Imaging roots and microorganisms in transparent soil using OPT and confocal microscopy.

<p>A. Projection image from OPT scan of <i>Nicotiana benthamiana</i> roots. Scale bar represents 1 mm. B. Root tracking algorithm is applied to the reconstructed data to segment and dilate (to improve visibility) the root (green) from the small air bubbles (blue). Scale bar represents 1 mm. C–F. Snapshots of volume renderings of confocal scans. C. <i>Arabidopsis thaliana</i> roots expressing GFP in plasma membranes (grey) in transparent soil with sulphorhdamine-B-dyed particles (orange) where scale bars represents 300 µm. Inset shows root skeletonisation and edge detection applied to scan C to detect roots and particles. D. GFP labelled <i>Escherichia coli</i> 0157:H7 cells and colonies on surface of <i>Latuca sativa</i> (lettuce) root with prominent root hairs. Scale bar represents 30 µm. E. Box shows enlarged region of lettuce root in D with Nafion particles visible in orange. Scale bar represents 100 µm. F. <i>Arabidopsis thaliana</i> root tip with nuclear RFP expression linked to auxin reporter <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044276#pone.0044276-Federici2" target="_blank">[41]</a>. Inset with box shows enlarged region. Scale bar represents 54 µm.