AbstractA new method is presented for quantitative evaluation of hybrid aspen genotype xylem morphology and immunolabeling micro-distribution. This method can be used as an aid in assessing differences in genotypes from classic tree breeding studies, as well as genetically engineered plants. The method is based on image analysis, multivariate statistical evaluation of light, and immunofluorescence microscopy images of wood xylem cross sections. The selected immunolabeling antibodies targeted five different epitopes present in aspen xylem cell walls. Twelve down-regulated hybrid aspen genotypes were included in the method development. The 12 knock-down genotypes were selected based on pre-screening by pyrolysis-IR of global chemical content. The multivariate statistical evaluations successfully identified comparative trends for modifications in the down-regulated genotypes compared to the unmodified control, even when no definitive conclusions could be drawn from individual studied variables alone. Of the 12 genotypes analyzed, three genotypes showed significant trends for modifications in both morphology and immunolabeling. Six genotypes showed significant trends for modifications in either morphology or immunocoverage. The remaining three genotypes did not show any significant trends for modification.