Authors Accepted Manuscript

A new intelligent method for Minerals

segmentation in thin Sections based on A novel
incremental color clustering
Hossein Izadi, Javad Sadri, Nosrat-Agha Mehran
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http://dx.doi.org/10.1016/j.cageo.2015.04.008
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Received date: 16 October 2014
Revised date: 19 April 2015
Accepted date: 20 April 2015
Cite this article as: Hossein Izadi, Javad Sadri and Nosrat-Agha Mehran, A new
intelligent method for Minerals segmentation in thin Sections based on A novel
incremental
color
clustering, Computers
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A New Intelligent Method for Minerals Segmentation in Thin

Sections Based on a Novel Incremental Color Clustering
Hossein Izadi1, Javad Sadri2,3*, Nosrat-Agha Mehran4
1

Petroleum Exploration Department, Faculty of Mining Engineering, University College of Engineering, University of Tehran,

Tehran, Iran. hossein.izadi@ut.ac.ir

2*

McGill Center for Bioinformatics, School of Computer Sciences, McGill University, Trottier Building, Room#: 3140, 3630

University Street, H3A 2B2, Montreal, Quebec, Canada. javad.sadri@cs.mcgill.ca.

3

Department of Computer Engineering, Faculty of Electrical and Computer Engineering, University of Birjand, Birjand, Iran.

Department of Mining Engineering, Faculty of Engineering, University of Birjand, Birjand, Iran. namehran@birjand.ac.ir.

Abstract
Minerals segmentation in thin sections is a challenging, popular, and important research topic in
computational geology, mineralogy, and mining engineering. Mineral segmentation in thin sections
containing altered minerals, in which there are no evident and close boundaries, is a rather complex
process. Most of the thin sections created in industries include altered minerals. However, intelligent
segmentation in thin sections containing altered minerals has not been widely investigated in the literature,
and the current state of the art algorithms are not able to accurately segment minerals in such thin sections.
In this paper, a novel method based on incremental learning for clustering pixels is proposed in order to
segment index minerals in both thin sections with and without altered minerals. Our algorithm uses twelve
color features that are extracted from thin section images. These features include: red, green, blue, hue,
saturation and intensity, under plane and cross polarized lights in maximum intensity situation. The
proposed method has been tested on 165 igneous samples and the overall accuracy of 92.15% and 85.24%
*

Corresponding author: Javad Sadri,

Postal address: McGill Center for Bioinformatics, School of Computer Sciences, McGill University, Trottier Building, Room#:
3140, 3630 University Street, H3A 2B2 Montreal, Quebec, Canada,
Phone: 514-398-7071-XT: 09264
Fax: 514-398-7071-XT: 089545
Email: javad.sadri@cs.mcgill.ca

has been obtained for thin sections without altered minerals and thin sections containing altered minerals,
respectively. Experimental results indicate that the proposed method outperforms the results of other
similar methods in the literature, especially for segmenting thin sections containing altered minerals. The
proposed algorithm could be applied in applications which require real time segmentation or efficient
identification map such as petroleum geology, petrography and NASA's Mars explorations.
Keywords: Intelligent mineral segmentation, Thin sections, Incremental learning, RGB and HSI color
features, Image processing.

1. Introduction
The main purpose of studying thin section images is the segmentation of minerals (Fabbri, 1984; Allard
and Benn, 1989; Simigian and Starkey, 1989). Intelligent mineral segmentation in thin sections is a crucial
step for performing further processing on minerals such as minerals identification and naming rocks (Izadi
et al., 2013). In addition, it makes possible some quantitative measurements such as grain size and shape
analysis, which could be used to address a wide variety of geological problems (Goodchild and Fueten,
1998). Therefore, developing an algorithm for minerals segmentation in thin sections is an important step
in computational geology.
In recent years, some scholars have developed various algorithms and methods using color features for
minerals segmentation in thin sections (Heilbronner, 2000; Van den berg et al., 2002). Most of these
methods are based on color edge detection; however, this technique is not a perfect method and only works
well on clean materials like ceramics (Arnould et al., 2001). As one of the first attempts for segmenting
minerals in thin sections, Goodchild and Fueten (1998) proposed an algorithm based on such image
processing techniques as Gaussian smoothing, gradient calculation, thresholding and image
skeletonisation. Boundary detection of grains in thin sections based on gradient filtering and using Lazy
Grain Boundary (LGB) method was proposed by Heilbronner (2000). LGB method, which is public
domain image processing software, consists of a set of macro commands programmed for NIH images. In
2

another study, Van den Berg et al. (2002) suggested an alternative algorithm for boundary detection of
grains in digital images of thin sections by using maximum likelihood classifier. Another algorithm for
grains boundary detection in thin sections was developed by Zhou et al. (2004-A). They used image
processing techniques based on phi-image (rotation stage of petrographic microscope) and max-image
(maximum intensity of minerals) as the - methodology of their proposed algorithm. In another study,
(Zhou et al., 2004-B) developed a method based on edge finding and region growing techniques for
minerals segmentation. In their study, the color edges were created by combining results of edge operators
and a color edge detection algorithm, and then a region growing algorithm was used for image
segmentation. Another method based on the watershed algorithm for minerals segmentation in thin
sections was proposed by Barraud (2006). After applying the watershed algorithm, the map of the grain
boundaries was corrected manually. In another study, Obara (2007) proposed an algorithm based on color
system transformation, and image processing techniques. The watershed algorithm was also used for grain
segmentation in RGB, CIELab, CIELuv, YIQ and YUV color spaces. Fueten and Mason (2007) developed
an algorithm based on the method proposed by Goodchild and Fueten (1998). Moreover, they used
artificial neural network (ANN), and color and texture features for mineral segmentation. They used ANN
to also examine the edges of minerals. Their approach could significantly reduce the amount of manual
corrections after automatic edge detection process. Boundary detection of minerals using the level set
method (LSM) was proposed by Lu et al. (2009). LSM consists of two steps which are initializing the
curve and then evolving it by solving the level set equation. In another study, Yesiloglu-Gultekin et al.
(2012) suggested a computer program (TSecSoft) which segmented minerals by using minimum
birefringence color intensity and several pre-processing techniques. It creates a final segmentation map by
user feedback, and then determines the mineral percentages. Furthermore, Filho et al., (2013) developed a
semiautomatic algorithm based on image foresting transform (IFT) for minerals segmentation in thin
sections.

Most minerals in thin sections existing in industries such as petroleum geology and petrology are altered
minerals, in which mineral boundaries are not clearly evident and close. Segmentation of thin sections
containing altered minerals is a very difficult problem, and it also seems nearly impossible through
methods formerly used in the literature (Arnould et al., 2001). So far, a general method for minerals
segmentation in thin section containing altered minerals has not been proposed, and the current state of the
art techniques are unable to obtain high accuracy for minerals segmentation in such thin sections.
Therefore, developing an online and real time algorithm for minerals segmentation in thin sections
containing altered minerals could be of great help in carrying out research and in mining industries. In this
paper, using color features, a new intelligent method for minerals segmentation in thin sections is proposed
based on an incremental clustering algorithm. While clustering based segmentation is a new approach to
mineral segmentation, most of clustering algorithms are unable to cluster all the minerals in thin sections.
This is because they need the number of clusters (minerals) as the input parameter. However, it is
impossible to anticipate the number of minerals in thin sections. Incremental clustering algorithm is a
method of clustering that does not need to determine the number of clusters (minerals) as the input
parameter, and it is able to determine the number of clusters in incoming data incrementally (Sadri et al.,
2006). The proposed method is able to efficiently segment minerals in thin sections both with and without
altered minerals with high accuracy.
The rest of this paper is organized as follow: in Section 2, mineralogy background information is
described. In Section 3, the database collection and details of images are presented. In Section 4, the
proposed intelligent method for minerals segmentation in thin section is introduced. Then, in Section 5,
experimental results of the proposed method are discussed, and finally, in Section 6, conclusions are drawn
and suggestions for further works are presented.

2. Mineralogy Background Information

In order to examine the mineralogical properties of minerals in thin sections, a polarizer rotation stage or a
polarizer microscope (Fig. 1) is used, which works based on polarized light (Dyar et al., 2008). Optical
mineralogy is a branch of mineralogy in which thin sections are studied by polarizer microscopes with
rotation stage.

Fig. 1. A polarizer microscope with rotation stage. The light source (B) is embedded on a stand (A) and the light ray passes
through the polarizer (C). Thin sections are put on the rotation stage for examination (D) and their components arewatched by
objectives (E) and oculars (G). Analyzer (F) converts plane polarized light into cross polarized light.

In order to study rocks, some slices are turned into thin sections by special mineralogy techniques. Thin
sections are a 30m thick slice of rocks mounted on a glass microscope slide (Zhou et al., 2004). Minerals
in thin sections have specific optical properties which are different in plane and cross polarized lights.
Most minerals in the plane polarized light are colorless (Fig. 3). Hence, cross polarized light is used too for
studying minerals in thin sections.

3. Database Collection
To create a database for this study, images were captured in a maximum intensity situation by a digital
camera using a polarizer microscope with rotation stage at plane polarized and cross polarized lights. The
maximum intensity situation is defined as the maximum interference color that every pixel attains during a
180 degree rotation of the polarizers (Ross et al, 2001). In this study, 165 igneous thin sections consisting
of 28 igneous common minerals were collected (Table 1), and they were used to develop the proposed

algorithm. From each thin section, two images were captured in RGB color space under plane and cross
polarized lights with the size of 300250 pixels and the resolution of 96 dpi.
Table 1. Number of minerals samples used in this study

Number of
Row#

Number of

Mineral

Row#

Mineral

samples

samples

Amphibole

16

15

Leucite

Analcime

16

Chlorite

Andalusite

17

Muscovite

Actinolite

18

Nepheline

Apatite

19

Nosean

Biotite

20

Olivine

Cancrinite

21

Orthoclase

10

Chabazite

22

Plagioclase

Chloritoid

23

Pyroxene

12

10

Clinozoisite

24

Quartz

11

11

Enstatite

25

Sanidine

12

Kyanite

26

Sphene

13

Epidote

27

Topaz

14

Garnet

28

Zircon

4. Intelligent Mineral Segmentation in Thin Sections

In this paper, for the first time, an incremental learning technique is used for developing an intelligent
mineral segmentation algorithm. The proposed segmentation algorithm provides the number of mineral
clusters (which is the maximum number of detected mineral species) and the boundary of grain minerals in
thin section. Latter this information can be used for mineral identification. The flowchart of the proposed
segmentation method is shown in Fig. 2, and

details of each step will be described in the following

subsections.
6

Plane polarized light

Cross polarized light

Input: two digital images (Max-Intensity) from the thin

section, one under plane polarized and the other under
cross polarized lights, were captured by a digital
camera installed on the polarized microscope

Mapping RGB pixel values into [0, 1] in both

images
Histogram equalization (both images)
Median filtering (both images)

Pre-processing
steps

Image resizing (both images)

Converting RGB into HSI color spaces in

both images
Extracting twelve features for each pixel
including six features from plane
polarized and six features from cross
polarized lights in both images

Extracting
color features

Assigning each feature vector to a cluster

which has similarity greater than
Choosing clusters consisting of
index minerals

Clustering

Combining clusters whose similarities

are greater than 85%

Output: final segmentation map in black and

white images consisting of index minerals
Fig. 2. Flowchart of the proposed method for intelligent mineral segmentation. Two images under plane and cross polarized
lights are assigned to the algorithm as input data, and after pre-processing and color feature extraction steps, an incremental

clustering algorithm is applied for intelligent mineral segmentation. The output of the proposed method includes several black
and white images in which the index minerals are shown.

4.1 Pre-processing
In mineralogy laboratory, images are captured by different microscopes. Therefore, images are obtained
with various sizes and resolutions. The size of images is an important parameter because the running time
of the algorithm depends on it. Therefore, a general size should be determined. In this paper, after several
evaluations through trial and error, images are resized into 200150 pixels. In addition, a median filter
with the 33 mask size is used for smoothing the images and reducing their noise (Fig. 3).

Fig. 3. Applying median filter mask size 33. A: original image and B: filtered image

In order to give the same values to the features, the RGB and HSI components are linearly mapped
between 0 and 1 according to (Eq. 1) (Rashedi et al., 2009). Furthermore, histogram equalization is used
for enhancing the contrast of images (Fig. 4)

Vinput Vmin
eps
Vmax Vmin

(1)

CR

CG

CB

DR

DG

DB

Fig. 4. Histogram equalization. A: low contrast image, B: improved image contrast using histogram equalization, histogram of
low contrast image for Red (CR), green (CG) and blue (CB) components, histogram of improved contrast image for Red (DR),
green (DG) and blue (DB) components

4.2 Extracting Color Features

RGB color space is an important and common color feature for developing image processing algorithms;
however, some experimental studies have indicated that the RGB color space is very sensitive to the
fluctuations of the light (Thompson et al., 2001). Converting the RGB components into hue, saturation and
intensity (HSI) color space detaches the intensity component from the color information and reduces the
effects of variable lighting (Thompson et al., 2001). In this paper, thin section images are captured in
standard fluctuation of light which is confirmed by a qualified expert; therefore, RGB color features are
adequate for segmentation. However, to obtain more accurate results, HSI color features are also used in
the proposed method. Hence, images are first captured in RGB color space, and are then they are
9

converted into the HSI color space (for equations converting RGB color space to HSI color space, refer to
Gonzalez et al. (2009). Afterwards, the feature vector which is assigned to each pixel in thin section
images is a concatenation of 12 features including both RGB and HSI features in plane and cross polarized
lights. A schematic diagram of the feature vector is shown in Fig. 5. The details of these features are
presented in the next two subsections.
HSI color space

RGB color space

R

HSI color space

RGB color space

Cross polarized light

Plane polarized light

Fig. 5. The feature vector which is extracted from each pixel in the thin section images. It consists of six features from plane and
six features from cross polarized images

4.2.1

RGB color space

RGB color space is an MN3 array of color pixels, where each color pixel is a triplet containing red,
green and blue components of an RGB image at a specific spatial location (Gonzalez et al., 2009). RGB
components are important color features and are used by most of experts for studying minerals in thin
sections using polarizer microscopes.
4.2.2

HSI color space

HSI color space is an ideal space to develop image processing algorithm based on color descriptions that
are natural and intuitive for humans, who are the final developers and users of these algorithms (Gonzalez
et al., 2009). The hue of the color, as determined by wavelength, provides a measurement that directly
determines the color of the grain. Saturation is the amount of color that presents the degree to which a pure
color is diluted by white light (Thompson et al., 2001). Each pixel in thin section images has a unique
value of hue and saturation features, and these features are independent of the intensity of the microscopes
source light.

10

4.3. Clustering
Clustering is one of the most important problems in computer science (Prudent, Ennaji, 2005). It aims
toat discovering groups of similar patterns and to identifying meaningful structures or useful patterns in the
data. There has been a lot of research on clustering, and many algorithms such as k-means, Fuzzy k-means
and ART (Adaptive Resonance Theory) have been proposed in the literature (Xu and Wansch, 2005). The
proposed method is based on an incremental clustering algorithm, which will be explained in details in the
following subsections.
4.3.1 Incremental Clustering Algorithm
Anticipating the number of minerals in thin sections is too difficult. Thus, conventional clustering
algorithms such as k-means or ANNs are not appropriate for minerals classification. This is because in
these clustering algorithms, the number of clusters (minerals) must be determined before running the
algorithm. Thus, it is necessary to use an algorithm which does not need the number of clusters (minerals)
as the input parameter. Moreover, the algorithm must take new patterns and assign them into former
clusters or create a new cluster.
Since the ART algorithms have online incremental learning capabilities, the basic idea to design
proposed clustering algorithm is adopted from ART. In this paper, a slightly modified version of the
incremental clustering algorithm proposed by Sadri et al., (2006) is used for segmenting minerals in thin
sections. This algorithm can run faster than k-means because it scans (visits) all the data points just once to
find the centers of the clusters. This property of the algorithm makes it suitable for clustering of online
incoming data (Sadri et al., 2006). Incremental clustering algorithm proposed by Sadri et al. (2006)
includes only one parameter, as (minimum similarity threshold), that must be adjusted before running the
algorithm. The value of is between 0 and 1, which where 0 means there is no similarity and 1 means two
objects are completely similar. In our modified version of this algorithm, pixels of input image are read
one by one by the clustering algorithm, and based on Eq. 2, the similarity between each input pixel and the
center(s) of previously created cluster(s) is determined, and the input pixel will be included in the cluster(s)
11

such that its similarity is greater than . If there is no such cluster, a new cluster will be created for that
pixel.

Similarity

1 Euclidean _ dis tan ce 2

Where

0 Similarity 1

0 Euclidean _ dis tan ce

(2)

) , and n is the number of extracted features, X=[ x1, x2, ...,

xn] and Y=[ y1, y2, ...., yn] are the color features of two different pixels of X, Y. The steps of clustering by
the proposed algorithm are presented here, and a full description of it based on a simple example is also
presented in Fig. 6.
1. Adjust the minimum similarity threshold ().
2. Cluster-Centers-list .
3. Read the next input pattern.
4. Find similar clusters centers to the input pattern in the cluster-center-list with a similarity greater
than .
If found: assign the pattern to those clusters, and adjust the centers of those clusters.
If not found: build a new cluster and insert the input pattern to cluster-center-list as a new
cluster center.
5. Repeat steps in 3-4 for all the input patterns.

A six-pixel image is assigned to the proposed

clustering algorithm

Step 0: A simple image including six pixels is assigned to

the clustering algorithm

The first pixel creates the first cluster and

then is assigned to the cluster center list
as center of the first cluster

Step 1: Assigning the first pixel to the clustering algorithm

Step 2: Assigning the second pixel to the clustering algorithm:

If: similarity between the center of the first cluster and
assigned pixel
If: similarity between the center of the first cluster12
and
assigned pixel <

Then

The second pixel is included in the first cluster,

and a pixel which is closer to the average between
all members is selected and then assigned to the
cluster center list as center of the cluster

\
Then

Step 3: Suppose that the first state of Step 2 happens:

Assigning the third pixel to the clustering algorithm:
If: similarity between the center of the first cluster and
assigned pixel

Then

If: similarity between the center of the first cluster and

assigned pixel <, then:

Then

Step 4: Suppose that the second state of step 3 happens:

Assigning the fourth pixel to the clustering algorithm:
If: similarity between the center of each cluster and
assigned pixel , then:

A new cluster is created and a new pixel

is assigned to the cluster center list as the
center of new cluster

The third pixel is included in the first cluster,

and the center of the cluster is determined
like step 2

A new cluster is created and

the input pixel will be regarded
as its center

Then

The fourth pixel is included in both

clusters and the center of the clusters is
determined like step 2

If: similarity between the center of the first cluster and

assigned pixel

Then

Now, two clusters exist where the fourth

pixel is included in the first cluster

If: similarity between the center of each cluster and

assigned pixel <, then:

Then

The third cluster is created and the input

pixel will be regarded as its center

Step 6: In general, at the end of this algorithm, 1<the

number of the clusters<6. In a specific case: if =0, there
will be only one cluster, and if =1, there will be six clusters
(one for each pixel)

Figure 6. An example of the proposed incremental clustering for a simple image including six pixels.

4.3.2

Choosing clusters including index minerals

In order to segment thin sections containing altered minerals, some reported clusters are noisy clusters with
random pixel which normally cannot provide necessary information about index minerals. For example,
the noisy cluster presented in (Fig.7-C) is one of the reported clusters by the proposed algorithm in this
study for segmentation of images shown in (Fig. 7-A and 7-B). As can be seen here, this cluster (Fig.7-C)
does not provide any important information about index minerals. Therefore, a median filter with 33
mask size is used for removing salt and pepper noises, and slightly smoothing the boundary of the clusters.
13

In order to eliminate those blobs which are not removed by median filter, a threshold equal to 150 (which
this threshold is equivalent to 0.5% of the input image sizes) pixels is also used. After this stage, other
remaining clusters will be considered as candidate index minerals.

Fig. 7. An example of the noisy cluster. A: input image in plane polarized light, B: input image in cross polarized light and C:
noisy cluster which have not important role in final segmentation map. By using a median filter a threshold equal to 150 pixels
the noisy cluster is omitted and not used for creating final segmentation map

4.3.3 Combining Clusters

In the algorithm used in this study, pixels can be assigned to several clusters as the case shown in (Fig. 6).
Therefore, overlaps between some clusters can happen, which these overlaps make those clusters come
close together. Clusters whose overlaps are greater than 85% will be combined together and indexed as one
mineral. This combination threshold was fixed by trial and error on the training examples. Note that by
choosing small values for combination threshold, clusters will be combined more frequently, and by
choosing bigger values, fewer clusters will be combined together. More details of our combination
operation are shown in Fig. 8 and an example is also shown in Fig. 9. This operation is one of the most
14

important steps in the proposed algorithm because weathering and alteration effects create minor color
changing through minerals surfaces. Combining similar clusters with an overlap greater than 85% can
handle these kinds of color changing. It also produces more reliable results, which are closer to qualified
human expert judgment for minerals segmentation in thin sections containing altered minerals.

( )
( )
(

Clusters A and B
will be combined

Fig. 8. Combination of simple clusters A and B. n(A) and n(B) show the numbers of pixels in A and B clusters, respectively, and
AB shows their intersection.

Fig. 9. A: Bronzite in plane polarized light, B: Bronzite in cross polarized light, C and D: two clusters as a part of segmentation

15

map for A and B. The overlap of these two clusters is greater than 85%, and the proposed method combine them as one mineral
cluster.

5. Experimental Results
In order to evaluate the performance of the proposed algorithm in minerals segmentation, several
experiments were conducted on the images of thin sections from our database, which wasas explained in
Section 3. In the following subsections, first our evaluation method is explained. Then the details of
experiments for finding the best value of the parameter and the best combination of input features for the
proposed clustering algorithm are shown. Afterwards, the results of the experiments on thin sections with
and without altered minerals are presented, and in the end, results of the proposed method are compared
with similar methods in the literature.
5.1 Method of evaluation
The proposed segmentation algorithm produces a segmentation map for each thin section. Normally, the
number of detected clusters is more than the number of actual minerals existing in thin sections, and some
of the detected clusters belong to the same mineral. In order to evaluate the segmentation map or clusters,
an expert was asked to determine the actual existing minerals in test thin sections. At the output of the
proposed algorithm, all clusters which belong to the same mineral are aggregated; the number of pixels in
these clusters is summed; and the result is divided by the number of pixels of that mineral in the thin
section image determined by the expert. This gives the segmentation accuracy for that specific mineral.
This process is repeated for all minerals existed in the thin section. In addition, the average segmentation
accuracy of the proposed algorithm is calculated for each thin section. The results are reported in the
following subsections.
5.2 Choosing the optimum value of the parameter
In order to estimate the optimum similarity threshold parameter () in the proposed clustering algorithm,
four experiments have beenwere conducted using different input feature combinations. The details of
16

these four experiments are presented in following paragraphs. For these experiments, ten (10) thin sections
have been chosen including five thin sections without altered minerals (see Fig. 10) and five thin sections
containing altered minerals (see Fig. 11).

A1

A2

B3

B2

C1

C2

D1

D2

E1

E2

Fig. 10. Five thin sections without altered minerals are used for finding the optimum value of . A1 and A2 refer to Amphibole
index mineral in plane and cross polarized lights, B1 and B2 refer to Biotite index mineral, C1and C2 refer to Nosane index
mineral, D1 and D2 refer to Quartz index mineral and E1 and E2 refer to Sanidine index mineral.

A1

A2

B3

17

B2

C1

C2

D1

E1

D2

E2

Fig. 11. Five thin sections containing altered minerals are used for finding the optimum value of . A1 and A2 refer to Actinolite
index mineral in plane and cross polarized lights, B1 and B2 refer to Aegirin index mineral, C1and C2 refer to Amphibole index
mineral, D1 and D2 refer to Chlorite index mineral and E1 and E2 refer to Enstatite index mineral.

The first experiment was carried out using a 112 feature vector including RGB and HSI components in
plane and cross polarized lights for each pixel. The results of this experiment are given in Table 2. For
both types of thin sections, the =0.90 yields more accurate results. In Table 3, the results of the second
experiment using a 16 feature vector including RGB components in plane and cross polarized lights for
each pixel is presented.

Nonlinear _ combinatio n Color _ component

2
Plane

Color _ component

2
Cross

Where =0.90 produces

more accurate results for this experiment. Furthermore, Table 4 indicates the results of third experiment
using 16 feature vector including HSI components in plane and cross polarized lights for each pixel.
Where =0.90 has more accurate results. The final experiment was conducted using a 16 feature vector
including a nonlinear combination of RGB and HSI color components in plane and cross polarized lights
based on Eq. 4. The results are presented in Table 5 where =0.9 yields to the most accurate results.
(3)
18

Table 2. The results of finding the best value of . A 112 vector including RGB and HSI components in plane and cross
polarized lights is established for each pixel. Both states of the thin sections have higher total accuracy when =0.90
Thin sections

Thin sections

without altered

containing

minerals

altered minerals

Accuracy when

Accuracy

Accuracy

Accuracy when

Accuracy

Accuracy

=0.80

when

when

=0.80

when

when

=0.85

=0.90

=0.85

=0.90

Amphibole

0.57

0.86

0.88

Actinolite

0.50

0.58

0.67

Biotite

0.60

0.80

0.90

Aegirin

0.50

0.83

0.92

Nosane

0.57

0.71

0.86

Amphibole

0.63

0.75

0.88

Quartz

0.57

0.86

1.00

Chlorite

0.54

0.85

0.85

Sanidine

1.00

1.00

1.00

Enstatite

0.57

0.71

0.71

Total

0.66

0.85

0.93

Total

0.55

0.74

0.81

accuracy

accuracy

Table 3. The results of finding the best value of . A 16 vector including RGB components in plane and cross polarized lights
is established for each pixel. Both states of the thin sections have higher total accuracy when =0.90
Thin sections

Thin sections

without

containing

altered

altered minerals

minerals

19

Accuracy

Accuracy

Accuracy

Accuracy when

Accuracy

Accuracy

when =0.80

when

when

=0.80

when

when

=0.85

=0.90

=0.85

=0.90

Amphibole

0.41

0.80

0.90

Actinolite

0.50

0.53

0.58

Biotite

0.52

0.71

0.83

Aegirin

0.48

0.75

0.85

Nosane

0.42

0.60

0.90

Amphibole

0.55

0.71

0.84

Quartz

0.51

0.79

1.00

Chlorite

0.43

0.72

0.78

Sanidine

1.00

1.00

1.00

Enstatite

0.49

0.57

0.65

Total

0.57

0.78

0.93

Total

0.49

0.66

0.74

accuracy

accuracy

Table 4. The results of finding the best value of . A 16 vector including HSI components in plane and cross polarized lights is
established for each pixel. Both states of the thin sections have higher total accuracy when =0.90
Thin sections

Thin sections

without

containing

altered

altered minerals

minerals
Accuracy

Accuracy

Accuracy

Accuracy when

Accuracy

Accuracy

when =0.80

when

when

=0.80

when

when

=0.85

=0.90

=0.85

=0.90

Amphibole

0.57

0.85

0.87

Actinolite

0.50

0.62

0.70

Biotite

0.67

0.80

0.86

Aegirin

0.58

0.79

0.85

Nosane

0.43

0.78

0.87

Amphibole

0.73

0.74

0.90

Quartz

0.57

0.80

1.00

Chlorite

0.62

0.83

0.86

Sanidine

0.72

0.85

0.91

Enstatite

0.41

0.65

0.80

Total

0.59

0.82

0.90

Total

0.57

0.73

0.82

accuracy

accuracy

20

Table 5. The results of finding the best value of . A 16 vector including nonlinear combination of plane and cross polarized
lights in RGB and HSI components (Eq. 3) is established for each pixel. Both states of the thin sections have higher total
accuracy when =0.90
Thin sections

Thin sections

without

containing

altered

altered minerals

minerals
Accuracy

Accuracy

Accuracy

Accuracy when

Accuracy

Accuracy

when =0.80

when

when

=0.80

when

when

=0.85

=0.90

=0.85

=0.90

Amphibole

0.51

0.87

1.00

Actinolite

0.45

0.55

0.80

Biotite

0.64

0.85

0.95

Aegirin

0.65

0.75

0.90

Nosane

0.70

0.77

0.90

Amphibole

0.71

0.80

0.92

Quartz

0.60

0.80

1.00

Chlorite

0.77

0.77

0.86

Sanidine

1.00

1.00

1.00

Enstatite

0.51

0.75

0.80

Total

0.69

0.86

0.97

Total

0.62

0.72

0.86

accuracy

accuracy

The overall results of these four experiments are shown in (Fig. 12). As shown in (Fig. 12), =0.90 and
nonlinear combination of plane and cross polarized lights in RGB and HSI color spaces as input features
yield the best results. This setup is fixed and used for final evaluation of the proposed algorithm.

21

Fig. 12. The accuracy of four different experiments of input feature vectors when =0.90. A 16 vector as input data set based
on nonlinear combination in plane and cross polarized lights for RGB and HSI components (Eq. 3) presents better results in
overall accuracy. Therefore, in the proposed algorithm =0.90 and nonlinear combination of plane and cross polarized lights as
input feature vector are fixed and used for minerals segmentation in thin sections.

5.3 Final evaluation of the proposed algorithm

In this section all images of all thin sections (165 images) existed in the database are segmented one by
one by the proposed algorithm. The overall accuracy of segmentation results is given in Table 6. Two
examples of segmented thin sections without altered minerals and containing altered minerals are also
shown and described below.
As shown in (Fig. 13), a thin section without altered minerals is used to evaluate the results of the
proposed method results in minerals segmentation.

22

A2

A1

B1

B3

B2

B4

B6

B5

Fig 13. The results of a thin section without altered minerals including Quartz index mineral (D1 and D2 in Fig .10). A1 and A2
refer to input data that assign to the clustering algorithm including nonlinear combination of the plane and cross polarized lights
in RGB and HSI components (Eq. 3), respectively. B1-B6 refer to the output of the clustering algorithm. Every black and white
image indicates a mineral cluster in the thin section images.

On the other hand, a thin section containing the altered minerals is used to evaluate the proposed algorithm
performance. As shown in (Fig. 14), a thin section containing the altered minerals with noisy pixels was
segmented by the proposed algorithm. It is important to note that the previous methods in the literature are
unable to segment the thin sections containing altered minerals such as the one shown in (Fig. 14). As seen
in Table 6, the overall accuracy of 92.15% and 85.24% has been obtained for thin sections without altered
minerals and thin sections containing altered minerals, respectively.

23

A1

A2

B1

B2

B3

B4

B5

B6

B7

B8

B9

B10

B11

Fig 14. The results of a thin section containing altered minerals including Aegirin index mineral (B1 and B2 in Fig .11). A1 and
A2 refer to input data that assign to the clustering algorithm, including nonlinear combination of the plane and cross polarized
lights RGB and HSI components (Eq. 3), respectively. B1-B11 refer to the output of the clustering algorithm. Every black and
white image indicates a mineral cluster in the thin section images.
Table 6. The final accuracy of the proposed method based on the database used.
Thin sections without altered minerals

Thin sections containing altered

minerals

Number of thin sections

43

122

24

92.15

Overall accuracy (%)

85.24

5.4 Discussion and comparison

In this paper, the focus was on intelligent mineral segmentation in thin sections, with a particular attention
to the thin sections containing to the altered minerals. The proposed method is based on incremental
learning, and it aims at not only obtaining real time results, but also segmenting minerals in thin sections
containing altered minerals. Given the literature, the proposed method is one of the first attempts to deal
with minerals segmentation in thin sections containing altered minerals with respect to the intelligent
approach. Converting information about minerals inside thin sections from low level pixel-based into high
level cluster-based is a significant point which plays an important role in image processing and image
analysis applications (Fig. 15).

Segmentation
process:
converting low
level pixel-based
information to
high level
minerals cluster
information

Fig 15. The conversion of low level pixel-based information into high-level cluster information minerals

In order to compare the results of the proposed method with the two previous methods as Zhou et al.
(2004-A) and Fueten and Mason (2007), image samples in these papers were used. It is important to note
that the proposed method needs plane polarized and cross polarized images from the thin sections;
however, in most previous papers including these two studies, cross polarized images were not used.
Hence, the proposed method was run only on plane polarized images in order to compare with these two
25

methods. The comparison of the intelligent segmentation algorithm used in this study with the method
based on edge detection and region growing presented by Zhou et al. (2004-A) is shown in Fig. 16. In
addition, the comparison of the proposed method with edge detection and artificial neural network (ANN)
algorithm proposed by Fueten and Mason (2007) is shown in Fig. 17. As seen in these two figures, the
results of the proposed method compares favorably with these two methods.

Fig. 16 Comparison of the proposed intelligent method with edge detection and ANN techniques (Zhou et al., 2004). A1: input
image and A2: result of Zhou et al. (2004) method. The other black and white images (B1-B16) are a final segmentation map
created by the proposed intelligent method.

26

Fig. 17 Comparison of the proposed intelligent method with edge detection and ANN techniques (Fueten and Mason, 2007).
A1: input image and A2: result of the method proposed by Fueten and Mason (2007). The other black and white images (B1B11) are final segmentation map created by the intelligent method used in this study.

6. Conclusions and Future Works

Minerals segmentation in thin sections is an essential step for minerals identification, in which names of
rocks will be determinedare based on the identified segmented minerals. In this paper, an intelligent
mineral segmentation method was introduced which was based on a new incremental clustering algorithm
and color features. Unlike other techniques, the clustering algorithm is based on an incremental learning
approach which does not require the number of index minerals (clusters) to be specified as an input
parameter. Utilizing image processing techniques, we extracted several features based on RGB and HSI
27

color spaces which were used by incremental clustering algorithm. Although most of the thin sections
created in industry are those containing altered minerals, the current state of the art methods are not able to
accurately segment minerals in such thin sections. However, the proposed method is able to segment
minerals in both thin sections with and without altered minerals with highly accurate results. In addition, as
a full automatic method, the proposed algorithm can be used in geological purposes which require real
time segmentation map of thin sections. Experiments indicate that the proposed methods results
outperform the results of other similar methods used in other studies cited in the literature. This is
particularly true for thin sections containing altered minerals. We obtained the overall accuracy of 92.15%
and 85.24% for segmenting thin sections without altered minerals and those containing altered minerals,
respectively.
In future, we would like to enrich our features set using texture and shape features which are extracted
from the thin section images.
Acknowledgments
We would like to express our gratitude to mineralogy and petrography laboratory at University of
Birjand that had very close collaboration with us by providing the thin sections of minerals.
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Highlights

An intelligent method for minerals segmentation in thin sections is proposed.

We use an incremental color clustering algorithm.
Our method works well in both thin sections with and without altered minerals.
We create a full automatic and real time segmentation map.
Our method can be applied in the NASA's Mars explorers.

30