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All organisms, fundamentally, are made from the same raw material, namely the elements of the periodic table. Biochemical diversity is achieved with how these elements are utilized, for what purpose and in which physical location. Determining elemental distributions, especially those of trace elements that facilitate metabolism as cofactors in the active centers of essential enzymes, can determine the state of metabolism, the nutritional status or the developmental stage of an organism. Photosynthetic eukaryotes, especially algae, are excellent subjects for quantitative analysis of elemental distribution. These microbes utilize unique metabolic pathways that require various trace nutrients at their core to enable its operation. Photosynthetic microbes also have important environmental roles as primary producers in habitats with limited nutrient supply or toxin contaminations. Accordingly, photosynthetic eukaryotes are of great interest for biotechnological exploitation, carbon sequestration and bioremediation, with many of the applications involving various trace elements and consequently affecting their quota and intracellular distribution. A number of diverse applications were developed for elemental imaging allowing subcellular resolution, with X-ray fluorescence microscopy (XFM) being at the forefront, enabling quantitative descriptions of intact cells in a non-destructive method. This Tutorial Review summarizes the workflow of a quantitative, single-cell elemental distribution analysis of a eukaryotic alga using XFM.