Fig. 2.

Quantification of root–soil–bacteria interactions. Image data from lettuce root (A), transparent soil particles (B), and GFP-labeled B. subtilis (C). Processing of the data follows three steps. (Left) Raw data are acquired from the microscope. (Middle) Cross-sections are assembled into volume data through stitching and stacking. (Right) Image processing is subsequently performed to quantify temporal and spatial patterns of biological activity in the pore space. The metrics obtained from the data include distance from the root surface (A), pore size (B), and bacterial cell density (C). (Scale bar, 2 mm.)