Explainable growth stage classification of cacao (Theobroma cacao L.) leaves and key feature visualization using vision transformer and transfer learning.

Accurate and objective plant phenotyping is crucial for optimizing agricultural practices, understanding plant development, and enabling rapid responses to environmental changes. Traditional methods, often relying on visual observation, can be subjective, time-consuming, and may overlook subtle but important differences. This study demonstrates the power of combining digital imaging with deep learning to classify plant material with high accuracy, even when visual differences are minimal. We focused on differentiating between stage D (light green) and stage E (dark green) leaves of cacao (Theobroma cacao L.), which are visually very similar in size and overall structure. Using cleared and stained leaves of the SCA 6 genotype to highlight the venation network, we trained a Vision Transformer (ViT) model, a deep learning architecture, on image patches. At the patch level, the model achieved an overall accuracy of 97.03% on an independent test set, with a recall of 96.0% for stage D and 98.3% for stage E. At the whole-leaf level, majority voting correctly classified 14 of 15 independent test leaves (93.3%). Attention maps indicated that image regions containing the midrib and primary lateral veins contributed strongly to classification. These attention maps identify discriminative image regions, but they do not by themselves determine the biological mechanism underlying the signal. The major-vein signal may reflect developmental differences in vein-associated structure, stage-associated differences in Safranin O uptake or optical density, tissue thickness, or a combination of these factors. Because vascular anatomy, lignification, hydraulic conductance, phloem loading, and source-sink status were not directly measured, these mechanisms are treated as hypotheses requiring future anatomical, histochemical, and physiological validation. Thus, this study provides a proof-of-concept for interpretable image-based classification of stage D and stage E leaves within greenhouse-grown SCA 6 cacao. Extension to other cacao genotypes, field-grown plants, independent seasons, staining batches, stress detection, species identification, genotype discrimination, or precision-agriculture deployment will require external validation.