Improved Contrast and Clarity in Plant Microscopic Images using Contrast Limited Adaptive Histogram Equalization
DOI:
https://doi.org/10.52436/1.jutif.2026.7.1.5333Keywords:
Biology, CLAHE, Image, Microscopic, QualityAbstract
This research aims to enhance the quality of microscopic plant images which often suffer from low contrast and noise, hindering both visual and automated analysis. We propose the application of the Contrast Limited Adaptive Histogram Equalization (CLAHE) algorithm to address this issue. Implementation was carried out using MATLAB, processing a dataset of microscopic images from the Biology Laboratory of Siliwangi University. The research methodology includes image pre-processing, applying CLAHE with a Tile Grid Size of 8×8 and a Clip Limit of 0.02, and a quantitative evaluation using full-reference metrics such as MSE, PSNR, SSIM, RMSE, and FSIM. The results show that the application of CLAHE consistently demonstrated a significant improvement in image quality. Based on calculations, the lowest MSE value was found in the “monokotil (L.S)” image with 644.046 and the highest in the Monocotyledon Stem image with 6,298,683. The highest PSNR value was achieved by the “monokotil (L.S)” image with 46.225 dB, while the lowest was in two Monocotyledon Stem images, at 25.174 dB and 23.422 dB. The highest SSIM value was also in the “monokotil (L.S)” image with 0.946, indicating a very high structural similarity. Likewise, the highest FSIM value was also found in the “monokotil (L.S)” image with 0.979. This enhancement is crucial for botanical analysis and bioinformatics applications, as it effectively increases contrast, reduces noise, and preserves structural integrity, thereby facilitating the identification of fine details in microscopic images. These results establish a reproducible enhancement baseline that strengthens downstream botanical analytics.
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M. W. Mirza, A. Siddiq, I. R. Khan, “A comparative study of medical image enhancement algorithms and quality assessment metrics on COVID-19 CT images,”. SIViP, vol. 17, no. 1, pp. 915–924, 2023, DOI: https://doi.org/10.1007/s11760-022-02214-2
Y. R. Haddadi, B. Mansouri, F. Z. D. Khoudja, "A Novel Medical Image Enhancement Algorithm Based on CLAHE and Pelican Optimization," Research Square, vol. nd, no. nd, 2023, DOI: https://doi.org/10.21203/rs.3.rs-2443705/v1
J. Guo, J. Ma, Á. F. G-. Fernández, Y. Zhang, H. Liang, "A survey on image enhancement for Low-light images," Heliyon Cellpress, e14558, pp. 1-26, 2023, DOI: https://doi.org/10.1016/j.heliyon.2023.e14558
F. Noor, Muhathir, Fadlisyah, D. Syahputra, "Analysis of Combined Contrast Limited Adaptive Histogram Equalization (CLAHE) and Median Filter Methods for Enhancement of CCTV Screenshot Image Quality," JITE (Journal of Informatics and Telecommunication Engineering), vol. 8, no. 2, pp. 335-345, 2025, DOI: 10.31289/jite.v8i2.14016
Y. Zhang, X. Zhao, J. Li, X. Jia, “Hyperspectral image sharpening using high-frequency modulation and guided filtering,” in Journal of Electronic Imaging, vol. 30, no. 1, pp. 13-18, 2021
J. Geng, W. Jiang, X. Deng, “Multi-scale deep feature learning network with Bilateral filter for SAR Image Classification,” ISPRS Journal of Photogrammetry and Remote sensing, vol. 167, no. 1, pp. 201–213, 2020, DOI:10.1016/j.isprsjprs.2020.07.007.
S. H. Anwariningsih, Wahyono, R. Sumiharto, "Enhancing Contrast Limited Adaptive Histogram Equalization Using Weighted Sum Cuckoo Search Algorithm," ICIC Express Letters, vol. 19, no. 5, pp. 475-488, 2025, DOI: 10.24507/icicel.19.05.475
S. Li, Y. Zhang, L. Wang, H. Zhang, “Robotic Weld Image Enhancement Based on Improved Bilateral Filtering and CLAHE Algorithm,” Sensors MDPI, vol. 22, no. 22, pp. 8845, 2022
C .H. Hsu, C. W. Chen, Y. K. Lai, “A real time hardware design for bilateral filtering,” Applied and Computational Engineering, Open Access Journal by AIJR Publisher, vol. 1, no. 1, pp. 1-10, 2024
Y. Zhang, J. Li, Y. Zhou, C. Wang, B. Zhang, “A novel 3D bilateral filtering algorithm with noise level estimation assisted by multi-temporal SAR,” Public Library of Science, PLoS ONE, vol. 20, no. 2, 2025
J. Chen, S. Paris, F. Durand, “A Fast Two-Stage Bilateral Filter Using Constant Time O(1) Histogram Generation,” IEEE Transactions on Image Processing, IEEE, vol. 32, pp. 2401-2413, 2023
P. A. Lyakhov, A. S. Voznesensky, E. D. Shalugin, A. R. Orazaev, V. A. Baboshina, "Bilateral and Median Filter Combination for High-Quality Cleaning of Random Impulse Noise in Images," 2022 11th Mediterranean Conference on Embedded Computing (MECO), Budva, Montenegro, pp. 1-5, 2022, DOI: 10.1109/MECO55406.2022.9797149.
K. Aurangzeb, S. Aslam, M. Alhussein, R. A. Naqvi, M. Arsalan, S. I. Haider, "Contrast Enhancement of Fundus Images by Employing Modified PSO for Improving the Performance of Deep Learning Models," IAEEEAccess, vol. 9, pp. 4793-47945, 2021, DOI: 10.1109/ACCESS.2021.3068477
F. Yan, H. Huang, W. Pedrycz, K. Hirota, "Review of medical image processing using quantum‑enabled algorithms," Artificial Intelligence Review, Springer, vol. 57:300, pp. 1-52, 2024, DOI: https://doi.org/10.1007/s10462-024-10932-x
H. Kaur, N. Kaur, N. Neeru, "A Comparative Study of Image Enhancement Algorithms for Abdomen CT Images," 2024 IEEE International Conference on Interdisciplinary Approaches in Technology and Management for Social Innovation (IATMSI), Gwalior, India, pp. 1-6, 2024, DOI: 10.1109/IATMSI60426.2024.10502768
K. S. Kumar, K. Bhagya, T. N. Kumari, G. Swathi, K. Dhanusree, "Image Enhancement using Adaptive Histogram Equalization for Medical Image Processing," Shodhsamhita: Journal of Fundamental & Comparative Research, vol. 7, no. 4, pp. 39-544, 2021, ISSN: 2277-7067
M. J. Alwazzan, M. A. Ismael, A. N. Ahmed, "A Hybrid Algorithm to Enhance Colour Retinal Fundus Images Using a Wiener Filter and CLAHE," Journal of Digital Imaging, Springer, vol. 34, pp. 750–759, 2021, DOI: https://doi.org/10.1007/s10278-021-00447-0
M. Hayati, K. Muchtar, Roslidar, N. Maulina, I. Syamsuddin, G. N. Elwirehardja, B. Pardamean, "Impact of CLAHE-based image enhancement for diabetic retinopathy classification through deep learning," in 7th International Conference on Computer Science and Computational Intelligence 2022, Procedia Computer Science, vol. 216, pp. 57–66, 2023
X. Liu, T. D. C. Nguyen, "Medical Images Enhancement by Integrating CLAHE with Wavelet Transform and Non-Local Means Denoising," Academic Journal of Computing & Information Science, vol. 7, no. 1, pp. 52-58, 2024, DOI: 10.25236/AJCIS.2024.070108
H. A. Majeed, A. M. Kadhim, H. G. Daway, "Enhancement of Microscopy Images by Using a Hybrid Technique Based on Adaptive Histogram Equalisation and Fuzzy Logic," International Journal of Intelligent Engineering and Systems, vol.16, no.1, pp. 246-253, 2023, DOI: 10.22266/ijies2023.0228.22
C. Li, H. Guo, Y. Liu, Z. Wang, “Retinex Jointed Multiscale CLAHE Model for HDR Image Tone Compression,” Sensors, MDPI, vol. 23, no. 20, pp. 8524, 2023
E. Prasetyo, R. Setiawan, O. D. Nurhayati, “Analisis Perbandingan He Dan Clahe Pada Image Enhancement Dalam Proses Segmenasi Citra Untuk Deteksi Fertilitas Telur,” Jurnal Teknologi Pertanian, no. 21, vol. 1, pp. 37-48, 2020
F. Noor, N. Muhathir, F. Fadlisyah, D. Syahputra, “Analysis of Combined Contrast Limited Adaptive Histogram Equalization (CLAHE) and Median Filter Methods for Enhancement of CCTV Screenshot Image Quality,” JITE (Journal of Informatics and Telecommunication Engineering), vol. 8, no. 2, pp. 335-345, 2025
M. A. Khan, F. Khan, U. Tariq, A. Hussain, A. Rehman, M. Nawaz, “Impact of CLAHE-based image enhancement for diabetic retinopathy classification through deep learning, Scientific Reports, Nature Portofolio, no. 13, vol. 1, pp. 4531, 2023
M. Pramita, “Implementasi Metode Bilateral filter Untuk Mengurangi Derau Pada Citra Magnetic Resonance Imaging (MRI),” Jurnal Informasi dan Teknologi Ilmiah (INTI), vol. 7, no. 3, 2020
E.Ranolo, A. Sebial, A. Ilano, A. C. Canillo, "Seagrass Blurred Image Enhancement and Detection using YOLO and CLAHE Algorithms Performance Comparison," in 2023 International Conference on Evolutionary Algorithms and Soft Computing Techniques (EASCT), Bengaluru, India, 2023, pp. 1-5, doi: 10.1109/EASCT59475.2023.10393080
N. A. Amalia, A. Afira, M. Ulfa, K. Muchtar, "Utilizing Edge Device and Streamlit for Comparative Evaluation of CLAHE-Based Underwater Image Enhancement Techniques," in 2024 IEEE 13th Global Conference on Consumer Electronics (GCCE), Kitakyushu, Japan, 2024, pp. 599-600, doi: 10.1109/GCCE62371.2024.10760315
J. S. Cardenas, W. M. F-. Amaris, C. A. S-. Centeno, Alejandro Castaneda, O. D. M-. Berna, D. R. Suárez, C. Martínez, "Image-Based Detection and Classification of Malaria Parasites and Leukocytes with Quality Assessment of Romanowsky-Stained Blood Smears," Sensor MDPI, vol. 25, no. 390, pp. 1-18, 2025, DOI: https://doi.org/10.3390/s25020390
M. W. Mirza, A. Siddiq, I. R. Khan, "A comparative study of medical image enhancement algorithms and quality assessment metrics on COVID-19 CT images," Signal, Image and Video Processing, vol. 17, pp. 915–924, 2023, DOI: https://doi.org/10.1007/s11760-022-02214-2
Y. A. Najjar, "Comparative Analysis of Image Quality Assessment Metrics: MSE, PSNR, SSIM, and FSIM," International Journal of Science and Research, vol. 13(3), pp. 110–114, 2024, DOI: https://dx.doi.org/10.21275/SR24302013533
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Copyright (c) 2026 Eka Wahyu Hidayat, R Reza El Akbar, Muhammad Adi Khairul Anshary
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