The high costs and the focus on analyzing human and animal cells certainly did not encourage the rapid spread of FCM in the plant sciences. But at least equally important obstacles were, and in many ways continue to be, the difficulties associated with sample preparation, as a consequence of the plant body design and cell structure. Plants are built of complex three-dimensional tissues of various types of irregularly shaped cells with rigid cell walls, which are held together by extracellular matrix. However, a sample for FCM must be in a form of liquid suspension of single particles. Additional problems are posed by the chemical composition of cells. Plant cells produce a vast array of secondary metabolites which may interfere with staining of particular cell constituents and/or exhibit autofluorescence, thus hampering quantification of signals from fluorescent probes. Provided that analysis at the cellular level is not required, a frequent alternative is to isolate the organelles of interest and treat them separately.
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