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Plant Seedlings Classification using Transfer Learning

Conference Paper · July 2021
DOI: 10.1109/ICEEM52022.2021.9480654

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 2nd IEEE International Conference on Electronic Engineering, Menoufia University, Egypt
ICEEM2021, 3-4 July 2021

Plant Seedlings Classification using Transfer

Learning
Esraa Hassan 1, Mahmoud Shams1 Noha A. Hikal 3 Samir Elmuogy 4

1 Dept. of Machine Learning and Information Retrieval, Faculty of Artificial Intelligence, Kafrelsheikh University, Kafrelsheikh, Egypt
2 Dept. of Information Technology, Faculty of Computers and Information, Mansoura University, Mansoura, 35516, Egypt
3 Dept. of Computer Science, Faculty of Computers and Information, Mansoura University, Mansoura, 35516, Egypt

Abstract
Agriculture is essential for human survival and continues to be a major economic engine in many countries around the world. The
number of macro organism species on the planet is estimated to be about ten million. Automatic plants image recognition is the
most promising solution for closing the botanical taxonomic gap, and it has gotten a lot of attention from the botany and computer
communities. Previous machine vision systems for selective weeding have struggled to identify weeds reliably and accurately.
Traditional classification workflows are sluggish and error-prone; classification expertise is held by a small number of expert
taxonomists; and, to make matters worse, classification expertise is held by a small number of expert taxonomists. In recent years,
the number of taxonomists has gradually decreased. Automated organism identification has thus become more than a wish, but a
necessity for better understanding, using, and preserving biodiversity. This paper gives an overview of recent attempts to classify
species using computer vision and machine learning techniques. It concentrates on identifying plant species using leaf images.
With a dataset containing 4,275 photos of 12 species at various growth stages, we present approaches for plant seedling
classification. We compare the results of two commonly used image classification algorithms: The Convolutional Neural Network
(CNN) and transfer learning. Our proposed model achieved 0.9754,0.9742,0.9766,0.9754 In terms of, Accuracy, Sensitivity,
Specificity, Fscore, respectively. Both standard machine learning approaches and those using Convolution Neural Networks
compare the results.
Keywords: Deep learning, CNN, Plant Seedlings, Automatic classification.

1.Introduction
Weeds have little nutritional or medicinal value but have rapid growth and compete parasitically with actual crops for
nutrients and space. Inefficient practices such as hand weeding resulted in substantial losses and rising manual
laborrelated costs. The world suffers from a shortage of the experts of plants classification that requires specialized
experts. The robots and the vision machines must be able to identify a weed from the useful plants with accuracy and
reliability. Built machine vision technologies for selective weeding face a challenge of effective and accurate weed
detection. Owing to uncertain crop borders, with varying rocky or sandy backgrounds, it is not easy to recognize
weeds, and as a result, conventional methods of classification are likely to fail in this mission. The use of traditional
machine learning techniques for image classification suffers from some challenges in processing original input
data[1].The use of new technology based on deep learning technology helps to classify plant images and create new
plant classification tools that help non-specialists to identify them. The smartphones with high-resolution cameras
allow a huge amount of raw images to be easily collected and available plants dataset over the internet. Deep learning
applications, that have brought important breakthroughs in image classification and image segmentation, have also
shown a great performance in plant classification. Comparing with shallow learning, Deep learning is distinctive for
extracting high-level and useful features which simulated the human visual cortex[2][3]. Figure (1) shows how neural
networks imitate the human visual processing neural structure. The edges of an object are recognized in the retina as
the parts with the greatest difference in strength of reflected light, and the result is sent to the lateral geniculate nucleus
(LGN). The proposed model improves the pre-training that enhanced by adding a large set of unlabeled tiny images to
layer-features on a large set of Plants images. The exploration of the graphical processing units and applying a pre-
trained model became the starting point of CNN’s success in the field of image classification. Great advancements in
image classification were also made with deeper CNNs. The ability to predict previously unseen data is central to the

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CNN concept. Deep neural networks require millions of input data to be trained from scratch, which necessitates high-
performance hardware and takes one or more weeks. These issues can be solved with transfer learning. is fine-tuned
by using a pre-trained model that already exists Classify a new set of images[4]. When opposed to training a network
from the ground up, transfer learning is usually much quicker and easier to implement. In plant species classification
tasks, transfer learning demonstrated a high degree of accuracy[5]. Just a few people looked into plant seedlings.
Inception v3, ResNet50, and VGG19, three pre-trained deep learning models, were fine-tuned to identify images of
plant seedlings in this paper. The proposed model ensemble should have better output and generalization and should be
able to simulate real-world conditions with less error prediction. We can be used to solve a variety of image
classification problems by automatically generating deep neural networks for various image classification datasets and
optimizing the network structure as it evolves[6][7].

Latest evidence on deep learning architecture has shown that image classification models based on deep learning
models outperform models learned using CNN classifiers. None of the studies listed above have looked into the
benefits of deep learning architecture. The main goal of this paper is to use a model to implement an accurate DL
model for classifying plant seeding images to 12 types of plants. This study contributes to the classification of malaria
parasites by developing a more effective model when compared to previous research. Nkemelu [8]present approaches
to classification of plant seedlings with a dataset containing 4,275 images of approximately 960 distinct plants
belonging to 12 species at multiple growth stages. [] Compare the outputs of two standard algorithms and a
Convolutional Neural Network (CNN), a deep learning technique commonly applied to image recognition. Jeon [4]
present three deep learning models for classifying photos of indigenous Philippine plant seedlings into five species.
Throughout this end, AlexNet, GoogLeNet, and ResNet50 have been finely tuned. The weight and bias learning rate
factors of the fully linked layers were both increased to 20 for accelerating learning in the three pre-trained models.
Enhancement methods such as rotation, random.

Lateral Geniculate Nucleus

LGN

Retina

Figure (1): Human visual structure.

This paper is organized as follows, In Section 2 presents the proposed work. Section 3 and section 4 show the
experimentations and its results. Section 5 discusses conclusions and future work.

2. Preliminaries
Seedling classification is a discipline that has gained a lot of traction in precision agriculture because it allows for field
observation from afar, laying the groundwork for more effective weed control. Fine-grained weed control relies
heavily on the precision of the classification process, so that the crops are not affected while the weeds are being

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 2nd IEEE International Conference on Electronic Engineering, Menoufia University, Egypt
ICEEM2021, 3-4 July 2021

handled. As a result, misclassification would have an immediate effect on crop yield. Multiple linear and nonlinear
transformations of input data are used to construct DL algorithms, with the aim of creating more abstract and
discriminative representations. These techniques have greatly enhanced state-of-the-art speech recognition, visual
object recognition, object detection, and a number of other areas, including drug discovery and genomics. The DL
model was trained on over one million images, and its success has brought in a revolution in computer vision. DL
applications for solving complex, real-world problems have become more feasible as a result of recent developments
in the field. In the literature, classification of crop and weed species has been suggested as a strategy that relies on
deep learning techniques to classify plant seedlings. flip, and random horizontally and vertically translations were
performed to training images to avoid the effects of overfitting. Figure (1) illustrates the proposed DL model, which is
structured of four main steps, namely, (i) Data Preparation (DP) (ii) Pre-Trained model (PT), (iii) Feature Extraction
(FS), and (iv) Classifier and loss function (CL). During DP, neural networks are processed to prepare the data by using
pre-processing and data augmentation for use in training and testing. PT is used to resolve the question of a lack of
training data while also reducing overall training time. FS is used to choose the most efficient features for detection
and, as a result, decreases the detection model's complexity as well as the input data's dimensionality. During the
learning process, CL minimizes the error for each training data.
Data Collection
Plant Seedings dataset are splitted to (60,20,20)

Data Preparation
Resize images Data augmentation Normalization

Pre-Trained model
VGG(19) Resnet(50) Inception V3

Feature Extraction
Training Features Testing Features

Classification
Trainer Classifier

Figure (2): The main outlines of the proposed work.

2.1. Data Preparation (DP)

The data is prepared for use during model training and testing in the Data Preparation (DP) phase. The information
gathered is then stored in a csv excel file. The data is then further processed in order to prepare it for use in the
following phases. I Since the resizing of images in the data set is not always consistent, we must resize the images to
224*224 before feeding them to the neural network. Data augmentation is used not only to artificially increase the size
of our used dataset, but also to reduce the chance of errors. Even, to reduce the total noise in the data sets. Flip, rotate,
scale, flip scale, and histogram equalization are some of the image transformations we use. When the distribution of
our data isn't quite uniform or the number of samples to feed the model isn't sufficient enough, data augmentation will
be used[9]. The sample images rotation, distance, width, height, horizontal flip, vertical flip is randomly transformed,
and the size of the training data may be larger than before, thanks to crop, rotating, color, or something else to produce
more images based on the original data. A general overview of the applied deep learning models in this study is
discussed in this section. Data Normalization, which converts non-numeric data elements into a standardized numeric
representation.

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 2nd IEEE International Conference on Electronic Engineering, Menoufia University, Egypt
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2.2. Pre-Trained model (PT)

We use several pre-trained models, Inception V3, ResNet(50) model, and VGG(19) model. In this paper, the CNN
model is a robust model for most image processing tasks, including classification for different types of plant seeding.
In contrast to other methods, it involves a large amount of training data; however, the dataset we were given already
meets this criterion. A Convolutional Neural Network (CNN) is a deep learning algorithm that has three layers: an
input layer, hidden layers, and an output layer. All of the seedling images have been resized to 224x224 pixels (The
size of images can be resized empirically so as to get more satisfactory performance and fit to the input layer).And the
hidden layers consist of a lot of layers which will be illustrated in the following table: Following are the layers which
are used to construct the CNN model: The Convolutional layer will compute the output of neurons that are connected
to local regions in the input, each computing a dot product between their weights and a small region they are
connected to in the input volume. The Convolutional layers in this model have 32,64,128 filters. Pool layer conducts
downsampling operation along the spatial dimension (width, height), These are used to cut down on computing costs
and, to a degree, overfitting Each neuron in the dense layer, also known as the fully-connected layer, will be connected
to all of the neurons in the previous layer. Each dense layer node produces a score that corresponds to a class score.
The dropout layer is a regularization method for fighting over-fitting of the training package. It 'drops' neurons at
random (setting their weights to zero) for each iteration, resulting in a simplified version of the CNN and making it
impossible for the model to overfit. From pre-processing to classification, this section explains how we used deep
learning to classify plant images as shown in Figure (3). This section also discusses essential pre-processing steps, as
well as training and testing requirements. CNNs are predominantly used in agriculture for identification and
classification activities, and they have been shown to yield superior performance. In contrast to other methods, it

involves a large amount of training data; however, the dataset we were given already meets this criterion.

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ImageNet Dataset Convolutional Layers Full Connected Layers Predicted Labels

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Trained Weighted Transfer Train from Scratch

 2nd IEEE International Conference on Electronic Engineering, Menoufia University, Egypt
ICEEM2021, 3-4 July 2021

Convolutional layers Full connection layers

Plant Seeding Dataset Predicted labels

Figure (3): The main outlines of the proposed model depends on transfer learning.

2.2.1 Inception V3
A deep neural network must be designed appropriately to deal with a wide range of characteristic differences between
images. The image recognition model called Inception-v3 depends on feature extraction and classifier. Inception V3 is
used as pre-trained model by applying it with 1000 classes. The idea of transfer learning is based on reusing the
feature extraction section and re-training the classification section with new dataset[7].

2.2.2 ResNet50
Using the identity, residual blocks are used to reparametrize features. Adding residual blocks to a function increases its
complexity in a well-defined way. By having residual blocks transfer data via cross-layer, we can train an efficient
deep neural network that achieves an efficient result. Skip connection in ResNet50 relieves vanishing gradient by
adding an alternate shortcut way for gradient to flow over It teaches the model by showing that the higher layer can
perform at least as well as the lower layer, if not better. It is divided into five stages, each with a convolution and
identity block. Each identity block has three convolution layers, and each convolution block has three convolution
layers. There are over 23 million trainable parameters in it.

2.2.3 VGG19
A deep convolutional network for object recognition is generally referred to as VGG (19). Many other datasets use
VGG's overall architecture as a successful classification architecture. It can be updated for other related tasks now that
the authors have made it public. Other systems, such as Keras, have VGG (19) weights readily available. The proposed
architecture is based on VGG (19), which was built through a series of experiments involving deeper and faster
automatic classification.
2.3. Feature Extraction (FS)
Feature extraction is the process of reducing the amount of resources needed to represent a large amount of data. One of the major
issues with performing complex data analysis is the large number of variables involved. A study with a large number of variables
typically necessitates a lot of memory and computing power, it can also cause a classification algorithm to overfit to training
samples and perform poorly when applied to new samples. Feature extraction is a broad term that refers to methods for
constructing combinations of variables to get around these issues while still accurately representing the data. Many practitioners of
machine learning claim that properly optimized feature extraction is the secret to building successful models.

2.4. Classifier and loss function (CL).

The pre-trained model can be used to extract features from plant images as a standalone program. In fact, the derived features of
an image may be a vector of numbers that the model would use to represent the image's basic features. These characteristics would
then be used as feedback in the construction of a new model. The last few layers of the VGG (16) model are completely connected
before the output layer. These layers would have a complicated set of features to represent a given input image, which can provide
useful input when training a new image recognition model or other computer vision tasks. The image can be loaded and prepared
for the model, just as we did in the previous example.

2.5 Data Training and Network Architecture

ImageNet [10]is used to implement the deep learning network classifier in depth, ImageNet was used to categories
over a million images into 1000 classes using the ImageNet database for training. We trained our network using

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ImageNet for the classification of plant images using transfer learning, which involves using pre-trained models as a
baseline to create CNN networks. Transfer learning is typically a quicker and more convenient way to fine-tune a
network than teaching a device from scratch. This is accomplished by reusing the network, which has previously
learned the lowlevel features of images and is now learning specific features. The main stage in the proposed
architecture is the training stage in which the collected data is used to train network architecture. Each category needs
to be explained well enough so that the training can generalize to new inputs data. There are very restricted datasets as
well as limited practice in labeling the data specific to the virus in humans. It is not obvious which there are enough
plant images for achieving reliable learning at this early step of data collection despite the increasing critical
importance of this model. We all know it is easy to calculate the activation size, considering it’s merely the product’s
width, height and the number of channels in that layer.

3 System Design and Implementation

This study was implemented using python 3.2 on a computer equipped with Intel Core i7- CPU @2.50 GHz and 2.59
GHz and 8GB of RAM.

3.1 Dataset
The dataset used contains 4275 images of approximately 960 specific plants belonging to 12 species at various growth
stages, provided by the Aarhus University Signal Processing group in collaboration with the University of Southern
Denmark as shown in Figure (4) [11]. The information is mainly intended for research aimed at identifying plant
species in their early stages of development. The images are divided into 12 categories, as seen in the diagrams above.
Each class has rgb images of plants at various stages of development. The images are in png format and come in a
variety of sizes. As a result, in our project data preprocessing, we'll resize the image, normalize it to match the model,
and convert the pixels to matrices.

Figure (4): The sample from the plant seeding dataset.

3.2 Implementation
As described in Section II, four deep learning models were used in this analysis, with the dataset being randomly
divided into 60 percent training, 20 percent validation, and 20 percent test sets. Every pre-trained network's last three
layers were fine-tuned to classify images of plant seedlings into 12 species. Except for the last three layers of each pre-
trained network, all of the layers were extracted. After that, a fully linked layer, a softmax layer, and a classification
output layer were added in place of the last three layers. Since transfer learning necessitates that the input images
match the network's scale, each image was resized accordingly. Input to AlexNet is 227 x 227, and 224 x 224 for
GoogLeNet and ResNet50. To speed up learning, the weight and bias learning rate factors of the fully connected layer

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 2nd IEEE International Conference on Electronic Engineering, Menoufia University, Egypt
ICEEM2021, 3-4 July 2021

were both adjusted to 20. A variety of label preserving image transforms were used to create a powerful image
classifier that avoids the effect of overfitting and prevents the network from memorizing the exact details of the
training images. These include image rotations of up to 30 degrees, random flips along the vertical axis, and random
horizontal and vertical translations of up to 30 pixels. With a mini-batch size of ten, stochastic gradient descent with
momentum optimizer was used for training. The learning rate is set to 0.0001 and the models are trained over a span of
up to 100 iterations.

4.Results and Analysis

The experiment used 4750 images of plant seedlings. The aim of this analysis is to see how well fine-tuning the three
deep learning models works when it comes to classifying images into 12 different species. The validation data was
used to evaluate and measure each model's results. Furthermore, the aim of this research is to find the best deep
learning model for output accuracy. The output accuracies obtained by each deep learning model are summarized in
Table I. All of the models performed admirably, with accuracy levels exceeding 90%. ResNet50 was the most reliable
of the four, with a score of 0.9708 percent. Plant seedlings that are native to the region. Figure The training behavior of
the three models ResNet50 managed to overcome the two models based on the accuracy performance and loss
function.

5.Performance measures
Several performance measures are used to validate the effectiveness of pre-trained DCNN models with transfer
learning by using Sensitivity, specificity, and accuracy which are the most chosen measures. Precise classification is
Related to the quality and specificity of the Terms: true positive (TP), true negative (TN) (FN), and (FP) false positive.
TP is the abnormal number of images that are categorized as irregular, TN is the normal number of Images that are
classified as regular, FP is the normal number of Photos that are labeled abnormal, and FN is the number of abnormal
photos that are labeled normal. The Accuracy sensitivity, specificity, and F1-score are presented in equation
(1), (2), (3), (4), (5). This experiment is mentioned in Table 1 for100 training epochs. Table 7 shows a comparison
between the same measures for 50 epochs and Table 9 and Table 10 shows the results of 100 training epochs. Training
the Proposed model with RGB images depends on different training epochs and image sizes achieves unsatisfied
results for malaria cell images.
Accuracy

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 2nd IEEE International Conference on Electronic Engineering, Menoufia University, Egypt
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-&’
=
(5)
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The above interventions are only effective in The Balanced Dataset Scenario. Unbalanced data sets necessitate further
research using additional performance metrics. Additional indices were determined using the uncertainty matrix,
which included the F-score.
5.1. Training using Several Pre-Trained Architecture

In this section, comparing MCN model with Residual and VGG common neural network architecture and by using
images for malaria cell images.

5.1.1 Inception V3
We use Inception V3 in this paper to concentrate on salient sections of the picture that may have a lot of size variance.
The classifiers didn't make much of a difference until near the end of the training phase, when precision was reaching
saturation, so add the ad delta Optimizer and Batch Standard to the Auxiliary Classifiers to boost the network. After
training proposed model depends on Inception V3 pre-trained model with using 50 epochs as shown in Figure (5).

(a) (b)

Figure (5): (a) The average accuracy of model depends on Inception, (b) Loss of model depends on Inception V3.

5.1.2 Residual Neural Network (ResNet50)

The principle of Residual (Skip Connection) is a fascinating addition to CNNs that has been shown to boost ImageNet
classification efficiency empirically. These layers can be used for image classification and other tasks that include
Deep networks. After training model depends on ResNet50 pre-trained model and RGB color mode with using 100
epochs not satisfied as shown in Figure (6).

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 2nd IEEE International Conference on Electronic Engineering, Menoufia University, Egypt
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(a) (b)

Figure (6): (a) The average accuracy of model depends on Inception, (b) Loss of model depends on ResNet(50).

5.1.3 Visual Geometry Group (VGG19)

In the first convolutional layer, VGG is concentrating on smaller window sizes and strides; the overall architecture is
mentioned above. Accuracy, precision, recall, and F-score were used to determine the model's best output using
VGG19. Increasing the number of training epochs is a good way to improve the model's efficiency without overfitting
it. After training MCNN model depends on ResNet50 pre-trained model and RGB color mode with using 100 epochs
as shown in Figure (40) the results of loss and accuracy.

(a) (b)

Figure (7): (a) The average accuracy of model depends on Inception, (b) Loss of model depends on VGG (19).

Table 1: Comparison between the four different pre-trained models.

Pre-trained models Accuracy Sensitivity Specificity F1 Score

Inception(v3) 0.9591 0.9508 0.9673 0.9587

ResNet(50) 0.9708 0.9742 0.9673 0.9708
VGG(19) 0.9754 0.9742 0.9766 0.9754

6. Conclusions

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Plant seeding classification is based on pathologist’s expertise and experience, and reports from various laboratories
performing manual examinations can differ. This paper introduced a proposed Deep Learning model for classifying
plant images, which has been shown to be an efficient and promising method for extracting and classifying features
from images. The findings are compared to both conventional machine learning approaches and CNN-based methods,
demonstrating the viability of deep learning-based image classification. The studies that are linked are mostly medical
studies. The classification of plant images was the subject of this article. The dataset conversion rate must be increased
in order to achieve this goal. The machine learning methods should be implemented more on plant images when this
data will be shared to literature.

References

[1] Y. Sun, Y. Liu, G. Wang, and H. Zhang, “Deep Learning for Plant Identification in Natural Environment,”
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[2] M. Umer, S. Sadiq, M. Ahmad, S. Ullah, G. S. Choi, and A. Mehmood, “A novel stacked CNN for malarial
parasite detection in thin blood smear images,” IEEE Access, vol. 8, pp. 93782–93792, 2020, doi:
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[3] S. Elmuogy, N. A. Hikal, and E. Hassan, “An efficient technique for CT scan images classification of
COVID19,” vol. 40, pp. 5225–5238, 2021, doi: 10.3233/JIFS-201985.
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[6] D. Nkemelu, D. Omeiza, and N. Lubalo, “Deep convolutional neural network for plant seedlings
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[7] S. Rajaraman et al., “Pre-trained convolutional neural networks as feature extractors toward improved malaria
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[8] D. Nkemelu, D. Omeiza, and N. Lubalo, “Deep convolutional neural network for plant seedlings
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[9] Q. Meng et al., “Weakly Supervised Estimation of Shadow Confidence Maps in Fetal Ultrasound Imaging,”
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[10] N. El-Rashidy, S. El-Sappagh, S. M. R. Islam, H. M. El-Bakry, and S. Abdelrazek, “End-To-End Deep
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[11] M. Dyrmann, H. S. Midtiby, S. Denmark, and T. Maersk, “A Public Image Database for Benchmark of Plant
Seedling Classification Algorithms,” 2017.

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