| Summary: | Chlorophyll fluorescence is interesting for phenotyping applications as it is rich in biological information and can be measured remotely and non-destructively. There are several techniques for measuring and analysing this signal. However, the standard methods use rather extreme conditions, e.g., saturating light and dark adaption, which are difficult to accommodate in the field or in a greenhouse and, hence, limit their use for high-throughput phenotyping. In this article, we use a different approach, extracting plant health information from the dynamics of the chlorophyll fluorescence induced by a weak light excitation and no dark adaption, to classify plants as healthy or unhealthy. To evaluate the method, we scanned over a number of species (lettuce, lemon balm, tomato, basil, and strawberries) exposed to either abiotic stress (drought and salt) or biotic stress factors (root infection using <i>Pythium ultimum</i> and leaf infection using Powdery mildew <i>Podosphaera aphanis</i>). Our conclusions are that, for abiotic stress, the proposed method was very successful, while, for powdery mildew, a method with spatial resolution would be desirable due to the nature of the infection, i.e., point-wise spread. <i>Pythium</i> infection on the roots is not visually detectable in the same way as powdery mildew; however, it affects the whole plant, making the method an interesting option for <i>Pythium</i> detection. However, further research is necessary to determine the limit of infection needed to detect the stress with the proposed method.
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