The rapid and accurate identification of pathogenic spores is essential for the early diagnosis of diseases in modern agriculture. Gray mold disease, caused by Botrytis cinerea, is a significant threat to several crops and is traditionally controlled using fungicides or, alternatively, by UV-C radiation. Classically, the determination of conidial germination percentage, a key indicator for assessing pathogen viability, has been a manual, time-consuming, and error-prone process. This study proposes an approach based on deep learning, using one-stage detectors to automate the detection and counting of germinated and non-germinated conidia in microscopy images. We trained and assessed the performance of three models under several metrics: YOLOv8, YOLOv11, and RetinaNET. The results show that these three architectures provide an efficient and accurate solution for the recognition of gray mold conidia viability. Selecting the best model, we performed the task of detecting and counting conidia for determining the germination percentage on samples treated with different UV-C radiation dosages. The results show that these deep-learning models achieved counting accuracies that closely matched those obtained with conventional manual methods, yet they delivered results far more rapidly. Because they operate continuously without fatigue or operator bias, these models begin to open possibilities, after widening field tests and datasets, for efficient and fully automated monitoring pipelines for disease management in the agro-industry.