Apple Trees Diseases Detection

Through Computer Vision in Embedded Systems

1,3
Denis Logashov, 1,2 Dmitrii Shadrin, 1,* Andrey Somov, 1,2 Mariia Pukalchik,
4
Anastasia Uryasheva, 5 Hari Prabhat Gupta, 4 Nikita Rodichenko
1
Center for Computational and Data-Intensive Science and Engineering (CDISE)
2
Digital Agriculture Lab
1
Skolkovo Institute of Science and Technology
Moscow, Russia
*
a.somov@skoltech.ru
3
State University of Aerospace Instrumentation
2021 IEEE 30th International Symposium on Industrial Electronics (ISIE) | 978-1-7281-9023-5/21/$31.00 ©2021 IEEE | DOI: 10.1109/ISIE45552.2021.9576438

Saint Petersburg, Russia

4
Tsuru Robotics
Moscow, Russia
5
Indian Institute of Technology (BHU)
Varanasi, India

Abstract—In this paper, we address the problem of detecting
diseases of apple trees. We report on a computer vision method
for apple trees leaves segmentation. For this reason we collect the
leaves images in the field using a thermal image camera. Data
analysis is carried out using Neural Networks (NN) optimized for
running on the embedded systems. We perform a comparative
study on the embedded systems, embedded systems enriched with
the GPU capability, and the PC. We achieved IoU=0.814. Our
results demonstrate that the NNs running on the embedded sys-
tems is a promising solution for detecting the trees diseases using
embedded systems and open up wide vista for its application in
precision agriculture.
Index Terms—Computer vision, embedded systems, precision
agriculture, disease detection
I. I NTRODUCTION
Nowadays, agriculture industry should supply the growing
human population with the increasing amount of food. Thus,
finding possibilities to increase quantity and quality of fruits
and vegetables yield is in high demand [1].
One of the way to do this is to increase the amount of used
agricultural areas. However, there is an obvious shortcoming
in this strategy: small countries, countries with unpleasant
climate conditions, and countries with the poor soil properties
are prone to use the agricultural areas inefficiently. Another
opportunity is to optimize the plants’ growth and to reduce
the harvest losses. Dramatic harvest losses due to the plant
diseases [2] is a problem of top priority for many countries.
Monitoring of the actual situation of plant diseases diversity,
spreading and elimination of them in time are in high demand
to provide the sustainable food production and minimize un-
suspected losses [3] [4]. Performing the monitoring activities
manually is quite time-consuming and ineffective if one needs
to cover huge amount of agricultural lands. Also, the problem
is that manual monitoring without special equipment is slow,
thus we can miss the important information of the epicenter
978-1-7281-9023-5/21/$31.00 ©2021 IEEE
and the moment of the beginning of rapid infection spreading.
By the means of manual monitoring it is nearly impossible
to assess the actual disease diversity and spatial distribution.
Indeed, this information is crucial due to the fact that, for
instance, fungal diseases take only two weeks for infecting
truly large areas [5]. Thus, there is a strong need in applying
the real-time diseases detection techniques for optimizing the
fungicide usage [6].
These problems can be addressed by using the auto-
matic monitoring systems equipped with the optoelectronic
devices [7] and Deep Learning (DL) algorithms for image
processing running on-board of the embedded systems [8] [9].
The most popular approach is processing of RGB images [10].
Moreover, those approaches process the single leaves that
significantly increase the performance of such systems, but
using the data collected in real conditions they have much
less performance because of the noise around leaves. One
of the example on segmentation leaves is reported in [11].
This method uses machine learning techniques to remove
the background and then apply methods such as k-means
to highlight the diseases. Among the important features of
plant disease development is that it can emerge and reveal
themselves at early stages in variety of electromagnetic spectra
which represent different physical basis of the physical disease
origin. This effect was shown in [3] [12]. Computer vision
systems can easily process any multi-spectral and hyper-
spectral data allowing for finding and quantitatively assessing
the features of interest automatically [13] [14]. Hyper-spectral
and multi-spectral image processing proved themselves as the
promising tools for disease detection and classification even
at the early stages [15] [16]. Deep learning techniques such as
Convolutional Neural Networks (CNN) and Recurrent Neural
Networks (RNN) and, in particular, long-short term memory
neural networks did not show their practical feasibility in
accurate and robust disease detection applications [17] [18].

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 In this research, we focus on the detection of the apple achieved results in terms of leaves segmentation and perfor-
tree diseases, e.g. the apple scab being one of the typical mance of embedded systems. Finally, we provide concluding
fungal disease and the most harmful. The proposed approach remarks and discuss our future work in Section IV.
is generic and can be easily transferred for detecting and
quantitatively evaluating other diseases. II. M ETHODS
DL approach has been used recently for the detection of In this research, we have realized the following pipeline
apple diseases and demonstrated high accuracy. However, the for the data collection and analysis to address the problem of
disease was detected as it appeared visually [19]. In the detection of apple trees diseases:
following research [20] the authors describe the features of • data collection,
apple scab and show how those features can be detected. This • data pre-processing,
work provides thermography which enables the detection of • launching the models on the desktop computer,
scab signs in thermal range before the visible signs. These • transfer a model to the embedded system,
discovered spectral properties were chosen for detecting the • compare the performance.
apple scab by using Fully Convolutional Neural Networks During this work the images of apple leaves were collected
(FCNN) to process the images from a thermal camera and using a thermal camera. Then a part of the obtained im-
detect the diseased leaves. ages was chosen for further processing. These images were
Among the limitations of DL techniques is the availability labeled to train a CNN. After the labeling procedure we
of the labeled datasets. Although there is a lack of labeled identified several state-of-the-art architectures of CNN for the
datasets some recent datasets exist and can be used for DL assessment. Upon accomplishment of the training procedure
models training [21] [22]. The most popular approach is the we have identified the most accurate model. Obtained model
usage of datasets of single leaves for solving classification was tested on all the available devices including the PC
related problems [19] [23] running the Artificial Intelligence and different embedded systems to compare the performance.
(AI) methods on a desktop or cloud facilities [24]. The most This comparative study has helped specify the advantages and
frequently used dataset in this case is PlantVilage [19] [25]. disadvantages of selected modifications of embedded systems.
We note here that in this work the lion share of dataset was
collected in field in contrast to similar research works [26] A. Embedded Systems
where the datasets are typically collected in laboratory condi- In this work, we have tested the proposed method on Rasp-
tions. berry Pi 4 (RPi4), Movidious Neural Compute Stick (NCS1
The advantage of proposed approach includes not only the and NCS2), and NVIDIA Jetson Nano. Table I summarizes
early disease detection, but implementation and evaluation main parameters of these devices.
of all the proposed DL methods on board of a low-power
embedded system [27] equipped with a GPU [28]. This in TABLE I
turn allows for the in-situ detection and analysis of diseases K EY PARAMETERS OF R ASPBERRY P I 4, M OVIDIOUS N EURAL C OMPUTE
diversity in the field and receiving the up to date information S TICK (NCS1 AND NCS2), AND J ETSON NANO .
in real-time. Moreover, such a low-power system allows for
RPi4 NCS1 NCS2 Jetson Nano
performing the monitoring for a long time remotely. Energy Quad core Quad-core
efficiency and long-term operation is crucial for autonomous CPU / VPU
ARM
Myraid 2 Myraid X
ARM
sensing systems [29] [30]: in terms of power consumption of Cortex-A72 Cortex-A57
1.5 GHz 2 GHz
embedded systems and their long-term operation in relevant RAM 2 GB 4 GB 4 GB 4 GB
applications, it was reported in recent research works [26] [28]. NVIDIA Maxwell
In fact, there is a lack of the experimental research and architecture
GPU - - - with 128
deployments of this kind, and just a few of them are available NVIDIA CUDA®
in the literature. In [31] the system for preventing the water cores
stress on plants was proposed. The authors used a thermal
camera with RaspberryPi (RPi) and a simple NN. NNs were RPi4 works on Raspberry Pi OS based on Linux system, it
used to classify the images with plants affected by water is equipped with the USB ports to connect external devices.
stress. Another work [26] reports on data collection using Jetson Nano also works on Linux based OS and as it is
an embedded system with the AI on board. As in the work shown in Table I it has a GPU on board which significantly
discussed earlier, only one system configuration was used for increases the performance of this device. In addition, NVIDIA
inference of NNs. provided all necessary tools to install the optimized versions of
In the proposed research, we perform the segmentation of libraries required to work with a NN. NCS1 and NCS2 work
each particular diseased leaf. We also carried out a comparative as the hardware accelerators and require additional OpenVino
study on several embedded devices for processing the deep software to convert and optimize the CNN. Since NCS1 is
neural networks with millions of parameters. no longer supported in later versions of OpenVino and more
The paper is organized as follows: in Section II we present suitable version for NCS1 does not support required operations
the methods used in this work. In Section III we discuss the we had to use NCS2 only.

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 B. Data Collection and Pre-processing
Our dataset contains the images of apple leaves captured in
the field by the thermal camera. Initially we collected more
than 5000 images. These images were a video stream on
which the diseased leaves were pointed during recording. As
a result, only 260 images were chosen as there were a lot
of similar images in the stream. Labeling process was done
using labelme [32] package for Python allowing for creation
of the required point polygons. An example of raw and labeled
image is shown in Fig. 1.
Fig. 1. Example of raw (left) and labeled image (right).
To artificially increase the initial dataset the image aug-
mentation technique was used. The transformations of the
original dataset are as follows: horizontal flip, scale, rotation,
shift, applying of additive Gaussian noise, gamma changes,
sharpen changes, applying of blur and brightness changes. All
parameters of these transformations are shown in Table III
typically used in the segmentation tasks. This loss is obtained
by the dice coefficient function.
2|X ∩ Y |
DSC = (1)
|X| + |Y |
Python language and Pytorch library were chosen to train
the selected CNN. All models of chosen architectures were
obtained using Segmentation Models package for Pytorch [41].
III. R ESULTS
A. Segmentation of Diseased Leaves
The dataset was divided into 3 parts: training, validation
and test. The training part contains 208 images, validation
part contains 39 images and test part contains 13 images. The
training process starts with learning rate equal to 10−3 . In
order to achieve the best possible accuracy we decrease the
learning rate during the training stage. After the first 10 epochs
the learning rate decreases up to 10−4 , after 20 epochs up to
10−5 and after 30 epochs up to 10−6 .
Fig. 3 shows an example of IoU and loss graphs for FPN
and EfficientNet-b2.
After all training procedures the obtained models were
validated using the test part of the dataset. The results are
shown in Table III.
TABLE III
IOU SCORES FOR CHOSEN ARCHITECTURES ( ROWS ) AND DIFFERENT
FEATURE EXTRACTORS ( COLUMNS ).

TABLE II EffNet-b0 EffNet-b1 EffNet-b2 EffNet-b3 Xception

T RANSFORMATION PARAMETERS . FPN 0.693 0.754 0.801 0.814 0.774
LinkNet 0.493 0.713 0.743 0.782 0.799
Probability Parameters PSPNet 0.366 0.413 0.437 0.453 0.466
horizontal flip 0.5 – Unet 0.651 0.745 0.704 0.796 0.805
scale 1.0 scaling factor in (-0.2, 0.2)
rotation 1.0 rotation limit in (-45, 45)
shift 1.0 shift limit in (-0.2, 0.2) The best results shows the FPN with EfficientNet-b3. Fig. 4
mean equal to 0 demonstrates an example of segmentation using the best
Gaussian noise 0.2
variance equal to 10
gamma 1.0 gamma factor equal to 80 model.
sharpen 0.3 lightness factor in (0.5, 1) These results demonstrate that the modern architectures
blur 0.3 kernel size equal to 3 can successfully distinguish the diseased leaves. It is worth
brightness 0.9 brightness factor in (-0.2, 0.2)
noting that the best model contains huge amount of parameters
(12,474,073) for only 2 classes.
C. Neural Networks B. Performance Evaluation on the Embedded Systems
The goal of this research was to check the ability of the Among other tasks in this work, we aim at assessing the
state-of-the-art neural networks to perform the segmentation of performance of embedded systems with the trained NN on
diseased leaves at an early stage using the thermal images. For board. First experiments were done with RPi4. Pytorch library
this purpose several well-known architectures were chosen: was directly installed on this device and it was possible
FPN [33], Linknet [34], PSPNet [35], Unet [36]. Schematic to launch the trained model. To increase the performance
description of chosen NN is shown in Fig. 2. NCS2 was connected to RPI4 using its USB port. We faced
Also, different feature map extractors were tested including some challenges during the optimization and due to limited
EfficientNet (EffNet) [37] with different depth and Xception calculation resources of NCS2 the size of processed images
[38]. Different depths in EffNet denotes as b0, b1, etc., where was reduced from 640 × 480 to 128 × 128. On NVIDIA Jetson
b0 is the smallest extractor. Adam optimizer [39] was chosen Nano optimized version of pytorch was installed and it was
as a recommended for the segmentation task. Intersection over also possible to launch the trained model directly.
Union (IoU) score was chosen as the main metric for the Table IV shows the comparative study on the performance of
segmentation task. Dice loss [40] was selected because it is NN on different devices with the size of input image 128×128.

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 Fig. 2. Architectures of used NN.

Fig. 4. Example of segmentation: (a) Original image, (b) labeled mask, and
(c) predicted mask.

This table shows that the performance of microcomputer is

very low in comparison with the PC. That is why the hardware
Fig. 3. IoU and Dice loss dynamics over training and validation epochs. accelerators should be applied to increase the performance of
embedded systems. As shown in Table IV, NCS2 provides

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 TABLE IV
C OMPARISON OF DIFFERENT DEVICES .
NVIDIA 6-cores GPU
RPi4 with
RPi4 Jetson CPU 3.79 GeForce
NCS2 Nano GHz RTX 2070
Time
7.56 0.071 0.132 0.068 0.014
elapsed, s
computing performance that is close to the performance of a
modern processor. NVIDIA Jetson Nano can process images
of needed input size, but this device is characterized by lower
performance in comparison with NCS2.
Also, performance can be increased by the optimization of
NN. Since the obtained architecture has a huge number of
parameters it is obvious that the performance on a regular
devices will be low. One of the optimization approaches is
prunning [42]. This method allows for making zeros some
coefficients and make the model less complicated. Currently,
the performance after pruning cannot be improved using
pytorch library.
IV. C ONCLUSIONS
In this work, we have demonstrated how the apple trees
diseases can be detected by computer vision in embedded
system. We made a special emphasis on the apple scub disease
in this research.
We collected the dataset of apple leaves in the field condi-
tions and labeled the images. For images processing we have
chosen appropriate architecture of NN. The effectiveness of
CNN was demonstrated in the task of segmentation of diseased
leaves. It was shown that CNN can be also deployed on the
embedded devices to make system autonomous. Comparative
study on the performance of embedded devices running CNN.
Our future work includes the integration of the proposed
solution into a robotic system or an unmanned aerial vehicle
with consequent testing in real conditions.
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