| Summary: | Abstract The study of plant anatomy, which can be traced back to the seventeenth century, advanced hand in hand with light microscopy technology and relies on traditional histologic techniques, which are based on serial two‐dimensional (2D) sections. However, these valuable techniques lack spatial arrangement of the tissue and hence provide only partial information. A new technique of whole‐mount three‐dimensional (3D) imaging termed high‐resolution episcopic microscopy (HREM) can overcome this obstacle and generate a 3D model of the specimen at a near‐histological resolution. Here, we describe the application of HREM technique in plants by analyzing two plant developmental processes in woody plants: oil secretory cavity development in citrus fruit and adventitious root formation in persimmon rootstock cuttings. HREM 3D models of citrus fruit peel showed that oil cavities were initiated schizogenously during the early stages of fruitlet development. Citrus secretory cavity formation, shape, volume, and distribution were analyzed, and new insights are presented. HREM 3D model comparison of persimmon rootstock clones, which differ in their rooting ability, revealed that difficult‐to‐root clones failed to develop adventitious roots due to their inability to initiate root primordia.
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