Ecological Informatics 66 (2021) 101454

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Ecological Informatics
journal homepage: www.elsevier.com/locate/ecolinf

Towards the automatic monitoring of deforestation in Brazilian rainforest

L. Bragagnolo, R.V. da Silva, J.M.V. Grzybowski *
Federal University of Fronteira Sul, Rodovia RS 135 km 72, CEP 99.700-000, Erechim, RS, Brazil

A R T I C L E I N F O A B S T R A C T

Keywords: Deforestation is considered one of the main environmental threats to the ecological balance on the planet. At the
Forest cover change same time, monitoring changes in forest cover is a major challenge, especially in Brazil, a country with conti­
Semantic segmentation nental dimensions, a vast coverage of tropical forests, and an accelerated ongoing process of illegal deforestation.
Logistic growth
This study aims to propose and present an integrated automatic methodology for monitoring changes in forest
Sentinel-2
cover, to enable “near real-time” monitoring of vast territorial extensions. Based on the application of Fully
Convolutional Neural Networks (FCNs) combined with a logistic growth model, the methodology is aimed at
allowing accurate detection of changes in forest cover based on the multitemporal assessment of satellite images.
The results show that the combination of the two approaches make the methodology able to pinpoint defores­
tation processes. The applicability of the methodology is demonstrated for the Amazon and Atlantic Rainforest
biomes, which are important areas of tropical forests in Brazil. In addition to enabling the agile and accurate
identification of forest cover losses and providing efficient computing, the comparative results show that the
methodology can be applied to issue alerts of suspected deforestation activity in standalone automatic moni­
toring systems, and also as a complementary tool to existing systems currently under operation.

1. Introduction
Deforestation is one of the main threats to environmental and
ecological balance on the planet, as well as one of the primary sources of
greenhouse gas emissions (de Bem et al., 2020; Le Quéré et al., 2018;
Goulart et al., 2013). In Brazil, the illegal removal of vegetation repre­
sents a worrying environmental problem that affects all regions of the
country, in particular the Amazon and Atlantic Forest biomes, which are
predominantly constituted by tropical forests. The Atlantic Forest
biome, for example, has suffered significant degradation of its vegeta­
tion cover, to the point that less than 15% of its original forest area
remained (Dean, 1997; Wagner et al., 2020). According to Ribeiro et al.
(2009), more than 80% of the fragments remaining in the Atlantic Forest
were <50 ha, and further, natural reserves protected only 9% of the
remaining forest, and 1% of the original forest. The annual deforestation
report referring to the year 2019 identified the loss of 12,187 km2 of
vegetation cover throughout the Brazilian territory (MapBiomas, 2020).
In addition to the direct environmental and economic consequences,
deforestation has also caused indirect economic damage due to several
initiatives that have suspended the import of Brazilian products from
activities under suspicion of contributing to illegal deforestation (Sousa,
2016; Assunção and Rocha, 2019; Arruda et al., 2019).
Given this scenario, the generation of information that allows the
monitoring of forest resources at the most different scales of interest and
spheres of activity is fundamental to enable the adoption of effective
measures to mitigate and control illegal deforestation. Several defores­
tation mapping methodologies based on the use of multispectral satellite
images have been proposed and are used in current ongoing projects in
Brazil (Coutinho et al., 2013; MapBiomas, 2020; INPE, 2008; Diniz et al.,
2015). Since 1988, by means of PRODES (Program for the Monitoring of
the Amazon Forest by Satellite), the Ministry of the Environment (MMA)
and the National Institute for Space Research (INPE) monitor defores­
tation in the Amazon forest by means of the application of land use
classification methods based on satellite imagery (INPE, 2008). The
PRODES methodology is based on visual interpretation of land use
classes and it allows the identification of deforestation polygons with
minimum area from 6.25 ha. Based on such classification, a photoin­
terpreter delimits new deforestation polygons taking as a starting point
the deforestation maps of previous years in which areas of non-forest
and hydrography are properly identified. The deforestation rates
calculated by PRODES are released annually. More recently, the
DETER-B program (Diniz et al., 2015) started to provide the detection of
deforestation and other changes in vegetation cover with a minimum
area of about 1 hectare and a temporal resolution of 5 days, in which the

* Corresponding author.
E-mail address: jose.grzybowski@uffs.edu.br (J.M.V. Grzybowski).

https://doi.org/10.1016/j.ecoinf.2021.101454
Received 25 February 2021; Received in revised form 2 October 2021; Accepted 3 October 2021
Available online 12 October 2021
1574-9541/© 2021 Elsevier B.V. All rights reserved.
L. Bragagnolo et al.
updates in the vegetation cover in the Amazon area are generated almost
daily. Other complementary systems have been developed to control and
prevent deforestation, such as the Selective Logging Monitoring System
(DETEX) (INPE, 2008), and the TerraClass Project (Coutinho et al.,
2013). Recently, Map Biomas Alert was launched in Brazil. It consists of
an online platform that incorporates a system for validating and refining
alerts on deforested areas that covers all biomes in the Brazilian terri­
tory. The tool runs machine learning algorithms that are applied to
refine the deforestation polygons with high-resolution satellite imagery
from monthly deforestation alerts collected by the different systems in
the country: DETER (Diniz et al., 2015), which includes the biomes of
the Amazon and Cerrado, SAD/IMAZON (De Souza et al., 2008) and
SIPAMSAR (CENSIPAM, 2008), both covering the Amazon biome, and
Global Land Analysis and Discovery (GLAD) (Hansen et al., 2016), from
the University of Maryland, comprising the other biomes. Such alerts are
analyzed by means of visual inspection to eliminate false positives, and
are then forwarded to the supervised classification process, from Google
Earth Engine, with images from Planet satellites, which have a spatial
resolution of 3 m, with daily frequency.
With the improvement of machine learning techniques applied to
image processing, new potential methodologies started to be studied for
the detection of forest cover changes. In particular, convolutional neural
networks (CNNs) and, subsequently, fully convolutional neural net­
works have achieved promising results (de Bem et al., 2020; Grings
et al., 2020; Khan et al., 2017; Wagner et al., 2020), having even sur­
passed human performance in image classification tasks (Yu et al.,
2017). Amongst the different architectures of fully convolutional neural
networks, the U-Net stands out for several factors, being the most
important its segmentation and computational performances (Bra­
gagnolo et al., 2021a). The U-Net architecture has already been suc­
cessfully applied in studies involving the identification of deforestation
(de Bem et al., 2020; Lee et al., 2020; Wagner et al., 2020; Bragagnolo
et al., 2021c). de Bem et al. (2020) applied three CNN architectures
(U-Net, SharpMask, and ResNet) using images from Landsat-8 to detect
deforestation in the Amazon Forest. The authors found similar results for
the three architectures evaluated, having outperformed classical ma­
chine learning algorithms, such as random forest and multilayer per­
ceptron. The resulting metrics showed that the ResNet achieved slightly
better performance, with 0.9252–0.9358 (precision), 0.9617–0.9508
(recall), while the U-Net achieved 0.9223–0.9175 (precision) and
0.9003–0.9508 (recall) in the validation sets of the same areas for two
different time spans. In turn, Lee et al. (2020) mapped deforested areas
using high-resolution remote sensing (Kompsat-3 images with 0.7 m
resolution) and deep learning. They applied two CNN architectures
(SegNet and U-Net) to find landscape affected by human-induced
deforestation. The results showed that the U-Net architecture was
approximately 11% more accurate than the SegNet architecture trained
in the same database. Further, Wagner et al. (2020) mapped forest cover
and changes and two species of pioneer trees, Cecropia hololeuca, and
Tibouchina pulchra. The authors combined a dataset from WorldView-2
and WorldView-3 (spatial resolution of 0.5 m and 0.3 m, respectively)
and applied a U-Net architecture. The resulting metrics in his study were
precision (0.808–0.993), recall (0.801–0.995) and F1-score
(0.804–0.994), which indicate once more the fitness of the architec­
ture for the segmentation of satellite imagery. Abrams et al. (2019)
developed an FCN called Habitat-Net based on the U-Net architecture in
order to map images of tropical forest habitats using images of canopy
and understory for training. The higher mean Dice coefficient of
Habitat-Net (0.94 for canopy and 0.95 for understory) indicates that
accuracy of Habitat-Net is higher than U-Net (0.89, 0.94). Finally, Bra­
gagnolo et al. (2021c) evaluate six different FCN architectures (U-Net,
SegNet, DeepLabV3+, PspNet, VGG-PspNet, and FCN32) to map forest
and non-forest areas in the Amazon biome, using satellite imagery from
Sentinel-2 (using the 10 m resolution bands). The U-Net achieved the
best performance among the architectures tested, having scored 0.9470,
0.9356, 0.9676, and 0.9513 for accuracy, precision, recall, and F1-score,
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Ecological Informatics 66 (2021) 101454
respectively. Further metrics related to computational performance also
pointed to a superior performance of the U-Net architecture, thus indi­
cating that, beyond its better segmentation performance, its training
time was considerably shorter. Comprehensive and comparative evalu­
ations have also shown that the U-Net architecture can be applied ad­
vantageously in the identification of landslide scars from satellite images
(Bragagnolo et al., 2021a,c), among other image segmentation problems
that rely on satellite imagery.
Although methodologies based on fully convolutional neural net­
works and, in particular, the U-Net architecture, have been shown to
provide accurate results in the task of identifying and segmenting
deforestation areas (Bragagnolo et al., 2021c), there are limitations to be
overcome. The occurrence of false positives is the most important one in
this specific application, since they are responsible for most of perfor­
mance degradation observed in practice. In a way, the occurrence of
false positives and false negatives is expected and, from a certain point
on, very difficult to be overcome by merely fine-tuning the network. The
main routes available for seeking improved accuracy following current
conditions and existing architectures of CNNs are (i) larger and more
comprehensive image databases, with more thematic layers and with
better resolution, (ii) variations in training parameters (loss functions,
optimizers, learning rates), (iii) variations in architectures (number of
layers, layer characteristics, number of neurons, attention mechanisms)
and (iv) better equipment with greater processing power, which may
allow the training of a greater number of candidate CNNs. Thus,
although there is room for improving the performance of the method in
relation to previous attempts (Bragagnolo et al., 2021c,d; de Bem et al.,
2020; Wagner et al., 2020), it is understood that, within the current state
of the art, such improvements are of an incremental nature.
Considering these limitations, we offer a hybrid approach aimed at
improving image segmentation accuracy over deforestation areas. We
show that the identification of deforestation areas can benefit from the
application of a logistic model combined with vegetation indexes, which
have already been studied to assess forest growth (Richit et al., 2019,
2021). In general, logistic models describe the growth of a given pop­
ulation that is subject to limited resources (Verhulst, 1845, 1847), and
allow the characterization of the evolution of the population by means of
well-defined, intuitive, and physically understandable quantitative pa­
rameters. In the case of a forest environment, the model can be used to
assess the rate of growth of vegetation density over time, also allowing
to identify spots with negative growth in plant density or any other
anomalous condition whatsoever. Thus, the application of the logistic
growth model allows to improve the results obtained from semantic
segmentation and to promote increased classification accuracy through
the overlap of two different and complementary types of assessment of
forest cover. This hybrid solution is aimed at contributing to the
implementation of automatic systems for monitoring deforestation in
vast territories and in ‘near real-time’, thus enabling the timely issuance
of deforestation alerts. Such a tool can be of great help to authorities
against illegal deforestation by potentially identifying and pinpointing
ongoing activities, thus allowing more effective action by environmental
authorities.
Having presented the state-of-the art on the application of machine
learning techniques to the segmentation of forest and non-forest areas
from satellite imagery and having pointed the limitation of existing
methodologies in what regards real-world applications, we now
formulate the main scientific question under study in this work: would a
hybrid methodology based on a blend of image segmentation and
mathematical modelling offer a simpler and yet accurate and robust
framework to serve as backbone of highly automated deforestation
monitoring systems? Our initial hypothesis is that it would, based on the
fact that image segmentation and growth modelling are complementary
in the sense that while the former accounts for learned resemblances
among the spectral signatures, size and shape of deforestation polygons,
the latter allows the assessment of parameters whose values may point
to anomalies in forest growth, including the case of clear cut.
L. Bragagnolo et al.
This study aims to present and discuss a highly automated method­
ology for monitoring deforestation based on the application of fully
convolutional neural networks and the logistic growth model. While the
U-Net architecture is considered due to advantageous segmentation
accuracy and computational performance shown in previous studies
(Bragagnolo et al., 2021c), it is the case that the methodology is flexible
to admit any other architecture whatsoever. As illustration of the
methodology and of its application, case studies are carried out in the
tropical forests of the Amazon and Atlantic Forest biomes in Brazil under
the actual application conditions. In order to evaluate the results, we
compared the deforestation polygons output by the proposed method­
ology with those produced and made available by the MapBiomas Alert
project (MapBiomas, 2019), which uses and refines data from PRODES,
the official program supported and conducted by scientific institutions
of the Brazilian government (INPE, 2008). The results indicate that the
proposed methodology can contribute to increasing the effectiveness
and accuracy of the monitoring systems currently employed. Since the
proposed methodology is shown to enable the agile and accurate iden­
tification of forest cover losses and to provide efficient computing, it is
argued that it can allow the issuance of alerts of suspected deforestation
activity in standalone automatic monitoring systems, or else as a com­
plementary tool to existing systems currently under operation.
The text is organized as follows: Section 2 presents the materials and
methods; Section 3 presents the results obtained in the study and com­
parisons with the results of MapBiomas Alert (MapBiomas, 2019); Sec­
tion 4 discusses the implications of the results; finally, Section 5 makes
final considerations and summarizes the research contributions.
2. Materials and methods
The methodological procedure is presented in three main stages: (a)
description of the U-Net architecture and its training, which include the
mapping of the forest regions and the identification of clouds; (b)
description and application of a logistic model to identify areas with
decreasing vegetation density; and (c) presentation of the automated
system for mapping deforestation areas.
Fig. 1. U-Net architecture used for forest mapping in this article: 4 input channels of 512 × 512 pixels and 32 × 32 pixels at the lowest resolution. Each blue box
represents a multi-channel resource map. The number of channels is indicated at the top of the box. The x-y size is shown in the bottom left corner of the box. The
white boxes represent maps of copied resources. The arrows indicate the different convolutional filtering operations. The white areas in the segmented output image
represent the forest regions. Modified from Ronneberger et al. (2015). (For interpretation of the references to color in this figure legend, the reader is referred to the
web version of this article.)
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Ecological Informatics 66 (2021) 101454
2.1. U-Net
The U-Net is a Fully Convolutional Neural Network capable of per­
forming the semantic segmentation of images, which results in output
images that represent object classes spatially and with the same size and
resolution as the input image. The U-Net architecture was initially
proposed by Ronneberger et al. (2015) and it was used for the semantic
segmentation of biomedical images. Also, this FCN uses subsequent
convolution layers and sampling filters, which makes it possible to
extract the characteristics of the input image. Basically, the U-Net
structure consists of two main paths: a contraction path (left side), and
an expansion path (right side), as shown in Fig. 1. The contraction path
is responsible for extracting and identifying the characteristics and
classes existing in the image being processed. In turn, the expansion path
retrieves the spatial information of the identified classes, thus gener­
ating a segmented image, presenting the classes and their location.
The first stage (contraction) applies convolution filters that scan the
images in order to generate feature maps, allowing the identification of
existing patterns. It is worth mentioning that as the layers deepen, the
relative importance of the pixel decreases, and that of the set of pixels
increases, which potentially allows the identification of characteristics
at the object level. In the expansion path (right side of Fig. 1), the
transposed convolution method is applied, where each block passes
through the entrance of two convolution layers, followed by a sampling
layer. The number of expansion blocks is equal to the number of
contraction blocks. In the final layer, a 1 × 1 convolution layer is applied
to the map (Ronneberger et al., 2015). In total, the network has 24
convolutional layers and 31,032,837 trainable parameters.
2.1.1. Training
The training process and definition of the best U-Net to be used in the
present study is described in detail in Bragagnolo et al. (2021d). In
summary, the training phase requires image datasets, with their
respective masks, that is, a reference image representing the spatial
location of the class (forest and non-forest) to be identified. For the
creation of these reference images and training of U-Nets, some scenes
from Sentinel-2 Level 2A were selected and downloaded through the
L. Bragagnolo et al.
Copernicus Open Access Hub platform (ESA, 2020). The best band
composition to be inserted as an U-Net input was defined by the merging
of bands 4 (red), 3 (green), 2 (blue), and 8 (near-infrared) of Sentinel-2
scenes, according to (Bragagnolo et al., 2021d). The U-Net was trained
using images obtained from Atlantic Forest and Amazon Brazilian bi­
omes. The image datasets applied in the training stage are available at
Zenodo database (Bragagnolo et al., 2021b). In a previous work, Bra­
gagnolo et al. (2021d) evaluated the performance of a U-Net for the
mapping of forest cover to identify deforestation polygons. Towards that
end, we applied a supervised land use classifier algorithm to label the
satellite images in forest and non-forest areas. We found that the U-Net
could correctly classify forest spots that had not been flagged during the
masking procedure, suggesting the U-Net can identify and classify forest
cover even when facing inaccuracies in the training set. This finding is
consistent with Rolnick et al. (2017) that empirically showed deep CNNs
are robust to strong label noise. Besides, in our previous work, the U-Net
architecture showed the best performance among traditional methods
and even among other CNN architectures. Therefore, regarding these
findings, in our present manuscript, we consider reducing human
intervention in the masks generation task employing an unsupervised
algorithm for image classification.
For the creation of masks (location of the forest and non-forest re­
gions), the GRASS-GIS 7.6.0 software (GR Development Team, 2019)
was used. To this end, the supervised classification methodology was
applied to each of the scenes. The spectral signature was extracted from
the training map and then contextual image classification was per­
formed using Sequential Maximum a Posteriori Estimation (SMAP), by
means of the modules i.gensignet and i.smap from GRASS GIS, and the
10-meter resolution bands. The product of this classification refers to an
image representing the forest class in white and the background in black.
Once the classifications were made, the database for training the U-
Nets was generated from the subdivision of the original images. Sub-
images were generated under the dimensions of 512 × 512 pixels. The
need to subdivide images is due to the limitation of computational
memory. Thus, for each scene, 484 images of size 512 × 512 pixels were
generated. These were exported in.PNG format for the masks and.TIF for
the compositions to then be used as training matrices for each U-Net.
After the image databases were generated, they underwent a visual
evaluation to remove faulty images, such as those that were located at
the edges of the scenes, etc. Thus, after the inspection, the image data­
base for forest classification resulted in 619 images for the Amazon
biome, and 605 images for the Atlantic Forest biome.
The U-Net training process requires databases to be separated into
three sets: training, validation, and testing. Such a procedure is neces­
sary to allow the assessment of the neural network as to its performance.
Thus, 100 images of each biome were randomly selected to compose the
validation sets and 20 for testing each of the databases. The remaining
images constituted the training sets.
The training data (not considering validation and testing) were
submitted to the data augmentation process to be used as input to the
training algorithm. This process generates new images from the varia­
tion of the original characteristics, to increase the number of examples
available for training. Therefore, the images were rotated, vertically and
horizontally shifted, as well as the degree of brightness was varied. The
rotation was varied within the range − 180◦ to 180◦ , vertical-horizontal
shift and brightness were modified using factors of 0.5 and 0.2,
respectively. The ‘nearest’ method was applied to interpolate the im­
ages, keeping them at the original size of 512 × 512 pixels. It is worth
mentioning that the data augmentation process was used only for the
training set with the best band composition already defined.
For faster convergence, it is also necessary to normalize the input
values, which are stored as a floating-point. Thus, the 3rd and 97th
percentiles of the training data set were used, since satellite images may
present outliers or pixels without data due to orthorectification. Thus,
for each pixel (i, j) of each image 512 × 512 of band b, each b of each
input image k is normalized in the form:
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Ecological Informatics 66 (2021) 101454
( )
kb (i, j) − 3rd pct(b)
k′b (i, j) = (1)
97th pct(b) − 3rd pct(b)
The U-Net architecture implemented in the Keras library (Chollet
et al., 2015), a high-level API (Application Programming Interface) that
allows the implementation of neural network structures in the Python
programming language, was applied. The Keras library was applied with
the TensorFlow backend, an open-source machine learning library
(Abadi et al., 2015).The SGD (Stochastic Gradient Descent) algorithm
with Nesterov moment implemented in the Keras library was used as an
optimizer. The learning rate was set at 0.01. Simultaneously to the
training of each U-Net, 100 images were submitted to validation, in
which the ability to generalize the neural network is evaluated. In
addition, to avoid overfitting, the early stopping method was applied, in
which the network parameters are collected at the point of occurrence of
the absolute minimum of the validation error curve, based, in this case,
on the minimum value of the loss. A maximum of 1,000 epochs has been
set, as well as a batch size value of 2 during the training phase. The
U-Net training was interrupted if there was no improvement in the
validation loss value in the next 20 epochs. As a loss function, the
weighted binary crossentropy function associated with the weighted
dice loss function was applied.
In the same way, a second U-Net was trained to identify clouds and
their shadows, to be able to eliminate the interference that can cause the
generation of incorrect deforestation polygons. To this end, the same
preparation, image processing, and training procedure were adopted. In
this case, the (real) masks, created by using the same methodology
aforementioned, refer to the presence of clouds and background. The
image dataset used for training is available at Zenodo database (Bra­
gagnolo et al., 2020) and it contains 1,160 images for training, 100 for
validation, and 100 for testing.
Finally, the training, validation, and test procedures were performed
on a 3.6 GHz Intel Xeon processor workstation with 32 GB of RAM. The
calculations were performed in a GPGPU (General Purpose Graphics
Processing Units) using an NVIDIA GeForce GTX 1060 Ti graphic card
with 6 GB of RAM and 1,280 graphics processing cores, under CUDA
Toolkit version 10.0 (Zone, 2017).
2.1.2. Validation
The validation stage occurs simultaneously with the training stage,
using its own set of images (200 images (Bragagnolo et al., 2021b)) and
without data augmentation. This step is necessary as a way of verifying if
the network is being able to generalize the information and patterns
identified in its training. It is the validation metrics that are evaluated
(value of the loss function in the validation, in this case) to identify the
moment of training stop and then avoid the occurrence of overfitting.
2.1.3. Test
After the training and validation were completed, the trained U-Net
went through the testing stage, in which images not previously seen
were submitted to classification, to then be evaluated against the mask
images. To this end, 40 images (Bragagnolo et al., 2021b) covering the
Amazon and Atlantic Forest biomes were used.
2.1.4. Application
After the U-Net was trained and satisfactory segmentation perfor­
mance was obtained under the metrics considered, the network weights
were saved for application with the deforestation mapping algorithm. At
this stage, after the band composition, each image, it goes through the
classification process, resulting in a segmented binary scene that in­
dicates the forest and non-forest regions as entries 1 or 0, respectively, in
the matrix corresponding to the segmented image. The integrated forest
cover change monitoring methodology using U-Nets is further detailed
in Section 2.3.
L. Bragagnolo et al.
2.2. The logistic growth model
While the segmentation process performed by means of the U-Net is
aimed at allowing the generation of deforestation polygons by
comparing multitemporal segmented images, the logistic model was
applied to allow the detection of areas with declining vegetation density.
This complementary approach seeks to improve the identification of
false positives in the segmented images. In this study, we apply the
Enhanced Vegetation Index (EVI) to convert the multilayered imagery
into a flat matrix that serves as a proxy to the density of forest cover. Sets
of multitemporal matrices corresponding to a given study area are then
evaluated by means of the logistic growth model, such that the growth
rate can be assessed. From this process, regions with declining vegeta­
tion density, represented by negative growth parameters in the logistic
model, are identified and pinpointed.
2.2.1. The equation
The logistic model, originally proposed by Verhulst (1845, 1847)
states that the rate of change of a population of size U, in the case of this
study represented by the value of EVI, submitted to a growth constant in
an environment of capacity K can be modeled according to Eq. (2):
( forest density over two consecutive images (ideal case). After the model
∂u u)
= ru u 1 − (2)
∂t K
where r refers to the growth rate intrinsic to the studied population, u
population size, and K the carrying capacity of the environment. Ac­
cording to Richit et al. (2021), the value of K would correspond to the
upper bound of vegetation index output for a given methodology for
calculating the vegetation index, being EVI, in the case of the present
study. Also, it shall be remarked that the value of K depends on the
vegetation type, such that the carrying capacity must be adjusted to the
range of the vegetation index in the area under study.
The solution of the logistic model in Eq. (2) can be determined
analytically and is given by:
u0 ert
u(t) = (3)
K + u0 (ert − 1)
being u0 the initial EVI value. In this stage, the objective is to determine
the value of r, that is, the parameter referring to the rate of growth or, in
this case, decrease in plant density. Based on two temporally spaced EVI
images, the value of r is determined using the model, allowing the
identification of regions of decreasing vegetation density, in the case of
r < 0.
2.2.2. The Enhanced Vegetation Index
The application of the EVI to assess vegetation density is an alter­
native to the classification of land use. According to Richit et al. (2017),
the advantages of applying the EVI are that: (i) the referred index results
in a density of vegetation pixel by pixel and (ii) can be readily scaled to
the range of the forest density variable u(t) in the diffusive-logistic
model. Besides, the vegetation indexes are better indicators of exuber­
ance and health of the vegetation cover. In general, the EVI seeks to
optimize the vegetation signal by intensifying the response in regions
with biomass concentration. The equation for obtaining the density of
vegetation in an image is given by:
NIR − RED
EVI = G (4)
NIR + C1 RED − C2 BLUE + L
where G is the vegetation gain scaling factor; C1 and C2 are aerosol
resistance coefficients, in order to minimize their interference on data
quality; L is the reflectance correction parameter of surface radiation;
NIR is the spectral band of the near infrared (B8); and RED and BLUE are
the spectral bands of the red (B4) and blue (B2) bands, respectively. The
variables G, C1, C2, and L were previously established by the study of
Huete et al. (1994) as G = 2.5, C1 = 6, C2 = 7.5, and L = 1.
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Ecological Informatics 66 (2021) 101454
2.2.3. Application of the logistic growth model to the identification of
potential deforestation areas
After the calculation of the EVI for each of the scenes (initial and
final), the logistic growth model is calibrated pixel-by-pixel. This pro­
cess provides the corresponding map of the growth parameter r to the
period. The regions with negative growth rates over the period are used
to generate polygons, which are then compared to those output by the
image segmentation. Polygons identified in the image segmentation
stage that do not feature negative growth (r < 0), representing
decreasing vegetation density, are then reclassified as false positives.
Fig. 2 illustrates the idea of applying the logistic model to obtain in­
formation on the loss of vegetation density in the areas considered in this
study. Detailed information on the application of a logistic model
combined with vegetation indexes to assess the behavior of plant density
over time can be found in Richit et al. (2019, 2021, 2017). Some figures
of the performance improvement provided by the application of the
logistic growth model are provided in the results section.
The logistic growth model was applied to forest areas only, after
water bodies, crop lands and other areas where perennial vegetation
were removed using the Sentinel SCL layer. This forest area is the study
area and the logistic model is calibrated to evaluate the behavior of
is fitted (pixel-by-pixel), one can draw polygons based on the observed
growth rates. Whenever negative growth rate is identified between two
(temporally near) images, one has elements to believe that a defores­
tation process is under way. Some polygons obtained by means of the
logistic growth model will naturally superpose to those obtained by
means of the image segmentation process, and that is a strong indication
of deforestation. Thus, the logistic growth model was implemented as
complement to broaden and better the segmentation process.
For the detection of false positives by means of the logistic model, the
growth rate was applied as an indication of potential deforestation
areas. Although this could arguably be accomplished by means of an
decrease in the average values of EVI, the growth rate is way more
informative in the sense that the logistic growth model maps to the
development stage of the vegetation under study and thus provide a
more reliable evaluation of the status of the vegetation relatively to its
growth curve. For example, it is known that vegetation in early stages
tend to increase in density faster than those fully-developed ones whose
growth has stabilized. Thus, for instance, while zero growth rate is ex­
pected in fully developed vegetation areas, it is not in vegetation during
early stages. This can help establish expected growth rates for each type
of vegetation/biome/region which can serve as reference for the iden­
tification of unjustified anomalies.
2.3. The integrated forest cover change monitoring methodology
Now that the main constituting parts of the framework were explored
in the previous sections, this section presents how they are combined in
an integrated methodology for forest cover change monitoring. Fig. 3
shows the flowchart indicating each step of the methodology applied for
the generation of deforestation polygons from multitemporal satellite
images. A more detailed description of each step is given in the following
subsections.
2.3.1. Datasets and preparation of the satellite imagery
After the download of each scene, before the classification by the U-
Nets (for identification of forests and clouds), the composition of bands
is performed, using bands 4, 3, 2, and 8, as previously mentioned. Then,
the scene is cut and transformed into 484 new sub-images of size
512 × 512 pixels to meet the required input standard of the U-Net. It is
also important to note that it was not necessary to apply atmospheric
and topographic corrections, since the scenes of Sentinel 2 Level-2A are
made available with the necessary corrections.
L. Bragagnolo et al. Ecological Informatics 66 (2021) 101454

Fig. 2. Exemplification of calculating

the r values using the initial and final
EVI matrices of the biomes studied
with the logistic model. The values
with negative r (outlined in red, in the
last column) represent the areas
where there was a reduction of vege­
tation density. These regions are used
to eliminate false positives from
deforestation polygons mapped by
images classified by U-Net. (For
interpretation of the references to
color in this figure legend, the reader
is referred to the web version of this
article.)

Fig. 3. Flowchart of the methodology for generating deforestation polygons using U-Net and a logistic growth model.

2.3.2. Segmentation of deforestation polygons
Then, from the moment the algorithm finds an older classified image,
the map of differences between the two segmented scenes is generated
from the subtraction of the oldest by the most recent. If the pixel, in the
difference matrix, is greater than zero, the difference matrix receives the
value 1, indicating loss of forest cover, otherwise, the pixel receives the
value 0.
In order to reduce the occurrence of false positives and noisy pixels,
the segmented images output by the trained U-Net were corrected based
on the assessment of the presence of clouds and other interferences,
eliminating possible polygons generated in these situations. To this end,
two different features were used: (a) the SCL layer (Scene Classification
Layer), a product that is obtained with the other bands of the down­
loaded scenes, and represents the classification of certain objects in the

6
L. Bragagnolo et al.
scene (such as clouds, water, etc.), having a resolution of 20 m; and (b)
the segmented cloud image obtained from the classification of the U-Net
trained for this purpose and which is applied right after the U-Net for
mapping forest areas.
In the case of SCL layers, these are automatically resampled to a 10 m
resolution before being applied as masks. Furthermore, this layer elim­
inates areas with clouds, defective pixels, dark areas, cloud shadows,
water, and snow. Although SCL identifies objects in the scenes as clouds,
it still has some inaccuracies as identified in preliminary tests. There­
fore, the U-Net trained to identify clouds was applied in order to improve
the quality and accuracy of the results.
Thus, from these images and the layers of deforestation polygons, the
regions with clouds and other interferences were eliminated from the
final products, where the pixels in these areas received a value of 0 if
they have been misclassified. To eliminate noisy pixels (usually located
in transition areas between classes, for example), image erosion was
applied, using the Python OpenCV library (Bradski and Kaehler, 2000).
Still, to identify the best kernel size to remove the noisy pixels without
excluding important characteristics, different sizes of kernels were
tested: 2 × 2, 5 × 5, 7 × 7, and 9 × 9.
The same images submitted to the classification by U-Net also were
applied in the logistic model, to eliminate misclassified polygons.
Likewise, from the moment the algorithm identifies the presence of an
older image, it calculates the EVI for both images, then applying them to
the logistic model to determine the value of r. Negative values of r are
indicative of loss of vegetation density within the period evaluated,
whereas positive values represent a gain of vegetation density. The
product of this step is an image with characteristics similar to those
obtained by U-Net, however, in this case, the binary matrix will repre­
sent the location of the regions where negative values of r were identi­
fied. In this way, polygons identified by U-Net that do not contain
negative r values are eliminated as false positives.
Also, because of the model characteristics, the equation can be
applied pixel-by-pixel.
2.3.3. Performance metrics
To assess the performance of the proposed method, the following
standard metrics were applied: accuracy, precision, recall and F1-score.
They are defined as follows:
Tp + Tn
Accuracy = (5)
Tp + Fp + Tn + Fn
Tp
Precision = (6)
Tp + Fp
Recall =
Tp
(7)
Tp + Fn
precision × recall
F1 = 2 × (8)
precision + recall
where Tp is the number of true positives, Tn the number of true nega­
tives, Fp the number of false positives, and Fn the number of false neg­
atives. Values closer to 1 indicate good performances.
2.4. Comparison to MapBiomas Alert
In order to further evaluate the results obtained by means of the
proposed methodology, we compared the deforestation polygons
resulting from the application of the proposed methodology with those
generated by the most sophisticated official deforestation tools in
operation in Brazil, MapBiomas Alert (MapBiomas, 2019). To this end,
we directly compared the shapefiles of the deforestation polygons pro­
vided by Map Biomas Alert to those generated as output by our proposed
framework. Given its agility, accuracy and the state-of-the-art approach
upon which it is built, and the renowned deforestation programs it gets
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Ecological Informatics 66 (2021) 101454
data from, MapBiomas is a very suitable standard for comparison.
Thus, beyond the usual metrics of accuracy, precision, recall and F1-
score, which evaluate the intrinsic performance of the proposed meth­
odology, we further evaluate its performance against an official state-of-
the-art deforestation monitoring tool supported by the Brazilian
government.
2.5. Study areas
The definition of the study areas was based on the assessment of the
density of deforestation polygons through the information available on
the MapBiomas Alert platform (MapBiomas, 2019). Areas with the
highest concentration of deforestation were selected and the scenes were
obtained from the Sentinel 2 Level-2A image catalog, as specified in
Table 1. Also, images with low cloud cover were chosen to facilitate the
visualization of the methodological application.
3. Results
3.1. U-Net training
The U-Net trained with images from the Amazon and Atlantic Forest
biome achieved performance metrics values as presented in Table 2,
which are consistent with those found a previous study (Bragagnolo
et al., 2021d). Also, Fig. 4 presents the training history considering the
values of the loss function and the metrics evaluated for the trained
U-Net. It is observed that, for all the metrics evaluated (second column),
all values are close to 1, indicating a good performance of the networks,
especially by the validation set, demonstrating the generalization ca­
pacity of the U-Nets for unknown images.
Another observation about the performance of U-Net in this seg­
mentation task is that it does not improve upon the application of larger
datasets. Following previous results (Bragagnolo et al., 2021c) and
further rounds of training, we chose to apply a small dataset in order to
reproduce more closely one of the limitations that are likely to be found
in practice. The scarcity of datasets (let alone large ones) would be
prohibitive to the application of the methodology under a requirement
of large image datasets. Further, since we are dealing with only two
classes, the training process is much simpler than that of multiclass
object segmentation as applied to autonomous driving, for instance. In
addition, the U-Net is known to do well in small datasets, as opposed to
other architectures, e.g., Inception, Xception. As a matter of fact, one of
the reasons the U-Net architecture was selected as backbone of the
deforestation identification framework is precisely that it can achieve
satisfactory learning over limited datasets, which means that perfor­
mance metrics stabilize quite well during the training.
3.2. Step-by-step performance evaluation of the algorithm
Fig. 5 presents the intermediate maps generated for each of the steps
of the methodology, allowing to identify the influence of each step in the
final deforestation polygons. It can be observed that generating only the
difference between the multitemporal images classified by U-Net results
in a series of misclassification and noisy pixels, the latter being more
pronounced in the transition areas between one class and another
(Fig. 5a). This behavior is expected and can be justified by the spectral
Table 1
Tile number fields, number of images and inital/final date for each site corre­
sponding to the Sentinel scenes applied in this study.
Tile number field Number of images Initial date Final date
T20NRG (Amazon) 7 Jan 24, 2019 Oct 17, 2020
T22MDB (Amazon) 6 Jul 23, 2019 Sep 05, 2020
T20LNP (Amazon) 6 Jul 30, 2019 Sep 27, 2020
T22JCS (Atlantic Forest) 11 Jan 18, 2020 Oct 19, 2020
L. Bragagnolo et al. Ecological Informatics 66 (2021) 101454

Table 2 the final maps of a given study region were obtained (Fig. 5) and
Training, validation and test metrics for U-Net forest/non-forest classification. compared with the real deforestation polygons, as shown in Table 4. In
Precision Recall F1-score Accuracy general, the larger the size of the kernel, the more degraded the classi­
fication becomes, reducing the accuracy, recall, and F1-score values,
Training 0.9827 0.9876 0.9851 0.9896
Validation 0.9721 0.9793 0.9756 0.9892 with only an increase in precision values. However, as precision and
Test 0.9871 0.9876 0.9882 0.9880 recall are metrics that need to be evaluated together, based on the
harmonic mean obtained by means of the F1-score, it was found that the
kernel size that maximizes the number of correct classifications is 5 × 5
disturbances that occur between the different temporal satellite images, px. In contrast, a too small kernel size was also found to be inadequate,
as well as on account of the vegetation density gradient that exists in the
transition areas. As the corrections are applied (cloud correction in
Fig. 5b; noise removal in Fig. 5c; removal of false positives by means of
Table 3
the outputs of the logistic growth model in Fig. 5d; and removal of Metrics for each image generated in the intermediate stages of the methodology,
clusters smaller than 10 pixels in Fig. 5e, results very close to the real as shown in Fig. 5.
polygons are obtained, these marked in red (reference data). Table 3
Stage Accuracy Precision Recall F1-
presents, in numerical terms, the improvement in the delimitation of score
polygons after the application of each of the stages of the proposed
1 (Just difference t + 1 and t) 0.9469 0.6120 0.8957 0.6650
methodology. It can be seen that the main steps that result in a more 2 (Clouds removal) 0.9470 0.6116 0.8926 0.6643
significant improvement in the polygons delimitation are those that 3 (Noisy pixels removal – kernel 0.9844 0.7693 0.8300 0.7964
involve the elimination of noisy pixels (step 3) and the application of the 5 × 5 px)
logistic model (step 4) to remove false positives. 4 (Logistic model application) 0.9922 0.9409 0.8443 0.8900
5 (Final after removal of clusters 0.9940 0.9402 0.8570 0.8941
In order to identify the best kernel size to be used for the removal of
<10 pixels)
noisy pixels, different values were tested. For each size, the metrics for

Fig. 4. Training history for the U-Net using images from Atlantic Forest and Amazon biomes.

Fig. 5. Intermediate maps for each stage of the methodology application: (a) difference between the temporal images classified by U-Net; (b) applying the correction
for the presence of clouds; (c) removal of noisy pixels (using the 5 × 5 size erosion method); (d) removal of false positives by the logistic growth model; and (e) final
map with clusters removal filter smaller than 10 pixels.

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L. Bragagnolo et al. Ecological Informatics 66 (2021) 101454

Table 4
Calculated metrics for the deforestation polygons obtained by the proposed
methodology using different kernel sizes for removing noisy pixels (Fig. 5c).
Kernel size (px) Accuracy Precision Recall F1-score

2×2 0.9905 0.8246 0.9279 0.8689

5£5 0.9940 0.9402 0.8570 0.8941
7×7 0.9925 0.9602 0.7854 0.8516
9×9 0.9908 0.9661 0.7233 0.8007

Best overall performance significance in bold.

as it does not eliminate the noisy pixels in necessary quantity, causing

false positive polygons to remain.
Fig. 6 illustrates the deforestation polygons generated by our pro­
posed methodology considering two images temporally spaced for the
same region. It is possible to identify by visual inspection that the
method is able to map areas with loss of forest cover with accuracy,
which agrees with the high values obtained for the performance mea­
sures. This can be better visualized and corroborated by means of Fig. 7,
which maps the successes and errors for each area under study. Still, to
demonstrate the potential of the methodology to carry out deforestation
monitoring, Fig. 8 shows, in a sequence of temporally spaced images, the
increments of deforested areas for each date considered. The metrics
obtained refer to the 5 × 5 kernel size as shown in Table 4.
3.3. Application to multitemporal deforestation monitoring
To demonstrate the application of the methodology to areas of the
two biomes under study, the Amazon biome and the Atlantic Forest
Fig. 6. Deforestation polygons mapped, in red, by the proposed methodology,
for a region in the Amazon biome. (For interpretation of the references to color
in this figure legend, the reader is referred to the web version of this article.)
Fig. 7. True positives, true negatives, false positives and false negatives iden­
tified based on the polygons identified by the methodology (Fig. 6) compared to
the polygons identified manually (reference data).
biome, the methodology was applied to scenes with different time
spacings, as it can be seen from Figs. 9–11. As a means of comparison,
the polygons identified by MapBiomas Alert in the same period were
also overlaid (see figure legends). The visual evaluation allows to verify
that the methodology is capable of generating deforestation polygons by
means of the segmentation of temporally spaced images, which means
that it is sensitive enough to identify small differences in forest cover
from one image to the next. In addition, under the simultaneous training
for both biomes, which presented the best overall results, it is capable of
identifying deforestation under different characteristics of vegetation
and land use.
It is possible to observe that the framework allows to identify
deforestation polygons that were not identified by MapBiomas Alert,
and also the other way around. In some cases, the polygons mapped by
MapBiomas were not identified by our proposed methodology. Thus, in
a certain sense, they can eventually be applied as complementary to
each other or to existing ones, potentially improving the segmentation
performance of the next generation of deforestation monitoring systems.
Table 5 allows evaluating the performance of the methodology in
comparison with MapBiomas. It is possible to verify that the segmen­
tation by MapBiomas achieved better precision scores, while the pro­
posed methodology achieved better recall scores in most cases. In
practice, it means that MapBiomas obtained less misclassifications of the
type false positives, while the proposed methodology achieved less
misclassification of the type false negatives, proportionally to the
number of true positives. Both types of errors have undesirable practical
consequences; while false positives may issue false alarms, false nega­
tives cause an actual deforestation spot to be dismissed altogether. This
corroborates what was previously exposed, in which the methodology of
this study can be used as a complementary tool for mapping and
monitoring deforestation.
Although the methodology can satisfactorily identify deforestation
polygons in both biomes, it also presented some misclassification, as
shown by Figs. 12–14. Some errors occurred due to the presence of
clouds. This means that in some cases the cloud correction masks were
not sufficient to eliminate the effects of the presence of clouds upon the
segmentation process. This was observed mostly due to the presence of
cirrus clouds or to the shading resulting from thicker clouds (Figs. 12b
and 13). Another challenging issue worth mentioning is that the areas
considered in the study already had an advanced degree of degradation
and were not properly forest regions, as in Fig. 12a; regions where
deforestation occurred but the polygon did not define the area correctly,
as seen in Fig. 12c; and in agricultural regions, whose behavior is

9
L. Bragagnolo et al.
Fig. 8. Identification and increment of polygons for the same region of the Amazon biome for different periods (Tile number field T20NRG).
especially observed in the images of the Atlantic Forest biome (Fig. 14).
In this regard, it can be mentioned that in case a deforestation region is
not segmented accordingly (as in Fig. 12c), this does not render the
segmentation useless; rather it still can be treated as a deforestation area
whose polygon can be reshaped by a complementary process. In addi­
tion, regarding misclassifications originated by the presence of agri­
culture, they can be iterativelly corrected by periodic classification of
the corresponding area, in such way that areas destined to seasonal
crops are identified and segmented separately. These issues shall be
further discussed in a latter section.
3.4. Execution time
The application stage took about 20 min for each scene of Sentinel-2
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Ecological Informatics 66 (2021) 101454
with a resolution of 10 m and coverage area of 10,000 km2. This dura­
tion includes the download of the image (about 15 min) and the pro­
cessing by U-Net (about 5 min). The steps with the longest processing
time include downloading the scene, cropping the scene into smaller
images and applying the U-Nets (to identify the forest/non-forest classes
and cloud mapping - about 1.5 min for each U-Net). Although these steps
take a longer time for processing, all calculations are performed via
GPGPU, as well as the application of the logistic model, which sub­
stantially reduces the total processing time and, thus, facilitating the
application of the methodology to larger areas.
L. Bragagnolo et al.
Fig. 9. Mapping of polygons for the same region of the Amazon biome for different periods (Tile number field T22MDB).
4. Discussion
4.1. Deforestation mapping
Based on the combination of different techniques (U-Nets and lo­
gistic model) and satellite scenes from the Sentinel-2 mission, which
have an interesting frequency and resolution for the mapping and
monitoring of many environmental processes, this study developed a
methodology that provides highly accurate mapping and monitoring of
deforestation areas. The computational efficiency of the implementation
allows that such mapping can be readily obtained upon the availability
of new satellite imagery. In combination with the low revisit time of the
satellite missions, such as the Sentinel-2 and many other currently
operating satellites, the methodology can help enhance the rapid iden­
tification of deforestation activities in very large areas. The high values
obtained for the performance metrics evaluated (0.9402, 0.8570, and
0.8941 for precision, recall, and F1-score, respectively (Table 3)) indi­
cate that the framework was able to capture and reproduce the essence
of what is expected from the time-consuming photointerpretation
11
Ecological Informatics 66 (2021) 101454
process, which is to identify and segment deforestation areas. The results
showed that accurate deforestation polygons were generated both for
the Amazon and Atlantic Rainforest (Figs. 9–11), thus indicating that,
upon adequate training, other biomes and regions could also be
included. This remains to be tested in latter studies.
Back to the scientific question under investigation, it can be observed
that the application of the logistic growth model on the top of the image
segmentation network had a clear effect upon the reduction of false
positives. This can be observed on the data presented in Table 3, which
summarizes the incremental increase in segmentation performance in
each stage of the application of the methodology.
It can be noticed that the deforestation polygons managed to cover
nearly all the deforestation areas, having remained in some cases a
border of uncertain pixels corresponding to transition areas (forest/non-
forest), where the vegetation usually features an intermediate density
which renders such pixels hard to classify even by visual inspection.
Anyway, it is important to mention that mildly innacurate polygons
resulting from segmentation shall not render the result worthless in any
sense, since the polygons can be redrawn and refined by complementary
L. Bragagnolo et al.
Fig. 10. Mapping of polygons for the same region of the Amazon biome for different periods (Tile number field T20LNP).
processes. One can even argue that, once deforestation spots are pin­
pointed within areas covering several hundreds of square kilometers, the
worst part of the workload was accomplished. Such uncertainty
behavior had already been mentioned by Bragagnolo et al. (2021d) as
being the result of the vegetation density gradient between one class and
another. As the edges between classes are not well defined in terms of
their reflectance spectrum, they are difficult to classify, even by means
of qualified visual inspection. Also, there are uncertainties associated to
the visual and manual mapping of polygons that compose the masks
applied during the training and validation of the U-Net. This means that
the masks themselves can contain a certain level of distortions near the
edges between classes, which can slightly deteriorate the training of the
network. Regarding the false positives, some of them were associated to
the presence of clouds and the shades they projected on the ground.
Some instances in which they were not correctly mapped can be seen in
Fig. 13.
As a problem more specifically related to the Atlantic Forest biome,
the majority of false positives observed in the classification were ob­
tained in recently harvested agricultural areas that had been previously
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Ecological Informatics 66 (2021) 101454
misclassified as forest during the crop growth period. This seasonality
problem caused the neural network to classify cultivated regions as
forest, even though it was trained with images to differentiate cultivated
regions of forested regions. In fact, some phases of crop growth make
croplands hard to distinguish from dense forests, at least considering the
combination of bands applied in this study. Besides, the high degree of
fragmentation of the biome poses an extra difficulty to the mapping of
deforestation, since degradation can occur in small areas that can be
missed due to the resolution of the imagery. One way to get around this
problem whenever there is interest in the identification of small defor­
estation spots is to apply satellite imagery with higher resolution to such
areas. In this case, it is enough to re-train the U-Net and apply the
method to the new images.
Another possibility to achieve better performance in the identifica­
tion of deforestation polygons by reducing misclassifications is to inte­
grate the methodology with information and database systems that map
activities such as silviculture and extractive agriculture, for example,
such that they are not confused with deforestation due to having similar
reflective and spectral properties. Further, as official information about
L. Bragagnolo et al. Ecological Informatics 66 (2021) 101454

Fig. 11. Mapping of polygons for the same region of the Atlantic Forest biome for different periods (Tile number field T22JCS).

refined and reliable. A direct consequence is that alerts would not be

Table 5
issued for deforestation areas where the activities are legal, thus making
Metrics calculated in comparison with the reference (real) deforestation poly­
issued alerts more trustworthy.
gons, for the polygons generated by the methodology proposed in this study and
the polygons generated by MapBiomas. Another interesting point to be discussed refers to the way in which
the mapping of land use changes by machine learning techniques is often
Proposed methodology MapBiomas
carried out, by applying an image before and another after the event,
Tile number Precision Recall F1- Precision Recall F1- and using as a reference masks the polygons that feature class changes
field score score
(de Bem et al., 2020; Ma et al., 2016; Shi et al., 2020). In this case, the
T22MDB 0.8613 0.7032 0.7587 0.9962 0.8665 0.9211 composition of image datasets becomes more time consuming and
T20LNP 0.9438 0.8619 0.8986 0.9938 0.6121 0.6801 laborious, since the polygons must be generated manually and requires a
T22JCS 0.9118 0.9445 0.9274 0.9779 0.5579 0.5925
search job that makes the overall process more time-consuming. In turn,
the methodology proposed in this study proposes the use of two classes,
legal deforestation areas as well as other extraction activities become forest and non-forest, which facilitates the composition of datasets by
publicly available along with their period and location, the outcomes of allowing a greater volume of images with more diverse characteristics to
forest cover change monitoring systems can become increasingly more be pre-processed by means of semi-automatic methods. Further, it

13
L. Bragagnolo et al. Ecological Informatics 66 (2021) 101454

Fig. 12. Misclassifications identified for images of the Amazon biome for scenes from the Grid Sentinel T22MDB.

Fig. 13. Misclassifications identified for images of the Amazon biome for the scenes of the Grid Sentinel T20LNP.

Fig. 14. Misclassifications identified for images of the Atlantic Forest biome for the scenes of the Grid Sentinel T22JCS.

reduces the computational burden since the number of input matrices
becomes reduced (only one image is inserted in the input layer, not two).
Finally, it allows the model to be retrained and updated more frequently,
based on new images or features that become available to the study area.
We argue that, with sufficient development, machine learning al­
gorithms as combined with other resources, as presented in this study,
can provide a feasible backbone to automated methodologies of defor­
estation mapping. In particular, for the Amazon rainforest that is
monitored by means of projects such as PRODES, MapBiomas Alert and
TerraClass, our proposed framework can either work in parallel as a
complement to such systems or even as a standalone system to this or,
conceivably, to any other biome of interest. Due to the very character­
itics and nature of CNNs and FCNNs, not only deforestation can be dealt
applying machine learning tools but, under adequate training, possibly
any other dimension of the environment that might be of interest.
In general, the methodology presented in this study allows satellite
imagery to be readily processed and classified immediately after receipt,
with very reduced human intervention, thus allowing agile practical
applications for monitoring changes in forest cover and deforestation
warning systems. These systems can be effective in helping public
agencies and stakeholders to respond more quickly and effectively to
ongoing threats to forest cover.
Regarding the applicability of the proposed framework to other bi­
omes and other parts of the world, it can be pointed that it is straigh­
forward once an adequate image dataset is available. Such dataset can
be applied to fine-tune pre-trained networks (such as the ones developed
in this work) or to start a network and train it from the start. As a rule of
thumb, a pre-trained network would require less training effort and
could require smaller datasets to achieve its performance peak. Anyway,
it is important to note that none of the methods in any stage of the
framework is site-dependent, and thus the framework itself can be
transferred and applied to other regions of interest. This includes the fact

14
L. Bragagnolo et al.
that the framework is a standalone in the sense that it is not built on the
top of other monitoring systems, as it happens to be the case of Map­
Biomas Alert. As another point worth mentioning in what regards its
flexibility, the framework also allows any other architectures of image
segmentation networks to be applied in substitution to the U-Net. The
application of the U-Net, in particular, follows from previous works that
point to it as currently being one top-performer architecture in terms of
accuracy, learning and computation efficiency.
4.2. Comparison of results with MapBiomas Alert
Section 3.3 provided direct comparison of the results presented in
this research with the deforestation polygons generated by the Map­
Biomas Alert, a cutting-edge platform that provides agile information on
deforestation detection based on state-of-the-art methodologies, and a
publicly available and user-friendly search environment. As a result of
the comparison to a well-established high-level framework such as
MapBiomas Alert, we found that our proposed methodology can provide
a comparable performance. The visual inspection (Figs. 9–11) and nu­
merical evaluation (Table 5) of the resulting deforestation maps also
points to the fact that they can be regarded as complementary in the
sense that some deforestation areas identified in this study were not
mapped by MapBiomas Alert, and contrariwise. Thus, the next genera­
tions of increasingly accurate and automated deforestation monitoring
and mapping systems might consider using combinations of elements of
both frameworks in order to obtain further performance gains.
As another dimension of comparison, one can observe that the results
from MapBiomas Alert is built upon information generated by other
projects, while our proposed framework was conceived to be an end-to-
end standalone methodology. As a matter of fact, MapBiomas Alert was
conceived to work on the top of a series of coarser-level systems such as
DETER (Diniz et al., 2015), SAD/IMAZON (De Souza et al., 2008) and
SIPAMSAR (CENSIPAM, 2008). While such systems issue coarse-level
forest cover change detection alerts, MapBiomas Alert works by
refining them using high-resolution satellite imagery (3 m) with daily
periodicity. We evaluate that our proposed methodology may be ad­
vantageous for application in areas which are not previously covered by
publicly available data from deforestation detection programs. Further,
while the fact that the methodology was conceived as a standalone
end-to-end solution, there is nothing that precludes it from incorpo­
rating and taking advantage of pre-processed deforestation data for
reference or as a starting point.
Another element worth to mention is that despite this study chose to
apply satellite imagery with coarser spatial resolution than those applied
by MapBiomas Alert, to take advantage of the fact that they are free of
charge, the proposed framework can deliver the identification and
segmentation of deforestation areas with minimum size of 0.1 ha, thus
smaller than those delivered by MapBiomas Alert (0.3 ha). Since the
minimum size is a result of the satellite resolution and not an intrinsic
limitation of the methodology, upon the application of higher-resolution
images such minimum size can be made smaller upon demand. It is
worth mentioning, however, that this would imply in an increase in
computational cost, which scales accordingly.
4.3. Automated processing, scalability and computational requirements
The methodology presented in this article is aimed at offering an
automated alternative for mapping deforestation, having as case studies
portions of the Amazon and Atlantic rainforests and using images from
the Sentinel-2 satellite. Regarding the automation of the methodology,
the results presented in this paper were generated without human
intervention. Once the details of the methodology were iteratively
adjusted to what seems to be their optimal values (e.g., kernel size for
the removal of noisy pixels, image band composition), during the
development of each stage, the methodology was applied end-to-end
without the need for intervention of any kind. This includes all the
15
Ecological Informatics 66 (2021) 101454
way from the download and pre-processing of satellite imagery to the
generation of deforestation polygons as overlays to maps and reports.
Therefore, while the results could eventually benefit from some kind of
specialized supervision or intervention along the process, the method­
ology was shown to provide accurate results when working autono­
mously. Hopefully, this might contribute to pave the way to highly
automated, efficient and accurate deforestation monitoring systems that
can be applied to vast areas at low cost.
Regarding the scalability of the methodology, it is worth mentioning
the possibility of adapting the methodology to increased workload by
rapidly ramping up outputs. Since the process is highly automated,
ramping up outputs will be largely dependent upon processing power,
while very little depending on specialized human work. Further, pre-
trained network parameters can be readily applied as starting point to
the fine-tuning of FCNs that are to operate in a newly covered region. As
such, the critical elements for scalability can be readily solved. In this
research we considered the application of a single U-Net to two Brazilian
biomes, since a previous study by Bragagnolo et al. (2021d) showed
evidences that a single neural network trained for both biomes was able
to achieve better identification performance in those two biomes than
two networks exclusivelly trained and applied for each biome. Yet these
results may not be conclusive or even applicable to other cases, they hint
that in some cases in which the vegetation characteristics are reasonably
similar, a single network trained over a larger and most diverse dataset
can outperform its biome-specialist pairs. In all cases, however, the
sensible and aware user must define the areas of coverage of his interest
and assess whether the methodology is responding satisfactorily. If it is
able to generalize the learning to regions with different characteristics,
as it happened to be the case in this study, the training and application
processes can be simplified.
About the computational requirements, the whole studied presented
in this paper was performed in an unexpensive workstation equipped
with a rather modest graphics card (to the current standards), which
means that the methodology does not require any extraordinary
computational facilities. It is true, however, that even a rather modest
GPU such as NVIDIA GTX 1060, as described above, can perform a huge
amount of computations in this case, since both the FCN and the logistic
growth model admit parallel implementation. As such, while an ordi­
nary office computer will suffice to apply the proposed framework to
monitor a rather vast area, it does pay off to have the GPU do the
computation. As an example, considering a single scene from the
Sentinel-2 satellite (100 × 100 km) and the machine configurations
employed for the development of the case studies, the whole process
(download, application of U-Net, and logistic model, post-processing)
took about 20 min, three quarters of which were spent in the down­
load of the scene. The remaining quarter, corresponding to about five
minutes, was the time taken to apply image pre-processing, image seg­
mentation, computation of growth parameter for each pixel and gen­
eration of the figures and the report on the deforestation areas
identified. The modest computational demand reinforces the potential
of the method to widespread applicability in monitoring systems.
4.4. Limitations of the proposed framework
Although a specific stage of the procedure was dedicated to treat the
presence of clouds and cloud shadows and it did contribute to improve
the classification performance, a relevant portion of false positives were
found in regions with the presence of clouds and cloud shadows. About
70% of false positives are related to the presence of clouds and their
shadows, considering as reference Fig. 8. Although such mis­
classifications can be corrected a posteriori, as soon as a new and cloud-
free image of the misclassified spot becomes available, this may take
quite a few passages of the satellite during the typical rainy seasons of
the Amazon biome. In this regard, alternative satellite products such as
ALOS-2 or Sentinel-1 imagery, which are not affected by the presence of
cloud cover since they have a synthetic-aperture radar (SAR) band, often
L. Bragagnolo et al.
feature low frequency (14 days of revisit time and a spatial resolution
ranging from 1 m to 100 m for ALOS-2, and 6 days for Sentinel-1 with a
spatial resolution of 5 m), and thus would frequently allow a posteriori
correction limited by the satellite periodicity (Reiche et al., 2018). Thus,
further studies are needed to overcome this limitation.
Another limitation related to the application of the Sentinel-2 im­
agery under the presence of thick clouds is that they may eventually hide
true deforestation areas. Therefore, although one can eventually prevent
false positives motivated by the presence of clouds and cloud shadows,
one can hardly avoid missing deforestation spots hidden by clouds. A
number of recent missions aim at providing satellite imagery not
affected by clouds, volcanic and fire smokes, as aforementioned.
As another important limitation, which is shared by all methodolo­
gies based on the analysis of satellite imagery, the outputs from the
proposed methodology point to areas whose spectral signature, as seen
by the combination of image layers, features high similarity to those of
deforestation areas. Therefore, although the methodology was found to
provide highly accurate results in terms of standard classification met­
rics, it might produce misclassifications, as any other existing classifi­
cation procedures (either manual or automatic) that deal with relevant
real-world problems. In this sense, it suffices to reinforce that the
objective of the presented segmentation methodology is to greatly
simplify, automatize and cheapen the process of identification and
location of deforestation spots within large forested areas, such as those
presented in the case studies.
5. Final remarks
This article aimed to present and discuss a methodology for mapping
deforestation using a fully convolutional neural network architecture
called U-Net coupled with the logistic growth model. By means of
application of free and openly available multispectral imagery from the
Sentinel-2 satellite for regions of the Amazon and Atlantic Forest bi­
omes, an automated processing chain for the generation of deforestation
polygons was proposed, tested, demonstrated and discussed. Case
studies illustrating realistic application of the methodology were pre­
sented, from which performance metrics for the methodology for pre­
cision, recall, and F1-score were in the range of 0.8613–0.9438,
0.7032–0.9445, and 0.7587–0.9274, respectively, indicating the po­
tential of the methodology to achieve accurate mapping of deforestation
polygons. Other important aspects such as the level of automation and
scalability were discussed on the basis of the comprehensive and
detailed information collected along the development of the case
studies.
As another conclusion, the application of a growth model on the top
of an image segmentation stage can be helpful in increasing the seg­
mentation performance. The results showed that a considerable count of
false-positives could be eliminated by means of the logistic growth
model.
It is hoped that this work can contribute to the discussion on
increasingly accurate, agile and computationally efficient methodolo­
gies for deforestation monitoring. To allow most widespread use and
evaluation, the methodology was entirely built on an open programming
language and tested using free satellite images. The satisfactory per­
formance achieved in such intended worst-case scenario is regarded as
encouraging. One can reinforce that the development of increasingly
accurate and automated deforestation monitoring tools can assist in the
most diverse spheres of governmental and non-governmental agencies
aimed at stopping illegal deforestation.
Declaration of Competing Interest
The authors declare no conflict of interest.
16
Ecological Informatics 66 (2021) 101454
Acknowledgements
The authors thank CAPES for the support.
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