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Currently, only non-imaging chlorophyll fluorescence measurements are used to identify the Lower Oxygen Limit (LOL) in Dynamic Controlled Atmosphere - Chlorophyll Fluorescence (DCA-CF) storage. The disadvantage of non-imaging fluorescence is that no statement can be made about the spatial heterogeneity of the sample. In contrast, chlorophyll fluorescence imaging can detect spatial heterogeneity of photosynthetic activity and has been established in research for some decades because the information benefit is higher. In this study, the chlorophyll fluorescence (Fo, Fm, Fv, Fv/Fm) of apples (Malus x domestica, BORKH.) was measured with a fluorescence imaging system in situ during storage. Intact apples of ‘Braeburn’ and ‘Golden Delicious’ were stored under low-oxygen stress conditions (< 1 kPa). The metabolic shift from aerobic to fermentative metabolism was made visible with the chlorophyll fluorescence imaging and was spatially localized on the sample. Furthermore, a method was developed to identify the LOL based on the chlorophyll fluorescence imaging combined with the histogram division method. This method considers the heterogeneity of the fluorescence and bundles the measured Fo data as histograms. Our results showed that the fluorescence imaging combined with the histogram division method can be a powerful tool for identifying the LOL.