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Two-dimensional sample entropy: assessing image texture through irregularity

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 Biomed. Phys. Eng. Express 2 (2016) 045002 doi:10.1088/2057-1976/2/4/045002

PAPER

Two-dimensional sample entropy: assessing image texture through

RECEIVED
17 November 2015
irregularity
REVISED
5 May 2016
ACCEPTED FOR PUBLICATION
L E V Silva1, A C S Senra Filho2, V P S Fazan3, J C Felipe2 and L O Murta Junior2
19 May 2016 1
Department of Physiology, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
2
PUBLISHED Department of Computing and Mathematics, Faculty of Philosophy, Science and Languages of Ribeirão Preto, University of São Paulo,
27 July 2016 Ribeirão Preto, SP, Brazil
3
Department of Surgery and Anatomy, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
E-mail: murta@ffclrp.usp.br

Keywords: sample entropy, texture quantifier, image irregularity, biomedical image analysis, sural nerve

Abstract
Image texture analysis is a key task in computer vision. Although various methods have been applied
to extract texture information, none of them are based on the principles of sample entropy, which is a
measurement of entropy rate. This paper proposes a two-dimensional sample entropy method,
namely SampEn2D, in order to measure irregularity in pixel patterns. We evaluated the proposed
method in three different situations: a set of simulated images generated by a deterministic function
corrupted with different levels of a stochastic influence; the Brodatz public texture database; and a real
biological image set of rat sural nerve. Evaluation with simulations showed SampEn2D as a robust
irregularity measure, closely following sample entropy properties. Results with Brodatz dataset
testified superiority of SampEn2D to separate different image categories compared to conventional
Haralick and wavelet descriptors. SampEn2D was also capable of discriminating rat sural nerve images
by age groups with high accuracy (AUROC = 0.844). No significant difference was found between
SampEn2D AUROC and those obtained with the best performed Haralick descriptors, i.e. entropy
(AUROC = 0.828), uniformity (AUROC = 0.833), homogeneity (AUROC = 0.938) and Wavelet
descriptors, i.e. Haar energy/entropy (AUROC = 0.932) and Daubechies energy/entropy
(AUROC = 0.859). In addition, it was shown that SampEn2D computation time increases with image
size, being around 1400 s for a 600 × 600 pixels image. In conclusion, SampEn2D showed to be stable
and robust enough to be applied as texture feature quantifier and irregularity properties, as measured
by SampEn2D, seem to be an important feature for image characterization in biomedical image
analysis.

1. Introduction spatial structure is taken into account. Haralick

Entropy measurement is ubiquitous in signal and
image analysis fields, as the only requirement for
entropy calculation is a probability distribution (Tsal-
lis 2009). A motivation for entropic methods relies on
the fact that these probabilities can be defined in
several ways, according to the problem under study.
Entropy is often computed from image using Shannon
entropy, where probability distribution is easily esti-
mated from image histogram. Although there are
some alternative approaches (Zhao and Ngo 2009,
Celik 2014), in most cases probability distribution
accounts only for individual pixels occurrence and no
entropy descriptor computes Shannon entropy from
an image co-occurrence matrix, and therefore
accounts for spatial pixel distribution, i.e. texture
patterns on image.
Measurement of entropy rates is usual in time ser-
ies analysis standing for systems complexity. Kolmo-
gorov–Sinai (KS) entropy is a theoretical definition of
entropy rate (Sprott 2003). KS entropy defines prob-
ability distribution as probability occurrences of each
system trajectory, calculated from phase space, and
computes the limit of Shannon entropy for n  ¥
and ò → 0, where n is the system time and ò is the size
of phase space hypercubes, i.e. state similarity

© 2016 IOP Publishing Ltd

Biomed. Phys. Eng. Express 2 (2016) 045002
tolerance. However, n  ¥ limit makes KS entropy
not applicable to finite time series.
Approximate entropy (ApEn) and sample
entropy (SampEn) emerged as computationally
feasible alternatives for KS. They can be applied to
finite time series, becoming widely used entropic mea-
sures (Pincus 1991, Richman and Moorman 2000).
SampEn was proposed as an improvement of ApEn,
which is known to have important biases (Richman
and Moorman 2000). Nevertheless, both ApEn and
SampEn are essentially irregularity measurements
(Pincus and Goldberger 1994). SampEn approaches
zero for signals with highly periodic patterns while is
higher for very irregular series, such as white noise.
SampEn is largely applied to analyze data series
such as heart rate variability and brain structural
measures (Richman and Moorman 2000, Chen and
Pham 2013).
In this paper, we propose the concept of two-
dimensional SampEn and evaluate its application for
image analysis. The method, namely SampEn2D, is an
extension of SampEn, and therefore is supposed to
quantify irregularity of two-dimensional pattern in
images. After defining the method, we present several
comparisons of SampEn and SampEn2D for the same
processes in one and two-dimensional cases. Finally,
we propose and evaluate the application of SampEn2D
to a public standard image set as well as to histological
images of nerves. These evaluations were performed
with the purpose of accessing its effectiveness as an
image texture descriptor.
2. Two-dimensional SampEn
SampEn was originally proposed as a measure of
irregularity for one-dimensional time series, and
quantifies the overall probability that two sequence of
m points that are similar will still be similar when the
following point is considered in both (i.e., m + 1
points). Two patterns are considered similar if the
absolute difference between each corresponding point
within the patterns is less than r. Eventually, SampEn
calculates the negative logarithm of this probability, so
that values close to zero indicate repeating patterns or
a predictive dynamics, i.e, regularity, whereas high
values point to nonrepeating patterns or unpredictable
dynamics, i.e. irregularity.
The probability described above can be computed
by counting the number of similar m and (m + 1)-
[# of x m + 1 (a , b) ∣ d [x m + 1 (i , j ) , x m + 1 (a , b)]  r ]
U im, j + 1 (r ) =
Nm - 1
length patterns, i.e. number of matches. Calculating
the ratio between (m + 1) and m matches, we obtain
conditional probabilities. One can note that, for
2
L E V Silva et al
signals where the number of matches for m is very
close to (m + 1)-length patterns, the ratio between
them will be close to one, and therefore, SampEn will
be close to zero. In this case of low SampEn, patterns
within the signals are very repetitive, predictable and
regular.
On the other hand, for signals where the number
of pattern matches for m is much larger than to m + 1,
the ratio between them is close to zero, resulting in a
large SampEn value. In this case, patterns within the
signals are very irregular, very unpredictable, as the
new points accounted for in (m + 1)-length patterns
are not similar at all.
Our extension of SampEn method for digital ima-
ges, considered a two-dimensional signal, was con-
cerned to maintain the original propose of SampEn as
a irregularity measure. Consider an arbitrary image u
(i, j) with W width and H height. Let xm(i, j) be the set
of pixels of u ranging columns j to j + m − 1 and lines i
to i + m − 1, i.e., x m (i , j ) = [u (i , j ), u (i , j + 1) ,...,
u (i , j + m - 1), u (i + 1, j ), u (i + 1, j + 1) ,... u
(i + 1, j + m - 1), ..., u (i + m - 1, j + m - 1)].
Shortly, xm(i, j) is the m-length square window with
origin at u(i, j).
Let Nm be the total number of square windows
within u that can be generated for both m and m + 1
size. It can be calculated by Nm = (W−m) * (H−m).
Note that the pixels in the last m lines and columns
cannot be used as pattern origins for both m and m + 1
sizes, following the same properties of SampEn (Rich-
man and Moorman 2000). Considering r a similarity
threshold, two-dimensional SampEn, namely
SampEn2D, is defined by
U m + 1 (r )
SampEn2D (u , m, r ) = -ln , (1)
U m (r )
where
i = H - m; j = W - m
1
U m (r ) =
Nm
å U im, j , (2)
i = 1; j = 1
U im, j (r )
[# of x m (a , b) ∣ d [x m (i , j ) , x m (a , b)]  r ] (3)
=
Nm - 1
and
i = H - m; j = W - m;
1
U m + 1 (r ) =
Nm
å U im, j + 1 (4)
i = 1; j = 1
, (5)
where a ranges from 1 to H−m, b ranges from 1 to W
− m and (a, b) ¹ (i, j). The distance function d is
defined by
Biomed. Phys. Eng. Express 2 (2016) 045002 L E V Silva et al

Figure 1. Example of SampEn2D pattern comparison scheme. A pattern match is obtained when all corresponding pixels within two
patterns are not different by more than r. In (a) there is a tridimensional example of MIX2D(p) process and in (b) a representative
window of pixels with amplification view. Dashed lines surround two patterns (m = 3). Those patterns are considered similar (match)
if all of the following conditions are satisfied: ∣u (12, 18) - u (9, 21)∣ < r , ∣u (12, 19) - u (9, 22)∣ < r , ∣u (12, 20) - u (9, 23)∣ <
r , ∣u (13, 18) - u (10, 21)∣ < r , ∣u (13, 19) - u (10, 22)∣ < r , ..., ∣u (14, 20) - u (11, 23)∣ < r .

d [x m (i , j ) , x m (a , b)] and Moorman 2000, Lake et al 2002, Costa et al 2005).

(6)
= max (∣u (i + k , j + l ) - u (a + k , b + l )∣) ,
where k and l ranges from 0 to m − 1.
In equations (3) and (5), the origin points (i, j) and
(a, b) must be different to exclude self-matches.
Equations (2)–(6) are almost the same defined in Sam-
pEn, except for Nm. Distance function is ideally the
same of SampEn, here extended for the two-dimen-
sional case, i.e., the differences are taken from each
corresponding pixels within the windows. Figure 1
illustrates the pattern comparison step. As similar to
original SampEn, r can be defined as a fraction of image
standard deviation as a normalization procedure.
The estimation of m and r parameters in SampEn
is a difficult task. Nevertheless, there are some studies
addressing this problem (Ramdani et al 2009, Liu
et al 2011). For signals such as those ones usually
found in heart rate variability analysis, values of m = 2
and r = 0.15 or r = 0.20 times the signals standard
deviation are common choices (Pincus 1991, Richman
As an irregularity measure, SampEn is expected to
increase with increasing amount of noise. On the other
hand, SampEn is expected to decrease with increasing
r, as it implies that more patterns will be considered
similar.
For SampEn2D, those parameters are expected to
play similar roles. However, changing m or r by the
same amount in one and two-dimensional methods
might have different aftereffect, once for m-length
time series patterns there are m comparisons, while for
images, m-length patterns correspond to m-square
matrix of pixels, and therefore, there will be m2 pixel
comparisons.
3. SampEn2D evaluation
In this section, we describe experimental procedures
for both parametric analysis and method validation in

3
Biomed. Phys. Eng. Express 2 (2016) 045002
Figure 2. Examples of images generated by MIX2D(p) process, sized 256 × 256 pixels, for (a) p = 0.1, (b) p = 0.5 and (c) p = 0.9.
Graphics in (d)–(f) represents the first row of each image, respectively. Note that as p  1, the resulting image gets closer to
completely random noise, i.e. an irregular image.
SampEn2D context. First, we describe a process to
generate two-dimensional image patterns with varying
level of white noise, namely MIX2D(p), used to analyze
the SampEn2D behavior with respect to r and m
parameters. The parameter evaluation is important to
validate SampEn2D. The use of other noisy images in
this analysis is also addressed. Then we describe the
public image set Brodatz, widely used to evaluate
texture analysis schemes and a methodological proce-
dure to determine the best parameters of SampEn2D
for a specific dataset. Finally, we describe a real
application to SampEn2D in a set of histological images
of rat sural nerve.
3.1. MIX processes
MIX(p) is a one-dimensional family of stochastic
processes which overlays sine function with comple-
tely random dynamics, according to the choice of
parametric probability p (0 < p < 1). The larger the p,
the more frequent is random dynamics (Pincus and
Goldberger 1994).
In order to evaluate SampEn2D and its parameters,
we introduce a family of two-dimensional MIX pro-
cesses, namely MIX2D(p), based on the one-dimen-
2pi 2pj
( )
sional definition. Let X i, j = sin 12 + sin 12 be a
sinusoidal image and Yi, j an image composed by uni-
form white noise pixels in the range [- 3 , 3 ]. In
addition, consider the random variable Zi, j, where Zi,
j = 1 with probability p and Zi, j = 0 with probability 1
−p. MIX2D(p) is defined by equation (7)
MIX2D ( p )i, j = (1 - Z i, j ) X i, j + Z i, j Yi, j .
In short, MIX2D(p) creates bidimensional sine
waves, replacing p of total number of pixels by random
L E V Silva et al
values uniformly distributed. According to the choice
of p, the resulting images present a specific degree of
spatial regularity, similar to what has been studied for
one-dimensional signals. MIX2D(p) was defined to
have zero mean and unit standard deviation for all p
values (Pincus and Goldberger 1994).
MIX2D(p) is a family of stochastic processes regu-
lated by the probability p. When p = 1, MIX2D(p) is
purely a random function, resulting in a highly irre-
gular image. The opposite occurs with p = 0, resulting
in a perfectly regular periodic image, i.e. bidimen-
sional sine function. Figure 2 shows sample images
generated by the MIX2D(p) process. Different levels of
irregularities might be detected by SampEn2D.
3.2. Noisy robustness
Besides MIX2D(p) process, we also evaluated
SampEn2D in a gray scaled reference image added with
different levels of noises. Uniform white noise and salt
and pepper noise were chosen for addition. Uniform
white noise consists of uniformly distributed uncorre-
lated values ranging from –127 to 127. Salt and pepper
is a binary uncorrelated noise, having values of 0 or
255. Figure 3 illustrates examples of reference images
( ) added by different levels of both noises. For uniform
white noise, the noise levels (p) correspond to the
attenuation of total noise. For example, uniform white
noise with intensity p = 0.5 correspond to random
values in the range [−64, 64]. After noise addition, the
final image is renormalized to guarantee the same
range values (0–255). For salt and pepper noise, the
(7) noise levels (p) correspond to the amount of pixels
replaced by binary values (0 or 255).
It is worth noting that salt and pepper noise addi-
tion procedure is quite similar to MIX2D(p) processes.
4
Biomed. Phys. Eng. Express 2 (2016) 045002 L E V Silva et al

Figure 3. Examples of a reference image, sized 256 × 256 pixels, added with different levels of uniform white noise (first row) and salt
and pepper noise (second row). Noise levels are 0.1 ((a) and (d)), 0.5 ((b) and (e)) and 0.9 ((c) and (f)). As can be seen, salt and pepper
noise result in more striking interferences in spatial pattern when compared with white noise.

Figure 4. Examples from Broadtz image dataset. Groups are numbered as in the original database: (a) 05, (b) 15, (c) 30, (d) 36, (e) 45,
(f) 75, (g) 93, (h) 95 and (i) 102. Each group is composed by 16 sample images with size 128 × 128 pixel.

However, in MIX2D(p) processes one has always the
same background image (sinusoid) and pixels are
replaced by uniform white noise, not by binary values.
On the other hand, addition of uniform white noise to
a reference image is different from MIX2D(p) because
in the latter pixels are replaced, while in the former
noise is added to original image values.
3.3. Brodatz image dataset
We accessed the effectiveness of SampEn2D in discri-
minating different texture patterns. Nine groups of
images representing different categories were selected
from Brodatz dataset (You and Cohen 1993, Abdel-
mounaime and Dong-Chen 2013, Jacob et al 2014).
From each group, we extracted 16 sample images sized

5
Biomed. Phys. Eng. Express 2 (2016) 045002
Figure 5. Examples of rat sural nerve transverse section for (a) a rat aged 30 days; and (b) a rat aged 720 days. Black horizontal bars
represent 10 μm.
Table 1. Definition of Haralick descriptors.
Descriptor Definition
Variance å i å j (i - j )2P (i , j )
Entropy å i å j P (i , j ) log P (i , j )
Uniformity å i å j P 2 (i , j )
(energy)
Homogeneity å i å j P (i , j ) (1 + ∣i - j∣)
3rd order moment å i å j (i - j )3P (i , j )
128 × 128 pixels. Figure 4 illustrates one image sample
from each category.
In order to compare the precision of SampEn2D,
we used Haralick and Wavelet descriptors. The Har-
alick descriptors are the most commonly used for
representing image texture: variance, entropy, uni-
formity (energy), homogeneity and 3rd order
moment. Their definition is shown in table 1. Coocur-
rence matrices were extracted considering four orien-
tations (0°, 45°, 90° and 135°) and ten interpixel
distances, i.e. ranging from 1 to 10 pixels. The inter-
pixel distance influences the result according to the
granularity of images. We decided to use a wide range
of distances to cover a larger variety of images. Each
Haralick descriptor was calculated for each coocur-
rence matrix and, to have a one-to-one comparison
with SampEn2D, we calculated the descriptor average
considering all the matrices. We also used Wavelets of
Haar and Daubechies in two levels of decomposition
and calculated the energy and entropy average from
the low-level images.
Group pairs were compared using ROC curves.
Area under ROC (AUROC) was used to measure the
quality of SampEn2D and the other descriptors in dis-
criminating groups.
3.4. Choosing the best parameters for SampEn2D
The best values of m and r might vary for different
datasets. Here we propose a simple methodological
L E V Silva et al
procedure to select those parameters according to the
Meaning image dataset. We illustrate the procedure with the
Brodatz database.
Contrast level First, SampEn2D is calculated for all images, vary-
Suavity ing r and m in a broad range. Here we chose
Uniformity 0.06 < r < 0.50 and 1 < m < 5. Next, for each m we
identify which r gives the best separation of groups. In
Homogeneity
this part, some distance or discriminant between
Distortion
groups must be used. We applied ROC curves for each
pair of groups and take de average AUROC for each r.
The best r is the one that gives the greater mean
AUROC, considering all pairwise comparisons.
In case of the Brodatz database we obtained:
AUROC = 0.958 (m = 1, r = 0.12), AUROC = 0.949
(m = 2, r = 0.32), AUROC = 0.969 (m = 3, r = 0.24),
AUROC = 0.967 (m = 4, 0.20) and AUROC = 0.952
(m = 5, 0.30).
Choosing the best m is a more difficult task. One
possibility is take the greatest AUROC considering all
m. However, one must be aware that the greater the m,
the greater the chance of no pattern matches in
SampEn2D calculation, and therefore, an undefined
SampEn2D value. For large m values, a large tolerance r
should be selected. For the Broadatz dataset, unde-
fined SampEn2D values were observed for r  0.06
(m = 2), r  0.14 (m = 3), r  0.20 (m = 4) and
r  0.24 (m = 5).
Here we choose the pair (m = 3, r = 0.24) for Bro-
datz database analysis, as it gives the greatest mean
AUROC without the risk of undefined SampEn2D.
3.5. Rat sural nerve image dataset
SampEn2D, Haralick and wavelet descriptors were also
applied to light microscopy images of rat sural nerve,
obtained from Wistar rats aged 30 (young group,
N = 12) and 720 days (elderly group, N = 16). A
semithin transverse section of sural nerve was obtained
for each rat and stained with 1% toluidine blue, which
is used to mark lipids, i.e. the myelin sheath. Images
were optically magnified with oil immersion lens
6
Biomed. Phys. Eng. Express 2 (2016) 045002
Figure 6. Entropy values for one and two-dimensional MIX processes. First row shows SampEn for MIX(p) process for (a) m = 1, (b)
m = 2 and (c) m = 3. Second row shows SampEn2D for MIX2D(p) process for (d) m = 1, (e) m = 2 and (f) m = 3. MIX(p) processes were
generated with 4096 points length and MIX2D(p) were generated with 265 × 256 pixels. As can be seen, both SampEn and SampEn2D
increases with increasing p for virtually all r values.
(100×), optovar (1.6×) and camera (0.5×), as well as
by computer (8×) (Jeronimo et al 2005, 2008). Figure 5
shows two examples of the images, obtained from rats
aged 30 and 720 days.
All images are sized 636 × 474 pixels. Descriptors
were computed for all images in both groups. Mean
values (standard error) are presented. SampEn2D para-
meters were set to m = 2 and r = 0.10 (10% of image
standard deviation) based on results obtained in a pre-
vious study (Silva et al 2014).
The ability to discriminate age groups were asses-
sed by Mann–Whitney rank sum test of median
values, as well as through ROC curves. The statistical
differences between the AUROC generated with
SampEn2D and the other descriptors were computed
using DeLong’s method (DeLong et al 1988, Sun and
Xu 2014). All p-values are reported.
4. Results and discussion
This section describes and discusses the results of
SampEn2D evaluation in three stages, namely valida-
tion of SampEn2D and its parameters, performance
with Brodatz database and application to sural nerves.
4.1. Validation of SampEn2D
Figure 6 shows entropy values for MIX(p) and
MIX2D(p) processes with increasing p, for three values
of m (1, 2 and 3) and different values of r. The higher
the p, the higher the amount of noise swapped in place
of deterministic component.
As MIX(p) represent periodic dynamics replaced
with stochastic values with a percentage p, SampEn, an
irregularity measurement, is expected to increase as p
7
L E V Silva et al
increases. Likewise, as SampEn2D was defined as an
extension of SampEn, it is also supposed to increase
with increasing p in MIX2D(p). Figure 6 shows that
SampEn2D resembles SampEn for this feature.
Although their similar curve profiles, SampEn2D
and SampEn present different absolute entropy values.
To understand that, consider m = 1. Both SampEn
and SampEn2D will compute the fraction of similar
patterns for m = 1 and m = 2, eventually taking the
ratio between those fractions (see equations (2), (4)
and (6)). For one-dimensional case, incrementing
m = 1 to m + 1 = 2 causes one more comparison for
similarity criteria. However, for two-dimensional
case, incrementing m = 1 to m + 1 = 2 cause three
more comparisons, as patterns are squared windows
of pixels. To satisfy the similarity criteria, all corresp-
onding pixels must be considered similar (see
equation (6)). Although the number of available pat-
terns is greater in the two-dimensional case, the incre-
ment from m to m + 1 requires more 2m + 1 pixels to
be all similar in the comparisons with other patterns.
Eventually, when ratio is calculated, SampEn2D is
likely to be higher than SampEn.
Figure 7 shows SampEn2D values for a sample
image (see figure 3), added with increasing amount of
uniform white noise and salt and pepper noise (also
indicated by p). Results are similar to findings with
MIX2D(p).
One can notice that the larger the number of
points of a signal, the larger the number of available
patterns the signal will have, and therefore, the better
the estimative of pattern occurrence probabilities.
Although the dependence of SampEn on signal length
has already been reported elsewhere (Richman and
Moorman 2000, Chen et al 2009, Yentes et al 2013), we
Biomed. Phys. Eng. Express 2 (2016) 045002 L E V Silva et al

Figure 7. SampEn2D values for increasing amount of salt and pepper noise (first row) and uniform white noise (second row). Results
are shown for m = 1 ((a) and (d)), m = 2 ((b) and (e)) and m = 3 ((c) and (f)). Horizontal axis (p) indicates the amount of noise added to
the reference image (see figure 3).

Figure 8. Dependence of SampEn on signal size. Six one-dimensional MIX processes were created for p = 0.3 (first row) and p = 0.7
(second row), with size ranging from 1000 to 21 000, step 4000. Results are shown for m = 1 ((a) and (d)), m = 2 ((b) and (e)) and m = 3
((c) and (f)).

calculated it for different lengths of MIX process and
compared to SampEn2D values obtained with different
sizes of MIX2D(p) process. Figure 8 show results for
SampEn and figure 9 for SampEn2D. MIX processes
were created with p = 0.3 and p = 0.7.
As can be seen, both SampEn and SampEn2D do
not vary much with signal and image size. Therefore,
SampEn2D can be considered robust for small image
sizes.
In some situations there is no entropy value due to
the absence of pattern matches. For example, in
figure 9(f) (m = 3), SampEn2D is not defined for low
image size and low r values. As m increases, less pattern
matches are expected to occur. For MIX2D(p) process
with p = 0.7, patterns are highly contaminated with
random values, leading to undefined SampEn2D. On
the other hand, MIX2D(p) process with p = 0.3 present
more regular patterns and SampEn2D is defined for all
r and image sizes (figure 9(c)).
4.2. Performance with Brodatz database
Figure 10 shows mean SampEn2D values obtained with
Brodatz image dataset. Each image group is associated
with a number (see figure 4).

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Biomed. Phys. Eng. Express 2 (2016) 045002 L E V Silva et al

Figure 9. Dependence of SampEn2D on image size. Six squared MIX2D(p) processes were created for p = 0.3 (first row) and p = 0.7
(second row), with size ranging from 100 to 600, step 100. Results are shown for m = 1 ((a) and (d)), m = 2 ((b) and (e)) and m = 3 ((c)
and (f)).

Figure 10. Average SampEn2D values for Brodatz image groups. SampEn2D was calculated for (a) m = 1, (b) m = 2 and (c) m = 3.

The best parameters of SampEn2D for this dataset Table 2. Average AUROC values obtained with SampEn2D,
have already been chosen (m = 3, r = 0.24) using ROC Haralick and Wavelet descriptors. The ‘best’ case comprises
groups 15, 36, 45, 93, 102 whereas the ‘worst’ case comprises
curves and are described in the previous section. We groups 30, 45, 75, 102. ROC curves were calculated for each
evaluated the effectiveness of SampEn2D in dis- pair within the case and mean AUROC are showed.
criminating Brodatz image groups in two ways: first, Descriptor Best case Worst case
we visually selected five groups whose SampEn2D
curves were nearly equidistantly separated and com- SampEn2D (m = 3, r = 0.24) 0.975 0.924
Haralick variance 0.896 0.907
pared one to each other; we call it the ‘best case’
Haralick entropy 0.927 0.825
(groups 15, 36, 45, 93 and 102). Second, we visually Haralick uniformity 0.887 0.813
identified groups which SampEn2D curves are super- Haralick homogeneity 0.885 0.798
imposed or very close one to each other; we call it the Haralick 3rd moment 0.943 0.917
‘worst case’ (groups 30, 45, 75 and 102). Haar energy 0.796* 0.908
Haar entropy 0.791* 0.867
Table 2 shows mean AUROC for SampEn2D, as
Daubechies energy 0.701* 0.829
well as values of AUROC calculated using Haralick Daubechies entropy 0.791* 0.842
and Wavelet descriptors.
As can be seen, SampEn2D outfits wavelet Note: *P < 0.05 compared to SampEn2D within each case.
descriptors for the best case (table 2, first row). For
the worst case, although no statistical difference was 4.3. Application to sural nerves
found, SampEn2D tend to have the highest mean Considering the sural nerve dataset, table 3 shows
AUROC. Therefore, even for very close SampEn2D mean values (standard error) for SampEn2D, Haralick
curves, it is possible to separate groups with high and wavelet descriptors, as well as the AUROC values
performance. calculated using each descriptor. Statistical

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Biomed. Phys. Eng. Express 2 (2016) 045002 L E V Silva et al

Table 3. Mean values (standard error) and AUROC of SampEn2D, Haralick and Wavelet descriptors for sural nerve images (30 days and
720 days).

Descriptor 30 days 720 days AUROC p-value

SampEn2D (m = 3, r = 0.24) 2.38 (0.57) 0.84 (0.19)* 0.844 —

Haralick variance 15.9 (1.6) 14.3 (0.8) 0.578 0.08
Haralick entropy 1.99 (0.03) 1.80 (0.04)* 0.828 0.90
Haralick uniformity 0.03 (0.01) 0.07 (0.01)* 0.833 0.91
Haralick homogeneity 0.47 (0.01) 0.54 (0.01)* 0.938 0.31
Haralick 3rd moment 120.8 (18.2) 110.6 (7.8) 0.521 0.03
Haar energy 2297 (176) 1060 (165)* 0.932 0.39
Haar entropy 263.1 (12.6) 158.0 (14.1)* 0.932 0.39
Daubechies energy 3549 (185) 1516 (328)* 0.859 0.90
Daubechies entropy 348.7 (11.1) 190.1 (24.6)* 0.859 0.90

Note: *P < 0.05 compared to group aged 30 days. P-values represent DeLong’s statistical significance of AUROC compared to SampEn2D.

Figure 11. Average computation time of SampEn2D for m = 1, m = 2 and m = 3 and image sizes 100 × 100, 200 × 200, 300 × 300,
400 × 400, 500 × 500 and 600 × 600.

significance (p-values) for AUROC compared to 4.4. SampEn2D computation time

SampEn2D are also shown in the table.
As can be seen, SampEn2D is significantly higher for
rats aged 30 days than to the aged 720 days, indicating
that sural nerve images of elderly rats are characterized
by more regular pixel patterns than the ones of young
rats. Of note, only Haralick variance and 3rd moment
did not give different values between age groups. In
agreement, analysis using ROC curves revealed poor dis-
crimination performances with variance and 3rd
moment Haralick descriptors. All the other descriptors
were able to discriminate quite well the ageing of sural
nerves, using different texture properties.
Most analysis of nerve images comprise the extrac-
tion of morphometric measures, which is a manual or
semi-automated process (Jeronimo et al 2005, 2008).
SampEn2D has the advantage to be a completely auto-
mated method. In addition, the level of irregularity of
patterns seems to be a valuable metric for characteriza-
tion of those kind of images. Results encourage future
use of SampEn2D in problems involving classification
of nerve images according to diseases.
SampEn2D algorithm was implemented in Java version
7. Figure 11 shows SampEn2D computation time average
(over the range 0.06  r  0.50) for squared images,
computed in a desktop computer with Intel Xeon CPU
E5405 2 Ghz Quad Core and 3.9 Gb of RAM. Increasing
image size increases considerably the computation time
as there are more pattern comparisons. Moreover, there
is a tendency of computation time to decrease with
increasing m because only those patterns that match for
m-length will be compared to m + 1 and matches
become more difficult to be found as m increases.
5. Conclusions
In this paper we introduced the concept of SampEn2D
and evaluated it as a tool for spatial image analysis
derived from widely used one-dimensional SampEn
method. We demonstrated that SampEn2D follows
SampEn properties, and therefore can be considered a
measure of irregularity. SampEn2D has also demon-
strated to be robust for small image sizes. As a texture

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Biomed. Phys. Eng. Express 2 (2016) 045002
descriptor, SampEn2D demonstrated to be useful and
also outperformed Haralick variance descriptor in
some situations. SampEn2D was also applied to
histological images, showing that pixel patterns reg-
ularity level can be an important metric for biomedical
image analysis and classification.
SampEn2D proposed here defines m-length pat-
terns as m × m matrices, and two patterns match only
when all corresponding pixels differs no more than r.
There are other possibilities for such definitions. For
example, patterns could be defined differently: as
l × m (not squared) matrices, as pixel cross, etc. In
addition, matches could be alternatively considered
when a percentage of pixels differs no more than r.
These are directions for future studies.
Rotation is very frequent in images and difficult to
previously determine, therefore, it is expected for an
image qualifier to be invariant to rotations. Since rota-
tions promoted in images would also rotate reference pat-
terns in SampEn2D, match counts would be the same.
Therefore SampEn2D is invariant to rotation. The same
reasoning can be applied to image translation, allowing to
conclude that SampEn2D is translation invariant.
SampEn2D is an entropy rate measure that
accounts for image spatial information and might be
useful in biomedical image analysis. We believe that
irregularity properties of images might be related to
important image features, such as texture patterns.
Further application studies can be conducted to verify
its effectiveness for other image datasets.
Acknowledgments
The authors would like to thank FAPESP (grants
2013/15445-8 and 2013/01111-0), CNPq (grant
300900/2013-9) and CAPES (grant PNPD20131672)
for the financial support.
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