| Summary: | The potential of hyperspectral measurements for early disease detection has been investigated by many experts over the last 5 years. One of the difficulties is obtaining enough data for training and building a hyperspectral training library. When the goal is to detect disease at a previsible stage, before the pathogen has manifested either its first symptoms or in the area surrounding the existing symptoms, it is impossible to objectively delineate the regions of interest containing the previsible pathogen growth from the areas without the pathogen growth. To overcome this, we propose an image labelling and segmentation algorithm that is able to (a) more objectively label the visible symptoms for the construction of a training library and (b) extend this labelling to the pre-visible symptoms. This algorithm is used to create hyperspectral training libraries for late blight disease (<i>Phytophthora infestans</i>) in potatoes and two types of leaf rust (<i>Puccinia triticina</i> and <i>Puccinia striiformis</i>) in wheat. The model training accuracies were compared between the automatic labelling algorithm and the classic visual delineation of regions of interest using a logistic regression machine learning approach. The modelling accuracies of the automatically labelled datasets were higher than those of the manually labelled ones for both potatoes and wheat, at 98.80% for <i>P. infestans</i> in potato, 97.69% for <i>P. striiformis</i> in soft wheat, and 96.66% for <i>P. triticina</i> in durum wheat.
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