outcome is fully correct.</p>
        <sec id="sec-5-2-1">
          <title>So, proposed unsupervised criterion for the segmentation of 3D images of ceramic proppant allows providing high quality segmentation in automatic mode.</title>
        </sec>
      </sec>
    </sec>
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