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OPEN A CNN‑based model to count

the leaves of rosette plants
(LC‑Net)
Mainak Deb 1, Krishna Gopal Dhal 2, Arunita Das 2, Abdelazim G. Hussien 3,4,5,6*,
Laith Abualigah 7,8,9,10,11 & Arpan Garai 12

Plant image analysis is a significant tool for plant phenotyping. Image analysis has been used to
assess plant trails, forecast plant growth, and offer geographical information about images. The area
segmentation and counting of the leaf is a major component of plant phenotyping, which can be used
to measure the growth of the plant. Therefore, this paper developed a convolutional neural network-
based leaf counting model called LC-Net. The original plant image and segmented leaf parts are fed as
input because the segmented leaf part provides additional information to the proposed LC-Net. The
well-known SegNet model has been utilised to obtain segmented leaf parts because it outperforms
four other popular Convolutional Neural Network (CNN) models, namely DeepLab V3+, Fast FCN
with Pyramid Scene Parsing (PSP), U-Net, and Refine Net. The proposed LC-Net is compared to the
other recent CNN-based leaf counting models over the combined Computer Vision Problems in Plant
Phenotyping (CVPPP) and KOMATSUNA datasets. The subjective and numerical evaluations of the
experimental results demonstrate the superiority of the LC-Net to other tested models.

Recently, plant phenomics has attracted the rising attention of researchers. There is a need to increase the
capabilities of high-yielding plants to ensure our food security. Global agriculture has faced significant chal-
lenges, including the need for high-yielding plants that can adapt to future climates and identifying the specific
feedstock crop for biofuel p ­ roduction1. The nutrients, the supply of carbon, and the other outer environmental
­ lant2. Plant phenotyping can provide an understanding
factors affect the size of leaves as well as the growth of a p
of plant genes, correlations between plants and the environment, plant trails, etc. as well as new technologies
to increase the yield of plants to overcome those problems. Plant phenotyping is also useful for studying the
growth of a plant, the yielding rate of a plant, and also the internal structure of a plant. The traditional laborious
and costly plant phenotyping techniques have become a bottleneck in plant breeding techniques as well as in
functional ­genomics1. These phenotyping bottlenecks have prevented us from understanding the correlation
between expressed phenotypes, genetic factors, and the condition of the e­ nvironment3.
The possibility of connecting heritable traits to genetic markers depends on precise phenotypic a­ ssessment4.
Plant image analysis is also a valuable tool for plant phenotyping. Image analysis has been used to analyse the
plant trails and predict the growth of the plant, as well as give spatial information about the image. But meas-
uring the visual characteristics of a plant is very costly and needs a very detailed long-term investigation to
continue the observation. As a result, an automated approach for resolving the problem must be established. As
recent literature suggests, the deep-learning (DL)-based methods are one of the most contemporary artificial-
intelligence (AI) techniques and are currently a crucial component of plant phenotyping. There is a survey on
plant phenotyping using computer vision with D ­ L 5.
Leaf area segmentation is the key feature of plant phenotyping and can be used to analyze the growth of a
­plant2. However, the segmentation of the leaves has become challenging when the size of the leaves is tiny or a

1
Wipro Technologies, Pune, Maharashtra, India. 2Department of Computer Science and Application, Midnapore
College (Autonomous), Paschim Medinipur, West Bengal, India. 3Department of Computer and Information
Science, Linköping University, Linköping, Sweden. 4Faculty of Science, Fayoum University, Fayoum, Egypt. 5MEU
Research Unit, Middle East University, Amman, Jordan. 6Applied Science Research Center, Applied Science
Private University, Amman 11931, Jordan. 7Hourani Center for Applied Scientific Research, Al-Ahliyya Amman
University, Amman 19328, Jordan. 8Computer Science Department, Al al-Bayt University, 25113, Mafraq,
Jordan. 9Artificial Intelligence and Sensing Technologies (AIST) Research Center, University of Tabuk, 71491, Tabuk,
Saudi Arabia. 10Department of Electrical and Computer Engineering, Lebanese American University, 13‑5053,
Byblos, Lebanon. 11College of Engineering, Yuan Ze University, Taoyuan, Taiwan. 12Department of Computer
Science and Engineering, Indian Institute of Technology, Delhi, India. *email: [email protected]

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significant number of leaves are overlapped. Also, the angle of the images and the lighting effect on the leaves
can affect the efficiency of leaf area segmentation. Another crucial factor for analysing plant growth in plant
phenotyping is determining the leaf count of the ­plant6. It is also challenging and time-consuming process to
determine the number of leaves. A comprehensive plant phenotyping method for camera-captured images
contributes to the cost reduction and improvement of plant and agricultural production. As a result, numerous
researchers are looking into plant phenotyping using images recorded by cameras.
Furthermore, current CNN-based methods show their efficient performance in accurate leaf count predic-
tions. A CNN is a class of neural networks within the field of DL. CNNs are designed with one or more convo-
lutional layers and are mostly used for tasks such as image processing, classification, segmentation, and analysis
of auto-correlated data. CNNs are primarily employed for the purpose of extracting features from grid-like
matrix datasets, particularly in the context of image analysis. The CNN architecture encompasses various levels,
including the input layer, convolutional layer, activation layer, pooling layer, and completely linked layers. The
convolutional layer is responsible for applying filters to the input image in order to extract relevant features.
The activation function is then applied in an element-wise manner to modify the matrix values, specifically
converting negative values to zero. Following this, the pooling layer is employed to downsample the image,
thereby reducing computational requirements. Finally, the fully connected layer is used to make the ultimate
prediction. The process by which the network acquires the most effective filters is achieved through the use of
backpropagation and gradient descent.
Therefore, in this manuscript, a novel CNN-based model for leaf counting has been proposed called LC-Net.
The proposed model takes segmented leaf parts as additional input for achieving better leaf counting accuracy.
Hence, well-established ­SegNet7 is utilized as it performs better leaf segmentation compared to existing well-
established CNN-based models, namely, DeepLab V3+8, U-Net9, Fast FCN with Pyramid Scene Parsing (PSP)10,
and Refine N ­ et11. Lastly, the proposed LC-Net has been compared with the other state-of-the-art leaf count
models, and the performance of all tested leaf count models has been tested over the combined CVPPP and
KOMATSUNA datasets. The qualitative and numerical results indicate that the proposed LC-Net outperforms
the existing leaf counting results.
In a nutshell, the significant contributions of the proposed work are enlisted in the following:

– A novel CNN-based model to count the number of rosette plants’ leaves has been proposed which has been
provided two inputs i.e., segmented output and the original image for better accuracy
– The proposed LC-Net model is tested on the merged version of the dataset of KOMATSUNA and CVPPP
(annotated for the leaf counting task by the experts). It is seen that the proposed LC-Net model outperforms
existing state-of-the-art techniques.
– The proposed model use a normalization layer that is used to filter the unwanted pixels present in the images.
Application of this layer in the proposed LC-Net is discussed in detail in Sect. "CNN based leaf segmentation".

The remainder of this manuscript is structured as follows. Next, Sect. "Related work" summarises about the exist-
ing work in the related field. Thereafter, Sect. "Methodology" discusses the proposed technique. Furthermore,
Sect. "Experimental results" presents the experimental investigation. Lastly, Sect. "Conclusion and future work"
contains the final observations and concluding remarks.

Related work
The past few years have witnessed successful research work in the domain of phenotyping of plants. In the recent
past, several research papers have been published on this hot topic. For example, in Ref.12, Tu et al. developed
a leaf counting network architecture based on YOLO V3. They considered the problem of leaf counting as an
object detection problem. As a result, first they detected the leaves and drew the bounding boxes, and then they
counted the number of boxes. The proposed model achieved -0.32 of difference in count (DiC), 0.48 of Absolute
difference in count (AbsDiC), 0.80 of Mean Squared Error (MSE), and 64.00% of percentage agreement on the
CVPPP dataset. In Ref.13, another deep-learning based model called Eff-U-Net++ for leaf segmentation and
counting had been proposed by Bhagat et al. Eff-U-Net++ was an encoder-decoder-based network. It had applied
EfficientNet-B4 as the encoder sub-net. The model achieved 0.11, 0.03, 0.12 DiC and 0.21, 0.38, 1.27 AbsDiC on
the ­CVPPP14, MSU-PID15, and ­KOMATSUNA16 datasets, respectively.
In Ref.17, two novel DL approaches had been proposed, elaborated, and compared by Farjon et al. for visual
leaf counting tasks. The first model fed input image in different resolutions into the network that had ResNet-50
as the backbone network to estimate features of leaves at multiple scales. Next, in order to get the final count,
repetitive regression of leaf heat map got from the previous step. The second model counted the number of leaves
by locating the centers of the detected leaves and finally aggregating them. They got 1.17 MSE and 43.7% of the
percentage agreement on the CVPPP ­dataset14. Miao et al.18 proposed a dataset for maize leaf counting and also
proposed two DL methods to count the maize leaves. The first model counted the leaves by regression, and the
second model counted the leaves by detection. In Ref.19, Lu et al. came up with a better way to use DL to count
the dense leaves and leaves that overlap in natural environments. The developed approach was used to detect
the object by merging a space-to-depth module, an Atrous spatial pyramid pooling, and a convolutional block
attention module into the network. The experimental results showed that the improved DL approach achieved
96% accuracy. To improve the phenotyping process, in Ref.20, Karthik et al. introduced a unique semantic seg-
mentation pipeline for the segmentation task. In CVPPP14 competition, a number of deep CNN models such
as U-Net, Attention-Augmented Net, and Attention-Net were introduced. These networks were trained using
the Arabidopsis Thaliana plant dataset. The Attention-Net achieved a 0.985 dice score, which is the best among
others.

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In Ref.21, Kumar et al. came up with a new orthogonal transform domain-based method to segment the leaf
region and further counted it by fine-tuned deep CNN models. On the CVPPP dataset, fine-tuned AlexNet
and VGG19 had been used to count the leaves and got 25.51%, 33.67% of percentage agreement, 5.43, 2.03 of
MSE, 1.71, 1.03 of AbsDiC, and 0.39, 0.11 of DiC, respectively. In Ref.22, Buzzy et al. proposed a novel real-time
object detection approach for the identification, localization, and quantification of plant leaves. A comparative
analysis was conducted between a Tiny-YOLOv3 model and a faster R-CNN model. The Tiny-YOLOv3 and
Faster R-CNN models were evaluated based on several performance metrics, including DiC, AbsDiC, MSE, and
percentage agreement. The obtained values for these metrics were 0.25 and 0.0556, 0.8056 and 1.2778, 2.0833
and 2.8889, and 56% and 27.78%, respectively. Hati et al.23 presented a regression model for the purpose of leaf
counting. The images were subjected to segmentation and subsequent enhancement, resulting in the removal
of noise and transformation of the pixel data associated with the leaves. Subsequently, the images were inputted
into the regression model, which is founded upon the architecture of AlexNet. In Ref.24, Ayalew et al. presented
a domain-adversarial learning method in which a domain adaption technique was used to estimate a density
map for leaf counting. Due to its flexibility in accommodating variations in distribution across source and des-
tination datasets, the method exhibits potential for application in a broader spectrum of leaf counting and plant
organ counting scenarios. The method got -0.95 of DiC, 1.56 of AbsDiC, 5.26 of MSE, and 29.33% of percentage
agreement on the CVPPP dataset. Gomes and ­Zheng25 presented an experimental study on the limitations of
datasets used for phenotyping and the performance strategy of the leaf segmentation tasks. They also looked at
how test-time augmentation and model cardinality might help with single-class image segmentation. Another
investigation had been conducted in Ref.26 by Yang et al. where they utilized a mask R-CNN based model to
effectively segregate and classify leaf images that contained intricate backgrounds.
In the year 2019, a new a­ pproach27 to extract leaf regions from images of plants and count the number of leaves
had been introduced by Kumar et al. There were three phases to the proposed methodology which are statistical
image enhancing technique, a graph-based leaf area extraction approach, and a circular hough transform (CHT)
based technique. In Ref.28, Valente et al. presented a preliminary study showcasing the efficacy of a trained deep
neural network in accurately quantifying the number of leaves in plant images obtained by greenhouse workers
through the use of handheld equipment. They got 0.31 of DiC, 0.62 of AbsDiC, 0.77 of MSE, and 47% of percent-
age Agreement. A Google Inception Net V3 based CNN model had been used by Jiang et al. in Ref.29 to count the
number of maize leaves. To reduce redundant information, the Fisher Vector (FV) was used, and the Random
Forest (RF) method was used to get the final prediction. They got 0.0018 of DiC, 0.35 of AbsDiC, and 0.31 of MSE.
In 2018, Giuffrida et al. presented a single deep ­network30 that counted the number of leaves from multi-
modal 2D images of different species for any rosette-shaped plant. The model had a DiC of 0.19, an AbsDiC of
0.91, a MSE of 1.56, and a 32.9 percentage agreement. For the CVPPP dataset, the proposed approach achieved
a segmentation accuracy of 95.4%, a DiC of 0.7 and an AbsDiC of 2.3. In Ref.31, Ubbens et al. proposed a plant
phenotyping dataset by demonstrating that performance could be improved on the leaf counting task using 3D
synthetic plants. These synthetic plants were also applied to augment a dataset. They recreated the architecture
used in the reference experiment using the Ara2013-Canon dataset in the augmentation ­experiment3 for the
augmentation experiment. They also switched the real and synthetic image datasets utilized to both train and
test the DL-based model. Additionally, it was demonstrated that these datasets could be utilised in a comparable
manner for training a neural network to accurately quantify the number of leaves.
For the plant phenotyping task, Aich et al. developed a data-driven strategy in Ref.32 that could be employed
to a variety of plant species and imaging configurations. They used a deconvolutional network to segment the
leaves, and the predicted images were used in a CNN for leaf counting. The model got 0.73 of DiC, 1.62 of Abs-
DiC, 4.31 of MSE, and 24.0 of Percentage Agreement on the CVPPP dataset. A Data Augmentation technique
had been proposed by Kuznichov et al. in Ref.33 for segmenting the leaves followed by the counting the leaves
from the images of rosette plants. In Ref.34, Itzhaky et al. developed two novel deep learning algorithms designed
for the purpose of leaf item counting. The researchers utilised the CVPPP 2017 Leaf Counting Challenge dataset
to demonstrate the efficacy of these methods. The findings show that they defeated the CVPPP challenge winner
from 2017. In Ref.35, Pape and Kulkas introduced a methodology for leaf segmentation that utilises edge detection
techniques. Additionally, they devised a method to analyse images by employing the software ­IAP36 in order to
extract a multitude of image attributes that might be utilised for estimating the quantity of leaves.
The aforementioned discourse unequivocally illustrates the immense utility of performing precise tasks,
such as leaf segmentation and counting, in the field of plant phenotyping. Furthermore, it should be noted that
there exists a restricted range of CNN models and techniques that have demonstrated the capability to generate
precise outcomes across two widely utilised datasets, namely CVPPP and KOMATSUNA. It has been observed
that these algorithms frequently encounter difficulties in scenarios including a green background and/or a sub-
stantial amount of overlapping leaves. Consequently, in order to address this deficiency, the primary objective
of this research endeavour is to construct a Convolutional Neural Network (CNN) model, specifically referred
to as LC-Net. The LC-Net, as proposed, demonstrates the ability to achieve higher predictions in leaf counting
even when confronted with various types of backgrounds. Furthermore, LC-Net demonstrates the capability
to precisely quantify the number of leaves, even in cases when they are overlapping. The next part provides a
detailed description of the LC-Net model that has been proposed, as well as an overview of the dataset that was
utilised in this study.

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Methodology
The proposed LC-Net has been designed to count the number of leaves in the rosette plants. The suggested model
takes both the RGB image of a rosette plant and the segmented image of its leaves as input in order to enhance
accuracy. The subsequent subsections provide an exposition of the LC-Net architecture and an elucidation of
the design’s underlying reasoning.

CNN based leaf segmentation

The necessity of accurate leaf segmentation arises from the fact that the segmented leaf portion provides an addi-
tional benefit to the proposed LC-Net model, as detailed in Section 2.2. This study employs five well-known CNN
models, namely DeepLab V3+ V3++8, ­SegNet7, Fast FCN with P ­ SP10, U-Net9, and Refine N ­ et11, to accurately
segment the leaves of rosette plants. The effectiveness of an image segmentation CNN model is determined by
its backbone. The backbone network is used to estimate the feature maps from the image, and followed by, these
feature maps are further applied and processed in order to get desired r­ esult37. The backbone of the DeepLab V3+
model is the modified Aligned X ­ ception8,38. VGG-1639 serves as the backbone for SegNet, while ResNet-10140
is utilized as the backbone for both FCN with PSP and Refine Net. U-Net9 segments using its own backbone.
This paper adopts SegNet as the segmentation model for the proposed LC-Net because SegNet provides the best
visually and numerically segmented results. In the section on experimental results, the segmented results of the
tested CNN models are presented.

Normalization layer
The normalization layer has been utilized to improve the segmented outcomes. This normalization Layer’s pur-
pose is to eliminate any unwanted pixels from the images. The uneven background or light reflection could be
the cause of these unwanted pixels. The precision of segmentation and leaf count may be affected as a result of
these circumstances. The inclusion of the normalization layer has facilitated the construction of models that
exhibit enhanced predictive accuracy. Figure 1 shows the segmented outcomes of SegNet with and without using
normalization layer. Visual analysis clearly shows that utilization of normalization layer over SegNet’s output
enhances the results.

Proposed LC‑Net model for leaf counting

This work adopts the conventional workflow of traditional computer vision systems in which the segmented
output and counting model’s input are integrated as depicted in Fig. 2b which also indicates the entire archit-
edture of the proposed model. The counting model has obtained additional information from the segmented
output. Figure 2a indicates the structure of a Conv Block which is utilized in Fig. 2b. One Conv Block is made of
convolution layer, batch normalization, and activation function. Batch normalization is a technique employed
to enhance the speed and stability of the CNN. The leaf segmentation model and leaf counting model are trained
independently of each other. The training of the counting model relies on the segmentation model, as the output
generated by the segmentation model are utilised in conjunction with the RGB image input. Furthermore, the
CNN models under consideration are trained without the inclusion of supplementary information pertaining
to the specific species of the plant. LC-Net demonstrates a high level of accuracy in quantifying the quantity of
leaves in a substantial portion of the dataset by solely utilising the segmented leaf regions as input. Nevertheless,
it is worth noting that in certain instances, the segmentation model may generate inaccurate segmentations for
a subset of the data. Consequently, it has the potential to impact the precision of leaf counting in the proposed
LC-Net. Furthermore, the quality and texture of the original images are significant factors in CNN based leaf
counting models. It has been observed within the dataset employed that certain images exhibit suboptimal qual-
ity, particularly in relation to leaf area. The average intensity of certain images is poor. Hence, the exclusive utili-
sation of original images also impacts the efficacy of the leaf counting model being proposed. As a consequence,
both the original and segmented outcomes are inputted into the LC-Net in order to enhance the accuracy of leaf
counting. We have also used a Normalization layer, which is nothing but a filter which makes the pixel values zero
which are less than a threshold which is set to 0.5 from the experience during experiment. The Normalization
Layer is elaborated in the section Section 2.1. The two inputs are concatenated at the beginning of the model.
Then we have used one (1 × 1) Conv Block followed by three (3 × 3) Conv Block which is a replacement of one
(5 × 5) Conv Block to reduce the parameter size. After that a maxpooling layer is added then again one (1 × 1)
Conv Block followed by three (3 × 3) Conv Block. We have used (1 × 1) convolution with less filter size before
all (3 × 3) convolutions to reduce the number of parameters used in the model.

Experimental results
The model is trained and tested using a system containing an NVIDIA GeForce 1650 having cuDNN CUDA
10.0, a 256 GB SSD, 16 GB RAM, and an AMD Ryzen 5 3550H CPU. TensorFlow and Scikitlearn were used in
all of the studies. The experimental results have two folds: one is leaf segmentation and other is leaf counting.
Both the results are presented in the following sub-sections.

Dataset design
As stated earlier, experiments on both the leaf segmentation and leaf counting have been done on two well-known
datasets. They are (i) the KOMATSUNA [14] dataset, and (ii) the plant phenotyping benchmark dataset, known
as ­CVPPP14. In our experiment, these datasets are merged. The KOMATSUNA dataset has been annotated for
the leaf counting task by the experts. The CVPPP dataset have four sections. They are named as A1, A2, A3, and
A4. All sections are included with segmented ground truth. On the other hand, there are two portions in the the

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Figure 1.  Visual representation of the significance of the normalization layer.

KOMATSUNA dataset. Among them, one portion is made by capturing the images by a RGB-D camera, while
the images in the other segment of the dataset is captured by several RGB cameras. As a whole, there are total of
1200 images in these two categories. As a result, there are a total of 2010 images along with the corresponding
segmentation and leaf number ground truths in the the combined dataset. Bilinear i­ nterpolation41 has been used
to resize the images into 224×224. Subsequently, the combined dataset is partitioned into distinct subsets, namely
the training, validation, and testing sets of images. In our experiment, the training set consists of 1410 images,
whereas the validation and test sets each contain 300 images. In addition, a series of vertical flips, 90◦ and 180◦
clockwise and anticlockwise rotations are randomly applied in order to generate a greater quantity of images. In
Fig. 3, some of the samples from each of the dataset are shown. In order to compare more accurately with state-
of-the-art CNN models, another dataset is prepared using 160 images chosen randomly from the CVPPP dataset.

Results of leaf segmentation

This section presents the results of CNN based leaf segmentation models. The five common CNN models such as
Fast FCN with Pyramid Scene Parsing (PSP), DeepLab V3+, SegNet, U-Net, and Refine Net are employed for the
proper leaf segmentation. For all CNN based leaf segmentation models, the well known ‘binary cross-entropy’

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Figure 2.  (a) Conv Block, (b) Architecture of the proposed LC-Net model.

Figure 3.  Samples of both utilized datasets.

has been used as the loss function. In our experiment, the size of the input and output images are size 224 x 224
x 3 and 224 x 224 x 1, respectively. The batch size varies depending on the machine capacity and the architecture
of the applied model. The suggested and existing tested CNN-based models’ parameter settings are provided
in Table 1.
In order to evaluate and compare the performance of the segmentation process by the CNN models, three
commonly used metrics such as, (a) segmentation accuracy (AC); (b) intersection over union (IoU); and (c) dice
score (DI), are used. The quality metrics are summarised in Table 2.
In the training period, DeepLab V3+ shows the best performance among all. DeepLab V3+ achieves 97.38%
of train accuracy, 97.30% of test accuracy, and 0.0108 of train loss. But while the models have been tested on the
merged dataset and on the CVPPP dataset, the SegNet model shows the best results. Test results on the merged
and CVPPP datasets are shown in Tables 3 and 4, respectively. SegNet achieves a 95.04% dice score and a 90.58%
IoU. Therefore, the SegNet model has been chosen as the segmentation model for the proposed leaf counting

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CNN model Parameter setting

The input image has three channels and is (224, 224) in size. The backbone’s filters are identical to the ­original8. For predic-
DeepLab V3+
tion, the sigmoid activation function is utilised. DeepLab V3+ has 3.5M trainable parameters.
The input image has three channels and is (224, 224) in size. The backbone’s filters are identical to the ­original7. For predic-
SegNet
tion, the sigmoid activation function is utilised. We have 16.7M trainable parameters for the SegNet model.
The input image has three channels and is (224, 224) in size. The backbone and decoder filters are identical to the o­ riginal9.
U-Net Similar to the Fast FCN with PSP model, at the final level, the sigmoid activation function is applied in order to predict the
class levels of each pixel. There are 31.0M trainable parameter present in the U-Net model used for the leaf segmentation.
The input image has three channels and is (224, 224) in size. The backbone and decoder filters are identical to the
Refine Net ­original11. Similar to the above mentioned models, at the last layer, the final prediction is performed using the sigmoid
activation function. The Refine Net model have 89.1M parameters that are needed to be trained.

Table 1.  Parameters Setting of the existing CNN-based models used for leaf segmentation.

Sl. Parameters Remarks

AC is the ratio of the total of correctly identified pixels and the total number of Pixels. The higher accuracy value
1 AC
represents better ­results42.
The value of IoU ranges between 0 and 1. It indicates the amount of overlapping is present between predicted image
2 IoU and the ground truth. In the existing literature, if the IoU for the outputs of the model is more than 0.5, then it is
considered that the model is predicting ­well43.
Basically DI indicates the similarity of predicted image with the ground truth. It is calculated by matching the
3 DI overlapped region of the predicted image by the technique and the ground truth i­ mage44. A higher DI value better
performance of the participating technique.

Table 2.  The quality metrics for leaf segmentation.

Models Test loss (×10−3 ) Test accuracy (%) IoU Dice score
DeepLab V3+ 22.3 97.06 89.78 94.59
SegNet 17.6 97.29 90.58 95.04
Fast FCN with PSP 19.4 97.24 89.29 94.31
U-Net 58.0 96.40 86.50 91.87
Refine Net 222.0 97.10 89.23 94.27

Table 3.  Test result that are obtained by various architectures on merged dataset (Test set size = 300 images).
Significant values are in bold.

Models Test loss (×10−3 ) Test accuracy (%) IoU Dice score
DeepLab V3+ 23.7 97.21 85.11 91.79
SegNet 19.7 97.92 86.04 92.50
Fast FCN with PSP 21.1 97.57 85.94 91.54
U-Net 59.8 96.92 81.55 89.23
Refine Net 24.2 97.06 84.50 91.20

Table 4.  Test result that are obtained by various CNN model on CVPPP Dataset (Test set size = 160 images).
Significant values are in bold.

model, i.e., LC-Net. The outcomes of segmentation by the existing tested CNN-based models along with the
ground truth on the merged dataset are depicted in Fig. 4. From Fig. 4, it is quite clear that the SegNet model is
performing with a significant accuracy.

Results of leaf counting

This section presents the results of CNN based leaf counting models. The proposed LC-Net has been compared
to ­VGG21, Alex N­ et21, and the model proposed by Ubbans et. al.31 over merged dataset. In addition to that the
proposed LC-Net is also additionally compared to counting models developed by Ayalew et. al.24, Giuffrida et.
al.30, and Aich et. al.32 over CVPPP dataset for better comparison. The parameters settings for the mentioned
CNN models are performed as per Table 5. For both images i.e. original image and predicted image, the size is
considered as (224, 224). The batch size varied based on machine capacity and the model used.

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Figure 4.  Qualitative comparison of the segmentation of proposed method with existing approaches.

Four commonly used metrics ­namely28,21, (a) Mean Square Error (MSE); (b) Abstract DiC; (c) R2; and (d)
Percentage Agreement are utilized to study the performance of Leaf counting models. The brief descriptions of
the mentioned metrics are reported in Table 6.
After training, we have tested all models on our merged test dataset and the CVPPP dataset as well. We
have used four evolution measures, i.e., Abs DiC, MSE, R2, percentage Agreement (%) and testing loss. Table 7
shows the test results of the models on the merged dataset, and Table 8 shows the test results of the models on

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CNN model Parameter setting

The original input image has three channels and segmented mask has one channel. The size of both input image is
(224, 224). For prediction, the Linear activation function is utilised. We have 45M trainable parameters for VGG
VGG
model of Kumar et. al. and used loss function is half MSE and the optimizer is SGD with 0.0001 learning rate, 0.9
momentum (As mentioned in Kumar et. al.21)
The original input image has three channels and segmented mask has one channel. The size of both input image is
(224, 224). For prediction, the Linear activation function is utilised. We have 53M trainable parameters for Alex Net
Alex Net
model of Kumar et. al. and used loss function is half MSE and the optimizer is SGD with 0.0001 learning rate, 0.9
momentum (As mentioned in Kumar et. al.21).
The original input image has three channels and segmented mask has one channel. The size of both input image is
Ubbans et. al. (224, 224). For prediction, the Linear activation function is utilised. We have 45M trainable parameters for proposed
model of Ubbans et. al. and the loss function is MSE (As mentioned in Ubbans et. al.31).
The original input image has three channels and segmented mask has one channel. The size of both input image is
Proposed LC-Net (224, 224). For training, smooth L1 loss function has been used in Adam optimizer. We have 5M trainable parameters
for our proposed LC-Net.

Table 5.  Parameter settings of the CNN-based models for leaf counting.

Sl. Parameters Remarks

It’s calculated by taking the mean of the squares of the errors - i.e., differences between the predicated leaf number and the ground truth.
1 Mean Square Error (MSE)
Lower value indicates better results.
The calculation involves determining the average value of the absolute differences between the predicted leaf number and the actual leaf
2 Absolute DiC (Difference in count)
number. Lower value indicates better results.
3 Coefficient of determination ( R2) It measures how well the predicted values match the ground truth. High value indicates better results.
4 Percentage agreement It takes the percentage of how many times the predicted value is exactly same as ground truth. High value indicates better results.

Table 6.  Quality parameters for leaf count.

Models Test loss↓ Abs DiC↓ MSE↓ R2 ↑ Percentage agreement (%)↑

VGG21 0.6163 0.717 1.2325 0.9348 50.31
Alex ­Net21 0.728 0.7563 1.456 0.944 48.75
Ubbans et. al.3 4.3088 0.7203 1.1691 0.9493 46.72
Proposed LC-Net 0.2371 0.4313 0.5924 0.9726 63.75

Table 7.  Testing result of leaf count have obtained by different architectures on merged dataset (Test set size =
300 images). Significant values are in bold.

Models/Methods Abs DiC↓ MSE↓ Percentage agreement (%)↑

AlexNet21 1.71 5.43 25.51
VGG1921 1.03 2.03 33.67
Ayalew et. al.24 1.56 5.26 29.33
Giuffrida et. al.30 0.91 1.56 32.9
Aich et. al.32 1.62 4.31 24.0
Proposed LC-Net 0.65 1.13 51.39

Table 8.  Testing result of leaf count have obtained by different architectures on CVPPP dataset (Test set size =
160 images). Significant values are in bold.

the CVPPP dataset. The test results clearly show that the proposed LC-Net model is better than all other tested
models and methods on both datasets by a large margin.

Effect of the combined input

One of the major features of the proposed LC-Net is the combined input i.e. original image and segmented image.
Therefore this section discusses the influence of this combined input in the proposed LC-Net. As a result, to
study the consequences of combined input, a performance comparative study has been made with and without
combined input. Hence, two CNN models have been compared which are (i) LC-Net with combined input, and
(ii) LC-Net with original image input. Table 9 shows the numerical results of the LC-Net with combined and

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Models Abs DiC ↓ MSE ↓ Percentage agreement (%) ↑

LC-Net with combined input 0.65 1.13 51.39
LC-Net with original image input 1.06 3.98 42.87

Table 9.  Numerical result for measuring the effect of combined input over CVPPP dataset (Test set size = 160
images). Significant values are in bold.

LC-Net with original image as input over CVPPP datasets. It can be seen that when the segmented image is
combined with the original image the performance of the LC-Net model has been enhanced to some great extent.
Best outputs are highlighted in bold in the tables. The presence of the ↑ symbol following a measure signifies
that a higher value of that metric indicates a more favourable outcome. In contrast, the presence of the sign ↓
following the metric denotes the opposite.

Conclusion and future work

This paper proposed a CNN network based model called LC-Net for counting the number of leaves of the rosette
plants. The proposed LC-Net is both trained and evaluated using the images of KOMATSUNA and CVPPP data-
sets. It is seen that LC-Net performed with a good accuracy and produced a competitive outcome with respect to
the state-of-the-art leaf counting models. The main feature of the proposed LC-Net is that is takes original and
segmented leaf images as combined input which make it more robust for leaf counting because the segmented
leaf part provides additional information to the proposed LC-Net. SegNet is used for leaf segmentation for
the proposed LC-Net because SegNet provides the best visually and numerically segmented results compared
to the other peer models. However, the major limitation of the work is that the proposed model has not been
evaluated for too noisy images and which can be a great future work. In addition to that, further experiment
regarding network structure design and loss function design may lead to a more accurate and robust CNN-based
network for leaf counting. Last but not the least, a 3D convolution models may be used to analyze 3D leaf image
data and it may produce more significant results. In the future, Authors can use many optimization algorithms
and embedded them in the network for better accuracy. These algorithms can be any algorithm such as Snake
Optimizer (SO)45, Fick’s Law Algorithm (FLA)46, Jellyfish Search (JS)47, Dandelion Optimizer (DO)48, Aquila
­Optimizer49–51, Atom Search Optimization (ASO)52, Water Cycle Algorithm (WCA)53, Bald Eagle Search (BES)54,
African Vultures Optimization Algorithm (AVOA)55, Archimedes Optimization Algorithm (AOA)56, Beluga
Whale Optimization (BWO)57, Hunter Prey Optimization (HPO)58, ­INFO59, Supply Demand O ­ ptimizer60,61,
Reptile Search Algorithm (RSA)62, Golden Jackle Optimization (GJO)63, and more.

Data availibility
The datasets that support the findings of this study are publicly available. Link for CVPPP dataset is: http://
www.plant-phenotyping.org/datasets. Link for KOMATSUNA dataset is: https://limu.ait.kyushu-u.ac.jp/ agri/
komatsuna/.

Received: 23 August 2023; Accepted: 11 January 2024

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Author contributions
M.D.: Conceptualization, Methodology, Writing-original draft preparation. K.G.D.: Conceptualization, Visu-
alization, Investigation, Validation. A.D.: Conceptualization, Visualization, Investigation, Validation. A.G.H.:
Conceptualization, Visualization, Investigation, Validation. L.A.: Supervision, Validation, Writing-Reviewing
and Editing. A.G.: Software, Visualization, Writing-Reviewing.

Funding
Open access funding provided by Linköping University.

Competing interests
The authors declare no competing interests.

Additional information
Correspondence and requests for materials should be addressed to A.G.H.
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