Automatic Recognition of Commercial Tree Species from the Amazon Flora Using Bark Images and Transfer Learning
Abstract
1. Introduction
2. Materials and Methods
2.1. Areas of Study
2.2. Image Acquisition
2.3. Identifying Species and Collection Botanical Material
2.4. Extraction of Sub-Images (Patches)
2.5. Extracting Features from Original Images and Sub-Images
2.5.1. Local Binary Patterns (LBP)
- Uniform and rotation-invariant: , , ;
- Uniform and non-invariant: , , .
2.5.2. Transfer Learning
2.6. Algorithms, Cross-Validation and Performance Metrics
2.6.1. Classification Algorithms
2.6.2. Image Division and Cross-Validation
2.6.3. Performance Metrics
- Accuracy: represents the number of correct predictions made by the model:
- Recall or Sensitivity: Metric recommended when there is class imbalance. It represents the classification model’s ability to predict the positive class:
- F1—score is the harmonic mean between Recall and Precision (which represents the number of observations classified correctly). It is considered a suitable metric for problems with unbalanced classes:
3. Results
Performance of the Classifiers
4. Discussion
4.1. Images Sets: Characteristics, Sources of Variation and Dificulties
4.2. Local Binary Standards
4.3. Transfer Learning
4.4. Implications for Sustainable Forest Management and Future Perspectives
- Expansion of datasets to include regional and structural bark variability;
- Validation of models using mobile devices under field conditions;
- Integration of other plant organs (e.g., leaves, fruits) for multimodal classification;
- Development of lightweight architectures for deployment in remote forest environments.
5. Conclusions
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
Algorithm | Candidate Hyperparameters |
---|---|
Artificial neural networks | hidden_layer_sizes = (50), (100), (150), (200), (250), (300), (350), (400), (450) e (500) |
activation = relu e identity | |
solver = adam e lbfgs | |
alpha = uniform(loc = 0.0001, scale = 0.09).rvs(size = 20, random_state = 10) | |
learning_rate = constant, adaptive e invscaling | |
Support vector machine | C = uniform(loc = 0.1, scale = 10).rvs(size = 20, random_state = 10) |
kernel = linear, rbf, poly e sigmoid | |
degree = 2, 3 e 4 | |
gamma = scale e auto + list(np.logspace(−9, 3, 13) | |
Random forest | n_estimators = np.arange(40, 320, 20) |
max_depth = list(np.arange(10, 100, step = 10)) + [None] | |
max_features = list(np.arange(30, 60, 5)) + [‘sqrt’, “log2”] | |
criterion = gini e entropy | |
min_samples_leaf = np.arange(10, 110, 10) | |
min_samples_split = np.arange(2, 10, 2) | |
bootstrap = True e False | |
Linear discriminant analysis | solver = lsqr e eigen |
tol = 0.0001, 0.0002 e 0.0003 |
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ID 1 | Family | Scientific Name | Vernacular Name | Samples | N 2 |
---|---|---|---|---|---|
1 | Fabaceae | Apuleia leiocarpa (Vogel) J. F. Macbr. | Garapeira | 10 | 155 |
2 | Anacardiaceae | Astronium lecointei Ducke | Muiracatiara | 10 | 182 |
3 | Moraceae | Bagassa guianensis Aubl. | Tatajuba | 10 | 185 |
4 | Fabaceae | Bowdichia nitida Spruce ex Benth. | Sucupira | 10 | 194 |
5 | Meliaceae | Cedrela odorata L. | Cedro-Rosa | 10 | 198 |
6 | Fabaceae | Dipteryx odorata (Aubl.) Forsyth f. | Cumaru | 10 | 149 |
7 | Vochysiaceae | Erisma uncinatum Warm. | Cedrinho | 10 | 158 |
8 | Goupiaceae | Goupia glabra Aubl. | Cupiúba | 10 | 162 |
9 | Fabaceae | Hymenelobium petraeum Ducke | Angelim-Pedra | 10 | 179 |
10 | Lauraceae | Mezilaurus itauba (Meisn.) Taub. ex Mez | Itauba | 10 | 164 |
11 | Fabaceae | Parkia pendula (Willd.) Benth. ex Walp. | Angelim-Saia | 10 | 183 |
12 | Burseraceae | Protium acrense Daly | Amescla-Aroeira | 10 | 188 |
13 | Vochysiaceae | Qualea paraensis Ducke | Cambara | 10 | 168 |
14 | Simaroubaceae | Simarouba amara Aubl. | Marupá | 10 | 197 |
15 | Burseraceae | Trattinnickia burserifolia Mart. | Amescla | 10 | 176 |
16 | Fabaceae | Vatairea sericea (Ducke) Ducke | Angelim-amargoso | 10 | 165 |
Training Set (cv = 5, n = 2237) | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
Classifier | Vector size | Statistics | SVM | ANN | RF | LDA | ||||
Accuracy (%) | F1 (%) | Accuracy (%) | F1 (%) | Accuracy (%) | F1 (%) | Accuracy (%) | F1 (%) | |||
C1 () | 10 | Average | 26.14 | 25.68 | 31.54 | 31.11 | 22.26 | 21.52 | 17.58 | 16.17 |
sd | 1.24 | 1.40 | 1.51 | 1.62 | 1.39 | 1.12 | 2.10 | 1.84 | ||
C2 () | 18 | Average | 32.30 | 31.16 | 38.95 | 38.20 | 25.47 | 24.40 | 22.79 | 21.54 |
sd | 2.06 | 2.43 | 2.26 | 2.20 | 0.91 | 0.77 | 1.65 | 1.21 | ||
C3 () | 26 | Average | 34.57 | 34.03 | 41.58 | 41.21 | 26.19 | 25.14 | 26.59 | 25.41 |
sd | 2.60 | 2.79 | 2.09 | 2.04 | 2.04 | 1.83 | 2.01 | 1.62 | ||
C4 () All | 54 | Average | 43.89 | 43.57 | 50.23 | 49.96 | 28.55 | 27.00 | 35.15 | 34.48 |
sd | 2.97 | 3.06 | 1.93 | 2.05 | 2.70 | 2.64 | 2.35 | 2.35 | ||
C5 () | 59 | Average | 38.31 | 37.96 | 42.96 | 42.67 | 29.21 | 28.68 | 31.41 | 30.81 |
sd | 2.02 | 1.85 | 2.19 | 2.06 | 1.24 | 1.40 | 1.79 | 1.90 | ||
C6 () | 243 | Average | 48.75 | 48.27 | 52.36 | 52.04 | 32.43 | 31.81 | 40.81 | 40.48 |
sd | 1.24 | 1.55 | 2.58 | 2.54 | 2.32 | 2.35 | 2.51 | 2.86 | ||
C7 () | 555 | Average | 51.69 | 50.97 | 55.17 | 54.76 | 33.32 | 32.35 | 48.58 | 48.04 |
sd | 1.30 | 1.42 | 2.40 | 2.53 | 3.19 | 3.42 | 2.91 | 3.42 | ||
C8 () All | 857 | Average | 54.73 | 54.00 | 60.30 | 59.90 | 35.63 | 34.49 | 55.40 | 54.95 |
sd | 1.57 | 1.78 | 2.62 | 2.82 | 2.96 | 3.32 | 3.57 | 4.07 | ||
C9 (+) All | 911 | Average | 55.40 | 54.74 | 60.65 | 60.26 | 35.59 | 34.50 | 56.25 | 55.84 |
sd | 2.12 | 2.26 | 1.59 | 1.84 | 2.96 | 3.02 | 4.11 | 4.61 | ||
Test Set (n = 566) | ||||||||||
Classifier | Vector size | SVM | ANN | RF | LDA | |||||
Accuracy (%) | F1 (%) | Accuracy (%) | F1 (%) | Accuracy (%) | F1 (%) | Accuracy (%) | F1 (%) | |||
C1 () | 10 | 38.68 | 38.48 | 41.00 | 40.82 | 33.00 | 32.62 | 20.00 | 18.82 | |
C2 () | 18 | 41.71 | 40.98 | 50.00 | 49.81 | 34.00 | 33.63 | 29.00 | 27.57 | |
C3 () | 26 | 46.88 | 47.12 | 52.00 | 51.44 | 32.00 | 31.94 | 34.00 | 32.46 | |
C4 () All | 54 | 54.55 | 54.63 | 60.00 | 60.60 | 39.00 | 37.67 | 42.00 | 41.57 | |
C5 () | 59 | 47.06 | 47.18 | 60.00 | 60.03 | 41.00 | 41.38 | 37.00 | 37.14 | |
C6 () | 243 | 62.92 | 63.09 | 63.00 | 63.24 | 45.00 | 44.25 | 51.00 | 51.16 | |
C7 () | 555 | 65.60 | 65.66 | 66.00 | 66.13 | 44.00 | 43.14 | 56.00 | 55.92 | |
C8 () All | 857 | 67.91 | 68.10 | 72.00 | 72.42 | 48.00 | 48.23 | 64.00 | 63.79 | |
C9 (+) All | 911 | 68.63 | 68.79 | 72.00 | 71.89 | 45.00 | 45.17 | 65.00 | 64.91 |
Training Set (cv = 5, n = 2237) | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
Classifier | Vector size | Statistics | SVM | ANN | RF | LDA | ||||
Accuracy (%) | F1 (%) | Accuracy (%) | F1 (%) | Accuracy (%) | F1 (%) | Accuracy (%) | F1 (%) | |||
C1 () | 10 | Average | 50.03 | 49.58 | 47.84 | 47.22 | 44.04 | 43.37 | 31.12 | 29.27 |
sd | 2.48 | 2.66 | 4.13 | 4.29 | 3.60 | 3.68 | 2.36 | 2.19 | ||
C2 () | 18 | Average | 36.17 | 34.26 | 52.40 | 51.39 | 41.94 | 40.60 | 35.18 | 33.29 |
sd | 3.13 | 3.47 | 2.88 | 2.88 | 3.86 | 4.16 | 4.00 | 4.03 | ||
C3 () | 26 | Average | 36.88 | 36.80 | 56.60 | 55.85 | 48.82 | 47.75 | 38.81 | 37.31 |
sd | 1.52 | 1.52 | 2.22 | 2.23 | 3.01 | 3.16 | 3.09 | 3.05 | ||
C4 () All | 54 | Average | 57.84 | 57.54 | 72.56 | 72.36 | 54.72 | 54.09 | 55.43 | 54.94 |
sd | 2.51 | 2.63 | 2.71 | 2.80 | 3.80 | 3.97 | 3.08 | 3.19 | ||
C5 () | 59 | Average | 66.79 | 66.51 | 74.16 | 73.90 | 56.95 | 56.11 | 53.96 | 52.87 |
sd | 1.77 | 1.77 | 2.66 | 2.80 | 2.35 | 2.43 | 2.67 | 2.73 | ||
C6 () | 243 | Average | 67.81 | 67.47 | 81.72 | 81.55 | 59.28 | 58.56 | 61.74 | 61.08 |
sd | 0.63 | 0.64 | 3.12 | 3.19 | 1.92 | 2.11 | 3.89 | 3.97 | ||
C7 () | 555 | Average | 67.90 | 67.89 | 78.23 | 78.07 | 53.82 | 52.34 | 63.21 | 62.45 |
sd | 2.49 | 2.50 | 2.72 | 2.76 | 2.67 | 2.65 | 3.26 | 3.31 | ||
C8 () All | 857 | Average | 77.61 | 77.29 | 77.52 | 77.41 | 60.22 | 59.38 | 73.72 | 73.46 |
sd | 2.85 | 2.81 | 3.16 | 3.17 | 2.19 | 2.29 | 3.63 | 3.71 | ||
C9 (+) All | 911 | Average | 77.21 | 76.9 | 77.56 | 77.48 | 60.93 | 60.07 | 73.94 | 73.66 |
sd | 2.92 | 2.9 | 3.28 | 3.27 | 2.21 | 2.27 | 3.68 | 3.75 | ||
Test set (n = 566) | ||||||||||
Classifier | Vector size | SVM | ANN | RF | LDA | |||||
Accuracy (%) | F1 (%) | Accuracy (%) | F1 (%) | Accuracy (%) | F1 (%) | Accuracy (%) | F1 (%) | |||
C1 () | 10 | 47.00 | 46.00 | 49.00 | 48.00 | 42.00 | 42.00 | 31.00 | 29.00 | |
C2 () | 18 | 37.00 | 35.00 | 53.00 | 53.00 | 41.00 | 40.00 | 36.00 | 34.00 | |
C3 () | 26 | 30.00 | 30.00 | 55.00 | 55.00 | 49.00 | 48.00 | 39.00 | 37.00 | |
C4 () All | 54 | 56.00 | 56.00 | 73.00 | 73.00 | 54.00 | 53.00 | 53.00 | 52.00 | |
C5 () | 59 | 69.00 | 69.00 | 75.00 | 75.00 | 56.00 | 55.00 | 54.00 | 53.00 | |
C6 () | 243 | 66.00 | 66.00 | 79.00 | 79.00 | 57.00 | 55.00 | 61.00 | 60.00 | |
C7 () | 555 | 67.00 | 67.00 | 75.00 | 75.00 | 51.00 | 48.00 | 61.00 | 60.00 | |
C8 () All | 857 | 75.00 | 74.00 | 75.00 | 74.00 | 60.00 | 59.00 | 73.00 | 72.00 | |
C9 (+) All | 911 | 75.00 | 75.00 | 75.00 | 74.00 | 60.00 | 59.00 | 73.00 | 72.00 |
CNN | ResNet50 | VGG16 | Inception_V3 | MobileNet_V2 | ||||||
---|---|---|---|---|---|---|---|---|---|---|
Vector size | 2048 | 512 | 2048 | 1280 | ||||||
Statistics (%) | Average | sd | Average | sd | Average | sd | Average | sd | ||
Training set (cv = 10, n = 2237) | SVM | Accuracy | 67.36 | 2.53 | 56.94 | 2.32 | 51.94 | 1.48 | 60.30 | 1.69 |
F1 | 66.79 | 2.73 | 56.35 | 2.36 | 51.36 | 1.24 | 59.60 | 1.39 | ||
ANN | Accuracy | 69.33 | 0.44 | 60.39 | 1.57 | 52.58 | 2.43 | 61.28 | 1.68 | |
F1 | 68.73 | 0.78 | 59.94 | 1.44 | 51.83 | 2.47 | 60.60 | 1.47 | ||
RF | Accuracy | 57.65 | 2.09 | 53.47 | 2.56 | 45.92 | 2.28 | 48.95 | 2.25 | |
F1 | 55.74 | 1.93 | 50.71 | 2.53 | 43.38 | 2.39 | 46.29 | 2.58 | ||
LDA | Accuracy | 63.87 | 1.79 | 53.01 | 1.41 | 52.22 | 3.00 | 59.00 | 2.10 | |
F1 | 63.54 | 1.98 | 53.08 | 1.30 | 52.28 | 2.54 | 58.79 | 1.41 | ||
Test set (n = 566) | SVM | Accuracy | 82.69 | 73.67 | 63.43 | 73.32 | ||||
F1 | 82.63 | 73.78 | 63.25 | 72.87 | ||||||
ANN | Accuracy | 81.98 | 74.03 | 63.25 | 76.50 | |||||
F1 | 82.08 | 73.98 | 63.44 | 76.24 | ||||||
RF | Accuracy | 69.96 | 59.19 | 50.53 | 57.42 | |||||
F1 | 69.05 | 57.53 | 48.75 | 56.16 | ||||||
LDA | Accuracy | 77.74 | 60.42 | 63.78 | 71.55 | |||||
F1 | 77.83 | 60.78 | 64.14 | 71.62 |
CNN | ResNet50 | VGG16 | Inception_V3 | MobileNet_V2 | ||||||
---|---|---|---|---|---|---|---|---|---|---|
Vector size | 2048 | 512 | 2048 | 1280 | ||||||
Statistics (%) | Average | sd | Average | sd | Average | sd | Average | sd | ||
Training set cv = 10, n = 2.237) | SVM | Accuracy | 95.57 | 1.07 | 91.42 | 1.28 | 93.21 | 1.94 | 94.55 | 1.53 |
F1 | 95.57 | 1.07 | 91.38 | 1.27 | 93.2 | 1.97 | 94.53 | 1.57 | ||
ANN | Accuracy | 95.35 | 1.63 | 91.28 | 2.53 | 91.24 | 1.45 | 92.36 | 1.99 | |
F1 | 95.34 | 1.64 | 91.21 | 2.61 | 91.18 | 1.45 | 92.31 | 2.01 | ||
RF | Accuracy | 84.76 | 2.83 | 80.82 | 3.12 | 71.71 | 3.43 | 76.09 | 3.04 | |
F1 | 84.48 | 2.94 | 80.31 | 3.40 | 70.48 | 3.82 | 75.15 | 3.28 | ||
LDA | Accuracy | 90.93 | 2.23 | 80.33 | 2.44 | 84.94 | 2.21 | 85.97 | 2.22 | |
F1 | 91.01 | 2.24 | 80.46 | 2.56 | 84.87 | 2.28 | 85.90 | 2.22 | ||
Test set (n = 566) | SVM | Accuracy | 95.00 | 91.00 | 92.00 | 94.00 | ||||
F1 | 95.00 | 91.00 | 92.00 | 94.00 | ||||||
ANN | Accuracy | 94.00 | 89.00 | 90.00 | 91.00 | |||||
F1 | 94.00 | 89.00 | 90.00 | 91.00 | ||||||
RF | Accuracy | 83.00 | 81.00 | 67.00 | 74.00 | |||||
F1 | 83.00 | 80.00 | 66.00 | 73.00 | ||||||
LDA | Accuracy | 92.00 | 81.00 | 83.00 | 86.00 | |||||
F1 | 92.00 | 81.00 | 83.00 | 86.00 |
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Gama, N.C.; Oliveira, L.E.S.; Carvalho, S.d.P.C.e.; Behling, A.; de Paula Filho, P.L.; Hamada, M.O.d.S.; Leal, E.d.S.; Souza, D.V. Automatic Recognition of Commercial Tree Species from the Amazon Flora Using Bark Images and Transfer Learning. Forests 2025, 16, 1374. https://doi.org/10.3390/f16091374
Gama NC, Oliveira LES, Carvalho SdPCe, Behling A, de Paula Filho PL, Hamada MOdS, Leal EdS, Souza DV. Automatic Recognition of Commercial Tree Species from the Amazon Flora Using Bark Images and Transfer Learning. Forests. 2025; 16(9):1374. https://doi.org/10.3390/f16091374
Chicago/Turabian StyleGama, Natally Celestino, Luiz Eduardo Soares Oliveira, Samuel de Pádua Chaves e Carvalho, Alexandre Behling, Pedro Luiz de Paula Filho, Márcia Orie de Sousa Hamada, Eduardo da Silva Leal, and Deivison Venicio Souza. 2025. "Automatic Recognition of Commercial Tree Species from the Amazon Flora Using Bark Images and Transfer Learning" Forests 16, no. 9: 1374. https://doi.org/10.3390/f16091374
APA StyleGama, N. C., Oliveira, L. E. S., Carvalho, S. d. P. C. e., Behling, A., de Paula Filho, P. L., Hamada, M. O. d. S., Leal, E. d. S., & Souza, D. V. (2025). Automatic Recognition of Commercial Tree Species from the Amazon Flora Using Bark Images and Transfer Learning. Forests, 16(9), 1374. https://doi.org/10.3390/f16091374