Schematic representation of the in situ PCR pipeline. Plant tissue is fixed in an ethanol/acetic acid/formaldehyde solution, followed by embedding in agarose and sectioning. Sections are collected into a microfuge tube in which DNase treatment, reverse transcription and in situ PCR are carried out using a thermocycler. During in situ PCR, DIG labeled nucleotides are incorporated into the PCR products. An anti-DIG antibody conjugated with alkaline phosphatase and an alkaline phosphatase substrate are used for the detection of the DIG labeled PCR products. These are visualized under a microscope. Thin fragile sections are placed onto a glass slide after sectioning, while *non-embedded, non-sectioned samples (i.e. epidermal peels) are placed directly onto slides for all processes from fixation to the final PCR step (dotted arrow).