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Background  3D high-resolution X-ray imaging methods have emerged over the last years for visualising the anatomy of tissue samples without substantial sample preparation. Quantitative analysis of cells and intercellular spaces in these images has, however, been difficult and was largely based on manual image processing. We present here an automated procedure for processing high-resolution X-ray images of parenchyma tissues of apple ( Malus  ×  domestica  Borkh.) and pear ( Pyrus communis  L.) as a rapid objective method for characterizing 3D plant tissue anatomy at the level of single cells and intercellular spaces.    Results  We isolated neighboring cells in 3D images of apple and pear cortex tissues, and constructed a virtual sieve to discard incorrectly segmented cell particles or unseparated clumps of cells. Void networks were stripped down until their essential connectivity features remained. Statistical analysis of structural parameters showed significant differences between genotypes in the void and cell networks that relate to differences in aeration properties of the tissues.    Conclusions  A new model for effective oxygen diffusivity of parenchyma tissue is proposed that not only accounts for the tortuosity of interconnected voids, but also for significant diffusion across cells where the void network is not connected. This will significantly aid interpretation and analysis of future tissue aeration studies. The automated image analysis methodology will also support pheno- and genotyping studies where the 3D tissue anatomy plays a role.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-015-0650-y) contains supplementary material, which is available to authorized users.

Automatic analysis of the 3-D microstructure of fruit parenchyma tissue using X-ray micro-CT explains differences in aeration