Manuscript-05 15 19

DEVELOPMENT OF A FULLY-AUTOMATED BACTERIAL COLONY
COUNTER FOR Staphylococcus aureus USING IMAGE PROCESSING

TECHNIQUES
A Thesis Manuscript
Presented to the Faculty of the
Department of Computer Science and Technology
College of Engineering
Visayas State University
Visca, Baybay City, Leyte
In Partial Fulfillment of the

Requirements for the Degree of
BACHELOR OF SCIENCE IN COMPUTER SCIENCE
MICHAEL JAMES PORMANES ROJAS

JUNE 2019
TABLE OF CONTENTS
TITLE PAGE Title Page
LIST OF FIGURES
Figure No. Title Page
LIST OF TABLES
Table No. Title Page

2

TECHNIQUES
Michael James P. Rojas, June 2019

Visayas State University, Baybay City, Leyte, Philippines 6521-A
Michael Anthony Jay B. Regis, Adviser
Abstract
This study
Keywords:
2

TECHNIQUES
CHAPTER I
INTRODUCTION
Nature and Importance of the Study
Aba
Abaca fiber is considered as one of the strongest among natural fibers, which
is three times the lack of instruments for an objective measurement of fiber quality,
grading and classification have to be done by visual inspection, which is time-
consuming and costly.
Philippine Fiber Industry Development Authority (PhilFIDA) is a government
agency tasked to grade d
In a study by Sinon (2013), the grade of the abaca fiber image in the bundle
was predicted by
The study by Sinon (2013) did not determine the grade of the abaca fiber
based on its texture, which is
Tobias et. al. (2018) stated that CNN has achieved human-like performance in several
recognition tasks such
Convolutional Neural these layers can create a particular CNN architecture.
First, the convolution layer image/feature maps compare to other supervised
learning that learn

3
Statement of the Problem
The current abaca fiber grading procedure is done manually by visual
inspection. Hence, the lack of instrument in grading abaca fiber makes the manual
process not reliable, subjective, time-consuming and costly. In a previous study, abaca
fiber grade classifier system made by (Sinon, 2013) is only based on color using
abaca fiber colorimeter. This new study will find a new method in grading abaca fiber
by acquiring its raw input pixel values and the learnable filters will be applied.
Objectives of the Study
The study aims to develop an Abaca Fiber Grade Classification System that
can recognize the grade of abaca fiber based on its color and texture from a digital
image.
The specific objectives are to:
1. Implement a small version of VGGNet-16 convolutional neural network
architecture to be applied in the system as the classifier for the abaca fiber
grade bundle;
2. Make a photo box used for image acquisition of the bundled abaca fiber;
3. Design and develop an easy to use graphical user interface for the abaca fiber
grade classifier; and
4. Evaluate the performance of the classifier using accuracy and Cohen's kappa
statistic.
Significance of the Study
The method applied in the developed system can be used as an objective
measurement in the automation of abaca fiber bundle grading. The automated abaca
4
fiber grade classifier system would aid both the abaca producers and traders to fairly
grade the abaca produce.
Scope and Limitations of the Study
This study covers from counting of colonies in a petri dish that are circular in
shape, separation
Time and Place of the Study
The sample data gathered were from Ching bee Trading Corporation at Brgy.
Hilapnitan, Baybay City, Leyte. Images were taken in dark room at Brgy. Patag,
Baybay City, Leyte. The development and testing of the system were conducted at the
Department of Computer Science and Technology, Visayas State University from
February 2019 to May 2019.

5
CHAPTER II
REVIEW OF RELATED LITERATURE
Convolutional Neural Network
In the history of neural network, coming up with convolutional neural network
(CNN) is a
Furthermore, Rosebrock (2017) well explained the difference between feature-
based and CNN supervised learning methods. He mentioned that traditional feature-
based approach involves
Murugan (2017) stated that a CNN is a state-of-the-art machine learning
algorithm that reduces the number of parameters without compromising the
computational power of its
Convolutional Layer
This layer has two mechanisms that perform element-wise multiplication and
add up to bias:
Activation function
After convolutional
Pooling Layer
The most important information. Rosebrock, (2017) stated that this layer
operates in two
6
Fully Connected Layer
In this layer
VGG Very Deep 16 CNN Architecture
Zisserman & Simonyan (2015) are the creators of the VGGNet-16 architecture
shown in Fig. 3 above
Image classification of color texture
In image classif
Moreover, in a recent study by Cusano et al., (2016) they ensembled the hand-
crafted image
Classification using Different Neural Networks
In a study by (Sinon, 2013) the grade of the abaca fiber image in bundle was
predicted by two
7
CHAPTER III
MATERIALS AND METHODS
Materials and Requirements Elicitation
The abaca fiber samples (see Appendix A for the images) were obtained
through a letter request to the Ching bee Trading Corporation (see Appendix C.A) and
the actual grading of abaca fiber sample was done by Mr. Ariel C. Cinco (see Appendix
C.B). Twenty sample images of abaca fiber for each of the seven abaca fiber grades
were segregated for image acquisition. The ten sample images of each grade were used
for training and testing phase. A 16.0-megapixel phone camera Samsung S6 was used
to capture the abaca fiber images. And a photo box was created in acquiring abaca fiber
images (see Appendix B for design and bill of materials).
System Architecture Design
Shown in Fig. 5 below is the system architecture of the study. The abaca fiber
grade classifier
8
Figure 5. System Architecture of the Abaca Fiber Grade Classifier
Image Acquisition
The different viewpoint and illumination of the acquired digital image will
greatly affect the classification

9
a. b.
Figure 6. a. Location and b. Set-up in acquiring abaca fiber images
10
Figure 7. Proposed SmallVGGNet CNN Architecture Design

11
Training Phase:
Small VGGNet-16 CNN Architecture
The
Convolutional Layer
Convolution layer are set of parallel feature maps shown in Fig.8, formed after
sliding different
M −1 N −1 C
F=( I∗K )ij = ∑ ∑ ∑ Ii +m , j+n , c∗K p=cm,, q=0
n
+b i, j Eq. 1
m =0 n=0 c=0
Where:
F=( I∗K ) = feature map output after convolution
i = ith pixel in height of the feature map
j = jth
i,j
b = bias parameter
p,q
C =σ ¿ Eq. 2
m,n
Where:
M&N=
p ,q
b
Dim c
12
Where:
Figure 8. Left: learnable K kernels. Middle: Image. Right: After convolution the output,
called feature map.
Rectified Linear Unit
The weighted
Pooling Layer
The mechanism
13
Figure 9. An example of max pooling
Fully Connected Layer
After the poo
Initialization. From the
l−1 p ,q
a i =f (P ) Eqn. 7
Where:
Forward Propagation. All random weights values are set during this mechanism
and bias values is set 1 to make it the classification layer using in fully connected layers
that produces an estimate of the probability for each abaca grades as shown in Eqn. 12.
n
z =∑ wlij al−1
l
j
l
j +b j Eqn.8.1
i=1
l l
a j=σ (z j ) Eqn.8.2
Where:
14
z = linearly transformed net inputs of fully connected layer
l = first layers in the fully connected layer
j = single neuron in the l
l T
a =σ ( ( W ) a
l l−1 l
+b ) Eqn. 9
Where:
a =σ ( ( W ) a + b )
L L L−1TL
Eqn. 10
Where:
L=
Where:
Backward Propagation. After forward run, the output to the weights adjust from
its initial random value of weights and biases. During the update, the loss function of
final layer with respect to the parameters is computed first where the gradient of first
convolutional layer is computed last. And then, this process used a partial derivative of
15
one layer being reused in computation of partial derivative of another layers using chain
rule. In effect the loss function will decrease and the performance of the model increases.
This algorithm called backpropagation by updating its parameters to its best in order to
minimize the loss function. The nomenclature of every equation shown below:
Nomenclature of below formulas:
X = image/convolve feature maps
α = learning rate
σ = ReLU activation function
n = total number of training sample
L+ 1
ŷ i = predicted output value
y = matrix of actual labelled value of training set
y i = actual value from labelled training set
z = linearly transformed net inputs of fully connected layer
Loss function formula of ith neuron as the classification layer (L+1) with respect to the
predicted values ŷ iL+ 1:
∂ L ( ŷ L+1 , yi ) 1
i−n
yi 1− y i
= ∑ L+1
i
+ Eqn.14
∂ yi
L+1
n 1 ŷi L+1
1− ŷ i
Loss function formula with respect to weight w Li ,i−1 of ith neuron in the final layer L:
16
∂ L ( ŷ L+1 , yi ) 1
n
− y i 1− y i
i
∂ wiL,i−1
= ∑ ( L+ 1 +
n i=1 ŷ i 1− ŷ L+1
¿ )¿ ¿ Eqn.15
i
Loss function formula with respect to weights of every neuron in Lth layer:
[ ]
∂ L ( ŷ1 , y1 )
L+1
L
∂ L( ŷi
L+1
, y) ∂ w 1 ,i−1
L
= ⋮ =¿ Eqn.16
∂W
∂L(ŷ )
L+1
i ,y
i
L
∂w i ,i−1
Loss function formula with respect to bias b li in ith neuron in Lth layer:
∂ L ( ŷ L+1 , yi ) 1
n
∂ L ( ŷ iL+1 , y i ) ∂ ŷ iL+1
= ∑ =σ ( z L+1
i − yi )
i
Eqn.17
∂ bLi n i=1 ∂ ŷi L+1
∂ bi L
Loss function formula with respect to bias of every neurons at Lth layer:
[ ]
∂ L ( ŷ1 , y1 )
L+1
[ ]
σ ( z 1 ¿− y 1)
L L+1
∂ L( ŷi
L+1
, y) ∂b 1
L
= ⋮ = ⋮ Eqn.18
∂b
∂L(ŷ , yi ) σ (z ¿− y i)
L+1 L+ 1
i i
L
∂b i
Loss function formula with respect to weight of ith neuron at first layer l in fully
connected layer:
∂ L ( ŷ L+1
i , yi ) ∂ L ( ŷ iL+ 1 , y i ) ∂ ŷ L+1
i
l
y i−z i
= = Eqn.19
z i ( 1−z i )
l L+1 l l l
∂ wi ,i−1 ∂ ŷi ∂ w i ,i−1
17
Then, the loss function formula with respect to weight of all neuron at lth layer shown
below,
[ ][ ]
l
∂ L ( ŷ1 , y1 )
L+1
y1 −z1
z 1 ( 1−z 1 )
l l l
∂ L( ŷi
L+1
, y) ∂ w1 , o
l
= ⋮ = ⋮ Eqn.20
∂W l
∂L(ŷ )
L+1
i ,y
i
y i −z i
z ( 1−z i )
l l l
∂w i ,i−1 i
Loss function formula with respect to bias of ith neuron at lth layer l in fully connected
∂ L ( ŷ L+1
i , yi ) ∂ L ( ŷ iL+ 1 , y i ) ∂ ŷ L+1
i
l
= L+1 l
=z l−1
i − y i Eqn.21
∂b i ∂ŷ i ∂b i
Then, the loss function formula with respect to bias at the layer l shown below,
[ ]
∂ L ( ŷ1 , y1 )
L+1
[ ]
∂ L( ŷi
L+1
, y) ∂ b1
l
z l−1
1 − y1
l
= ⋮ = ⋮ Eqn.22
∂b l−1
∂L(ŷ , yi ) − yi
L+1
i
z i
l
∂b i
In performing the learning of CNN, it is necessary to update the learnable filters
and bias values in convolutional layers. But from the first layer in the fully connected
layer, the single long vectors from the pooled feature maps must be updated first. Below
is the loss function formula with respect to all input value:
∂ L ( ŷ L+1
n , yn ) ∂ L ( ŷ nL+1 , y n ) ∂ y nL+1
= Eqn.23
∂ ali ∂ y L+1
n ∂ al−1
i
18
After the single long vector updated, the reshaping of the long vector take place in
the pooling layer in Eqn. 24. Then, there are no parameters to be updated in this layer so
the up-sampling mechanism in Eqn. 25.
∂ L ( ŷn , yn)
L+1
p, q −1
P =f ( l
) Eqn. 24
∂ ai
∂ L ( ŷ L+1
i , yt )
p, q
=P p , q Eqn. 25
∂C m ,n
Then, the loss function formula with respect to the convolutional learnable filter
p ,q
k u ,v can be computed as shown in Eqn.26. Then, updated values of learnable filter k p ,q in
Eqn. 27.
∂ L ( ŷ L+1 , yi ) M −1 N−1
∂ L ( ŷ iL+1 , y n )
=∑ ∑
i
X m−u , n−v Eqn. 26
∂ k up,, vq m=0 n ∂C mp ,, qn
p ,q
°∗∂ L ( ŷ iL+1 , y n )
k =rot 180 Eqn. 27
∂ Cmp ,, qn
Finally, the loss function formula with respect to the bias b p ,q of the convolutional
learnable filter can be computed in Eqn.28.
∂ L ( ŷi , yi ) ∂ L( ŷi , yn )
L+ 1 M −1 N −1 L+1
b p ,q
= p ,q
=∑ ∑ p ,q
Eqn.28
∂b m=0 n ∂C m ,n
19
Model Optimizer and Training Regularization
In this part, the optimization techniques are developed for the model in order to
minimize the loss function in every update of the learning parameters such as WL+1, bL+1,
WL, bl, kp,q and bp,q at each iteration process on the basis of gradient descent. One of this is
the stochastic gradient descent optimization. The weight and bias update of fully
connected layer in classification layer L+1 in Eqn. 29.a & 29.b.
L+1 L+1
∂ L ( ŷ iL+1 , y )
W =W −α L
Eqn. 29.a
∂W
L+1 L+1
∂ L ( ŷ iL+1 , y )
b =b −α Eqn. 29.b
∂ bL
Where:
∂ L ( ŷ L+1
i , y)
L
= shown in Eqn.16
∂W
∂ L ( ŷ L+1
i , y)
= shown in Eqn.18
∂ bL
Then, the weight and bias update of fully connected layer in first layer l in Eqn.
30.a & 30.b.
l l
∂ L ( ŷ iL+1 , y )
W =W −α Eqn. 30.a
∂Wl
l l
∂ L ( ŷ L+1
i , y)
b =b −α Eqn. 30.b
∂ bl
20
Where:
∂ L( ŷi , y)
L+1
l
= shown in Eqn. 20
∂W
∂ L ( ŷ L+1
i , y)
= shown in Eqn. 22
∂ bl
Finally, the weight/pixel values and bias update of learnable filter in Eqn. 31.a &
31.b.
p ,q p, q
∂ L ( ŷ L+1
i , y)
k =k −α Eqn. 31.a
∂ k up,, vq
p .q
∂ L ( ŷ iL+1 , y )
b =α Eqn. 31.b
∂ k up,,qv
Where:
∂ L ( ŷ L+1
i , y)
= shown in Eqn. 26
∂ k up,v,q
∂ L ( ŷ L+1
i , y)
= shown in Eqn. 28
∂ k up,v,q
Importantly, a reminder for the overfitting when too many parameters of the
model can cause by having too few samples to learn in training process. Then, the
regularization techniques in training process such as data augmentation, dropout
regularization and batch normalization help to fight overfitting. Data augmentation

21
mechanism is to generate more training data from existing sample images, “augmenting”
the training data via a number of random transformations.
Dropout is one of the most effective and commonly used regularization
techniques. It works when applied after to a particular layer by simple consist of
randomly “dropping out” (i.e. setting the value to zeroed out if the value is less than or
equal to the initialize probability value). Then, the output values of a particular layer
break up the patterns that are not significant.
Batch normalization techniques is straightforward just centering the data in 0 by
subtracting the mean from the data and then giving the unit standard deviation by
dividing the data by its standard deviation. In result, the data follows a normal
distribution in which centered and scaled to unit variance. The advantage of this
technique is effective at reducing the number of epochs and large variety of learning rates
in every parameter in the network. But the drawback of this technique is the
computational time.
Implementation
The programming language used in this study was Python version 3.6 under
Spyder 3.3.3 integrated development environment within Anaconda distribution. Keras a
python deep learning library in python was used whose backend is Tensorflow API.
Additionally, Qt designer was used for the graphical user interface (GUI) and some
packages of python installed such as pyqt5, sklearn, imutils, matplotlib, numpy, pickle,
22
opencv, random, os and many more. Then, in evaluating the performance of the system
was done manually.
User Interface Design
The user interface
Figure 10. Use Case Diagram of the Abaca Fiber Classifier System
System Testing and Evaluation
The generated model and label files after several experiments will be subject for
testing in which uses a feed forward propagation. Ten sample abaca fibers per grade were
used as testing data to determine the performance of the system using kohen kappa
statistic and accuracy.by gathering the predicted output of the system and actual abaca
fiber grade based on the grading of PhilFIDA Inspector Mr. Ariel Cinco.
The evaluation of the system testing are follows:

23
1. Total False Prediction (TFP) – total false prediction in each grade of abaca
fiber when the system predicts.
2. Total True Prediction (TTP) - total true prediction in each grade of abaca fiber
when the system predicts

24
Table 1. Performance Evaluation using Confusion Matrix
Actual Abaca Fiber Grade based on PhilFIDA Inspector Mr. Ariel Cinco Total
Actual: S2 Actual: S3 Actual: I Actual: G Actual: H Actual: JK Actual: M1
Predicted: S2 (TTP) (TFP) (TFP) (TFP) (TFP) (TFP) (TFP) P:S2total
System Predicted: S3 (TFP) (TTP) (TFP) (TFP) (TFP) (TFP) (TFP) P:S3total
Predicted Predicted: I (TFP) (TFP) (TTP) (TFP) (TFP) (TFP) (TFP) P:Itotal
Grade Predicted: G (TFP) (TFP) (TFP) (TTP) (TFP) (TFP) (TFP) P:Gtotal
Predicted: H (TFP) (TFP) (TFP) (TFP) (TTP) (TFP) (TFP) P:Htotal
Predicted: JK (TFP) (TFP) (TFP) (TFP) (TFP) (TTP) (TFP) P:JKtotal
Predicted: M1 (TFP) (TFP) (TFP) (TFP) (TFP) (TFP) (TTP) P:M1total
Total A:S2total A:S3total A:Itotal A:Gtotal A:Htotal A:JKtotal A:M1total (Grand
Total)
25
To evaluate the performance, the computations formulae was conducted as follows:
1. Cohen’s kappa statistic – measures the precision between prediction of the system
and actual grading of abaca fiber. The kappa statistic value is calculated using
equation 4 and in table 3 shows an equivalent value.

i
TTP
∑ Pii= Grand total
Total
Eqn. 32
i=1
Where:
TTPtotal is the grand total of the Total True Prediction (TTP)
Grand Total is the total number of the test data.
[( )( )( )(
P : S 2total P :S 3 total P : I total P :Gtotal
i ∗A :S 2total ∗A : S 3total ∗A : I total
Grand Total Grand Total Grand Total Grand Total
∑ Pi +¿ P +i
=
Grand Total
+
Grand Total
+
Grand Total
+
Grand T
i=1
Eqn. 33
Where:
* = denotes S2, S3, I, G, H, JK & M1 grade
A:*total = grand total of each grade in the actual
P:*total = grand total of each grade
Grand Total = total number of the test data.

26
i ∑ Pi +¿P +i
κ=∑ Pii − i=1

i
¿ Eqn.
1−∑ Pi +¿ P ¿
i=1
+i
i=1
33
Where:
∑ Pii is the total proportion of main diagonal

i=1
∑ Pi +¿ P +i
¿ is the total proportion of marginal in the confusion matrix
i=1
Table 2. Cohen’s Kappa Equivalent Value
Value of Level of Percentage of Data that

Kappa Agreement are Reliable
0-.20 None 0-4%
0.21–0.39 Minimal 4-15%
0.40–0.59 Weak 15-35%
0.60–0.79 Moderate 35-63%
0.80–0.90 Strong 64-81%
Above .90 Almost Perfect 82-100%
2. Accuracy – measures on how the system corrects the prediction.
TTPtotal
accuracy= x 100 Eqn. 34
Grand Total
Where:
TTPtotal is the total number of correct identifications

27
Grand Total is the total number of test data
CHAPTER IV
RESULTS AND DISCUSSIONS
Building Virtual Environment
Before the actual implementation of the system, Anaconda Python distribution
which is open source and free must be installed. After installation set-up, virtual
environment must be
Keras is a one
Listing 1. Configuring keras.json file
{
"floatx": "float32",
"epsilon": 1e-07,
"backend": "tensorflow",
"image_data_format": "channels_last"
}
Importing Different Libraries
After the keras.json file configure, different libraries imported to one python file
only for the sake of simplicity in the throimplementation and to minimize its processing
time in accessing the classes and modules of different libraries.

28
Building Graphical User Interface Design
In the phase of implementation, Qt designer was used for the Graphical User
Interface (GUI) of the system. Then, the generated .ui file of the application is subjected
to conversion into python file using anaconda prompt as shown in Listing 2. The quoted
texts are subject to change. The generated python file for the GUI of the system was
imported to implementation of the system.
Listing 2. .ui file conversion to .py file

activate ‘createdVirtualEnvironment’
cd ‘directoryLocationOfTheUIFile’
python -m PyQt5.uic.pyuic -x ‘fileName’.ui -o ‘fileName’.py
Training Phase
Small VGGNet16 Architecture Implementation

The proposed architecture of the study was shown in Fig.7 in the methods section,
and the implementation is shown in Listing 3. Moreover, GUI design for the training
phase is shown in Fig. 10.
Listing 3. Small VGGNet16 Architecture Implementation
def smallVggModel(width, height, nChannels, abacaGrades):

genModel = Sequential()
inputShape = (height, width, nChannels)
changeDime = -1
genModel.add(Conv2D(32, (3, 3), padding="same",

input_shape=inputShape))
genModel.add(Activation("relu"))
genModel.add(BatchNormalization(axis=changeDime))
genModel.add(MaxPooling2D(pool_size=(3, 3)))
genModel.add(Dropout(0.25))
genModel.add(Conv2D(64, (3, 3), padding="same"))

29

genModel.add(Flatten())
genModel.add(Dense(1024))
genModel.add(BatchNormalization())
genModel.add(Dense(abacaGrades))
genModel.add(Activation("softmax"))
return genModel
30
Figure 11. Training Tab Interface of the system

When the user triggers the Load Image File Directory button a folder dialog is
prompted in order to locate the training dataset of the acquired images for training phase,
as shown in Fig. 11. After the start training button is triggered the training process begins,
as shown in Fig. 12.

31
Figure 12. Folder dialog when Load Image File Directory is triggered
Figure 13. Training process start when training button is triggered

32
If the user clicked the start training button without any file directory for training
dataset, it will prompt a warning sign in shown in Fig. 13 below.
Figure 14. A warning sign prompt when no file directory exists
After several experiments, the generated good model has training parameters of
learning rate set to 0.001, training epochs set to 100, random seed set to 42 and batch size
set to 32. At epoch 57 in the training process, achieved a minimum loss and then the
model is saved automatically using a poweful method called “callbacks” in Keras API.
Testing Phase
The generated model is tested with 70 images and the results are shown in Table
3. Confusion matrix is presented in Table 3 and the summary of performance in shown in
Table 5. Moreover, the interface design of this phase is shown in Fig. 14 below. Fig. 15
on the other hand shows when an image is loaded and the results of the prediction model.
33
Figure 15. Testing Tab Interface of the system
Figure 16. Prediction results of the abaca fiber image

34
While other feature of the system is to generate a model after the show
model button was click shown in Fig. 16and the detailed image shown in Appendix E.
Fig.17 and 18 shown the feature maps and specific feature map at every layer and Fig. -
19 shown the About Tab Interface of this system.
Figure 17. Model Summary of the model

35
Figure 18. Prediction results of the abaca fiber image
Figure 19. Specific feature map of a particular convolutional layer in the model
36
Figure 20. About Tab Interface
Performance Evaluation
Table 3. Results on the Abaca Fiber Grade Classifier System

Sample Actual Predicted Matched
No. Grade Grade Percentage Remarks
1 Current(I) Current(I) 79.99% Correct
11 Medium Brown(M1) Medium Brown(M1) 98.83% Correct
37

21 Seconds(JK) Soft Brown(H) 82.43% Wrong
22 Seconds(JK) Second(JK) 99.99% Correct
31 Soft Brown(H) Soft Brown(H) 100.00% Correct
41 Soft Second(G) Medium Brown(M1) 99.02% Wrong
42 Soft Second(G) Current(I) 75.12% Wrong
46 Soft Second(G) Current(I) 64.65% Wrong
51 Streaky Three(S3) Streaky Three(S3) 100.00% Correct
38

55 Streaky Three(S3) Medium Brown(M1) 82.29% Wrong
61 Streaky Two(S2) Streaky Two(S2) 100.00% Correct
39
Table 4. Confusion Matrix for the 70 images
Actual Abaca Fiber Grades based on PhilFIDA Inspector Mr. Ariel Cinco Total
Actual: Actual: Actual: Actual: Actual:
Actual: S3 Actual: I
S2 G H JK M1
Predicted: S2 10 0 0 0 0 0 0 10
System Predicted: S3 0 9 0 0 0 0 0 9
Predicted Predicted: I 0 0 10 2 0 0 0 12
Grades Predicted: G 0 0 0 0 0 0 0 0
Predicted: H 0 0 0 0 10 1 0 11
Predicted: JK 0 0 0 0 0 9 0 9
Predicted:M1 0 1 0 8 0 0 10 10
Total 10 10 10 10 10 10 10 70
Table 5. Summary of Performance Evaluation
Performance Measures Values

Accuracy 82.86%
Kappa Value 0.58
40
CHAPTER V
SUMMARY, CONCLUSION AND RECOMMENDATIONS
Summary
Classifying abaca fiber grades done by visual inspection based on its physical
features such as color and texture is difficult even with the aid of the expert. The process
is subjective, not reliable, time-consuming and costly. Thus, this study developed a
software that could be used to objectively augment the human capability in grading the
abaca fiber.
In a previous study, abaca fiber grade classifier system made by (Sinon, 2013) is
only based on color using abaca fiber colorimeter. However, Cusano et al., (2016)
implemented different kinds of image classification methods in raw food texture images
including CNN architectures under different lightning conditions. Results clearly showed
that the VGGNet-16 CNN architecture outperforms other with a high classification
accuracy of 98.21%. They concluded that the datasets taken under no variation in lighting
condition clearly boosts the performance of the different image classification methods.
The Python version 3.6 programming language with the aid of Spyder IDE 3.3.3
within Anaconda Python Distribution was used to develop the system. Specifically, Keras
deep learning library whose computational backend is TensorFlow for saving the trained
model and then pickle library for saving the grade labels of abaca fiber and many more
were installed within anaconda virtual environment.

41
Inspired by Cusano et al., (2016) paper, this study implements a small version of
VGGNet-16 architecture equipped with CPU Intel core i3 processor because the actual
architecture implementation uses high-end PC equipped with NVIDIA Titan GPU
processors. It consists of five convolutional layers followed by a rectified linear unit as
activation function, three pooling layers and 1024 inputs to fully connected layer and 7
outputs for different grades of abaca fiber. Moreover, a photo box is used for controlling
the illumination of the abaca fiber images.
Conclusion
The abaca fiber grade classifier system using a small version of VGGNet-16 CNN
architecture with the aid of photo box for acquisition set-up produce a result of 83%
classification accuracy and Cohen kappa level of agreement is weak. The developed
system was an effective alternative for the manual identification of abaca fiber grades
based on color texture classification provided by (PhilFIDA, 2016).
Recommendation
Based on the results, further study is recommended to build the high effectiveness
of the develop technique in order to improved its classification, through
1. Building an optimum model of the proposed small version of VGGNet-16
CNN architecture by tuning-in its training parameters with the aid of
GridSearchCV technique.
42
2. Actual implementation of VGGNet-16 CNN architecture in high-end PC
equip with GPU processors. Then, the image dimension from the acquisition
should not be large enough in order to retain the quality of the image when
rescaling technique apply.
3. Real-time implementation of the abaca fiber grade classifier system whether
in bundled or per strand.

43
LITERATURE CITED
Bianconi, F. (2011). Theoretical and experimental comparison of different approaches for

color texture classification. Journal of Electronic Imaging, p. 20.
Chollet, F. (2017). Deep Learning with Python. San Diego, USA: Manning Publications.
Cusano, C., Napoletano, P., & Schettini, R. (2016). Combining multiple features for color
texture classification. Journal of Electronic Imaging 25(6), p. 10.
Hakeem, K., Jawaid, R., & Rashid, U. (2014). Biomass and Bioenergy: Applications. In
R. Armecin, F. G. Sinon, & L. O. Moreno, Abaca Fiber: A Renewable Bio-
resource for Industrial Uses and Other Applications (pp. 108-119). Universiti
Putra Malaysia: Selangor , Malaysia: Springer International Publishing.
Ji, M., Liu, L., & Buchroithner, M. (2018). Identifying Collapsed Buildings Using Post-
Earthquake Satellite Imagery and Convolutional Neural Networks. MDPI, 20
pages.
Karpath, & Johnson. (2017). Convolutional Neural Networks. Retrieved 20 2018,
October, from CS231n: Convolutional Neural Networks for Visual Recognition:
http://cs231n.github.io/convolutional-networks/
Lecun, Bottou, Bengio, & Haffner. (1998). Gradient-Based Learning Applied to
Document Recognition. IEEE, 47.
Li, J., Liao, G., Ou, Z., & Jin, J. (2008). Rapeseed Seeds Classification by Machine
Vision. IEEE, pp. 146-149.
Mȁenpȁȁ, T., & Pietikȁnen, M. (2004). Classification with color and texture: jointly or
separately? Pattern Recognition, Pergamon, 12 pages.
Milan, P. P. (2005). Abaca and Rainforestation Farming: A guide to sustainable farming
management. Leyte State University, Baybay, Leyte,: Desktop Publishing.
Murugan, P. (2017). Feed Forward and Backward Run in Deep Convolution Neural
Network. arXiv:1711.03278v1 [cs.CV], 20.
Mussig, J. (2017). Industrial Applications of Natural Fibres: Structure, Properties and
Technical Applications. In F. G. Sinon, W. Muhlbauer, & F. GoltenBoth, Abaca -
Cultavation, Extraction and Processing (pp. 189 - 204). Department of
Biomimetics, Hochschule Bremen - University of Applied Sciences, Bremen,
Germany: A John Wiley and Sons, Ltd., Publication.
44
Naik, S., & Patel, B. (2013). Machine Vision based Fruit Classification and Grading - A
Review. International Journal of Computer Applications (p. 13). Uka Tarsadia
University, Bardoli, Surat, Gujarat, India: IEEE.
PhilFIDA. (2016). Abaca fiber: Grading and Classification – Hand-stripped and Spindle/
Machine stripped. Diliman, Quezon City: Philippine National Standard. Bureau of
Agriculture and Fisheries Standards.
PhilFIDA. (2018). Fiber Statistics. Retrieved October 28, 2018, from Philippine Fiber
Industry Development Authority: http://www.philfida.da.gov.ph/index.php/2016-
11-10-03-32-59/2016-11-11-07-56-39
Rosebrock, A. (2017). Deep Learning for Computer Vision with Python. California,
USA: Pyimagesearch.
Sinon, B. (2013). Development of an Abaca Fiber Grade Recognition System using
Neural Networks. Visayas State University (VSU), Baybay City, Leyte:
Undergraduate Thesis (Department of Computer Science and Technology).
TechSciResearch. (2018, October 28). Retrieved from Philippines Abaca Fiber Market
Forecast and Opportunities: https://www.techsciresearch.com/report/philippines-
abaca-fiber-market-forecast-and-opportunities-2019/390.html
Tobias, L., Ducournau, A., Rousseau, F., Mercier, G., & Fablet, R. (2018). Convolutional
Neural Networks for Object Recognition on Mobile Devices: a Case Study. IEEE,
p. 7.
Zisserman, A., & Simonyan, K. (2015). VERY DEEP CONVOLUTIONAL
NETWORKS FOR LARGE-SCALE IMAGE RECOGNITION. ICLR , 14 pages.
45
APPENDICES
46
APPENDIX A
ABACA FIBER IMAGES
STREAKY TWO (S2)

47
TRAINING SET IMAGES TESTING SET IMAGES
STREAKY THREE(S3)
48

49
CURRENT (I)

50
SECONDS (JK)

51
MEDIUM BROWN (M1)

52
SOFT BROWN (H)

53
SOFT SECOND (G)

54
APPENDIX B
PHOTO BOX DESIGN
Appendix Figure A. CAD Design of the Photo Box

55
Appendix Table B. Bill of Materials of the Photo Box

Quantity Unit Description Unit Cost Total Cost
(₱) (₱)
4 units LED Light 25.00 100.00
1 unit Lock 23.00 23.00
4 units Bisagra 9.00 36.00
3 m Wire 12.00 27.00
1 unit Adapter DC Plug 325.00 325.00
1 pc ½” x 2¾” x 45” lauan lumber 40.00 40.00
1 unit switch 25.00 25.00
Total Material Cost (TMC) 459.00

Labor Cost (35% of TMC) 160.65
TOTAL COST (TPC) 619.65
56
APPENDIX C
LETTER OF REQUEST
A. Gathering of Abaca Fibers
56
57
B. Grading of Abaca Fibers
57
58
APPENDIX D
Table 1. Normal grades of hand stripped abaca fiber
Grade Description
Name Alphanumer Fiber strand Color Stripping Texture
ic code size (in mm)
Mid current EF 0.20 – 0.50 Light ivory to a hue of very light brown to Excellent Soft
very light ochre
Streaky Two S2 0.20 – 0.50 Ivory white, slightly tinged with very light Excellent Soft
brown to red or purple streak
Streaky Three S3 0.20-0.50 Predominant color – light to dark read or Excellent Soft
purple or a shade of dull to dark brown
Current I 0.51-0.99 Very light brown to light brown Good Medium soft
Soft seconds G 0.51-0.99 Dingy white, light green and dull brown Good
Soft Brown H 0.51-0.99 Dark brown Good

Seconds JK 0.51-0.99 Dull brown to dingy light brown or dingy Fair
light yellow, frequently streaked with light
green
Medium brown M1 0.51-0.99 Dark brown to almost black Fair
Source: PhilFIDA. (2016). Abaca fiber: Grading and Classification – Hand-stripped and Spindle/ Machine stripped
58
59
APPENDIX E
59
60
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DEVELOPMENT OF A FULLY-AUTOMATED BACTERIAL COLONY

COUNTER FOR Staphylococcus aureus USING IMAGE PROCESSING

In Partial Fulfillment of the

MICHAEL JAMES PORMANES ROJAS

Figure No. Title Page

Table No. Title Page

DEVELOPMENT OF A FULLY-AUTOMATED BACTERIAL COLONY

Michael James P. Rojas, June 2019

Michael Anthony Jay B. Regis, Adviser

DEVELOPMENT OF A FULLY-AUTOMATED BACTERIAL COLONY

Nature and Importance of the Study

grading and classification have to be done by visual inspection, which is time-

consuming and costly.

Philippine Fiber Industry Development Authority (PhilFIDA) is a government

agency tasked to grade d

based on its texture, which is

recognition tasks such

Convolutional Neural these layers can create a particular CNN architecture.

First, the convolution layer image/feature maps compare to other supervised

learning that learn

Statement of the Problem

The current abaca fiber grading procedure is done manually by visual

Objectives of the Study

The specific objectives are to:

1. Implement a small version of VGGNet-16 convolutional neural network

grade classifier; and

Significance of the Study

The method applied in the developed system can be used as an objective

grade the abaca produce.

Scope and Limitations of the Study

Time and Place of the Study

Department of Computer Science and Technology, Visayas State University from

February 2019 to May 2019.

REVIEW OF RELATED LITERATURE

Convolutional Neural Network

In the history of neural network, coming up with convolutional neural network

Furthermore, Rosebrock (2017) well explained the difference between feature-

based approach involves

Murugan (2017) stated that a CNN is a state-of-the-art machine learning

algorithm that reduces the number of parameters without compromising the

computational power of its

Fully Connected Layer

VGG Very Deep 16 CNN Architecture

shown in Fig. 3 above

Image classification of color texture

Classification using Different Neural Networks

MATERIALS AND METHODS

Materials and Requirements Elicitation

images (see Appendix B for design and bill of materials).

System Architecture Design

Figure 5. System Architecture of the Abaca Fiber Grade Classifier

greatly affect the classification

Figure 7. Proposed SmallVGGNet CNN Architecture Design

Small VGGNet-16 CNN Architecture

F=( I∗K ) = feature map output after convolution

i = ith pixel in height of the feature map

Rectified Linear Unit

Figure 9. An example of max pooling

Fully Connected Layer

After the poo

Initialization. From the

z = linearly transformed net inputs of fully connected layer