Classification of Blackcurrant Genotypes by Ploidy Levels on Stomata Microscopic Images with Deep Learning: Convolutional Neural Networks and Vision Transformers

Aleksandra Konopka, Ryszard Kozera, Agnieszka Marasek-Ciołakowska, Aleksandra Machlańska

Plants vary in number of chromosomes (ploidy levels), which can influence morphological traits, including the size and density of stomata cells. Although biologists can detect these differences under a microscope, the process is often time-consuming and tedious. This study aims to automate the classification of blackcurrant (Ribes nigrum L.) ploidy levels—diploid, triploid, and tetraploid—by leveraging deep learning techniques. Convolutional Neural Networks and Vision Transformers are employed to perform microscopic image classification across two distinct blackcurrant datasets. Initial experiments demonstrate that these models can effectively classify ploidy levels when trained and tested on subsets derived from the same dataset. However, the primary challenge lies in proposing a model capable of yielding satisfactory classification results across different datasets ensuring robustness and generalization, which is a critical step toward developing a universal ploidy classification system. In this research, a variety of experiments is performed including application of augmentation technique. Model efficacy is evaluated with standard metrics and its interpretability is ensured through Gradient-weighted Class Activation Mapping visualizations. Finally, future research directions are outlined with application of other advanced state-of-the-art machine learning methods to further refine ploidy level prediction in botanical studies.