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Premise Herbarium specimens have been used to detect climate-induced shifts in flowering time by using the day of year of collection (DOY) as a proxy for first or peak flowering date. Variation among herbarium sheets in their phenological status, however, undermines the assumption that DOY accurately represents any particular phenophase. Ignoring this variation can reduce the explanatory power of pheno-climatic models (PCMs) designed to predict the effects of climate on flowering date. Methods Here we present a protocol for the phenological scoring of imaged herbarium specimens using an ImageJ plugin, and we introduce a quantitative metric of a specimen's phenological status, the phenological index (PI), which we use in PCMs to control for phenological variation among specimens of Streptanthus tortuosus (Brassicaceeae) when testing for the effects of climate on DOY. We demonstrate that including PI as an independent variable improves model fit. Results Including PI in PCMs increased the model R-2 relative to PCMs that excluded PI; regression coefficients for climatic parameters, however, remained constant. Discussion Our protocol provides a simple, quantitative phenological metric for any observed plant. Including PI in PCMs increases R-2 and enables predictions of the DOY of any phenophase under any specified climatic conditions.