A pipeline for processing hyperspectral images, with a case of melanin-containing barley grains as an example

• Published in: Vavilovskiĭ zhurnal genetiki i selekt͡s︡ii Vol. 28; no. 4; pp. 443 - 455
• Main Authors: Busov, I. D., Genaev, M. A., Komyshev, E. G., Koval, V. S., Zykova, T. E., Glagoleva, A. Y., Afonnikov, D. A.
• Format: Journal Article
• Language: English
• Published: Russia (Federation) The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences 01.07.2024; Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
• Subjects: barley grains; hyperspectral images; machine learning; Original; pigment composition; statistical analysis; pigment composition; barley grains; machine learning; statistical analysis; hyperspectral images
• ISSN: 2500-3259; 2500-0462; 2500-3259
• DOI: 10.18699/vjgb-24-50

Analysis of hyperspectral images is of great interest in plant studies. Nowadays, this analysis is used more and more widely, so the development of hyperspectral image processing methods is an urgent task. This paper presents a hyperspectral image processing pipeline that includes: preprocessing, basic statistical analysis, visualization of a multichannel hyperspectral image, and solving classification and clustering problems using machine learning methods. The current version of the package implements the following methods: construction of a confidence interval of an arbitrary level for the difference of sample averages; verification of the similarity of intensity distributions of spectral lines for two sets of hyperspectral images on the basis of the Mann–Whitney U-criterion and Pearson’s criterion of agreement; visualization in two-dimensional space using dimensionality reduction methods PCA, ISOMAP and UMAP; classification using linear or ridge regression, random forest and catboost; clustering of samples using the EM-algorithm. The software pipeline is implemented in Python using the Pandas, NumPy, OpenCV, SciPy, Sklearn, Umap, CatBoost and Plotly libraries. The source code is available at: https://github.com/igor2704/Hyperspectral_images. The pipeline was applied to identify melanin pigment in the shell of barley grains based on hyperspectral data. Visualization based on PCA, UMAP and ISOMAP methods, as well as the use of clustering algorithms, showed that a linear separation of grain samples with and without pigmentation could be performed with high accuracy based on hyperspectral data. The analysis revealed statistically significant differences in the distribution of median intensities for samples of images of grains with and without pigmentation. Thus, it was demonstrated that hyperspectral images can be used to determine the presence or absence of melanin in barley grains with great accuracy. The flexible and convenient tool created in this work will significantly increase the efficiency of hyperspectral image analysis.