Fig. 1

Schematic representation of the seed–soil contact calculation process. The original image shows contact areas in blue based on the overlap of dilated soil aggregates. a During the process of germination, seeds open to enable radicle penetration which is indicated with the schematic representation of the 2D slice. The standard process of segmentation was conducted with additional segmentation of the air space within the opening seed. The segmented surface was dilated by +1 voxel. b Brown objects indicate a simplified version of soil aggregates around the seed. Using surface determination, the soil aggregates were segmented and finally dilated by +1 voxel. c The dilated surface from step A was extracted as a volume and the segmented surface (3rd step of A) copied into the volume as a ROI. The surface area of the seed is now listed in determine properties as closed surface area. The dilated soil from step B is also copied into the new volume and the surface area determined via determine properties. d The previously determined surface properties (step C) were used to calculate a seed–soil contact percentage