Fig. 1.

Main steps of image processing in the 3-D reconstruction program (xylem vessels as an example). (A) Colour images of the root stele are converted to grey-scale images, then loaded into the AMBIOS program and adjusted to optimal brightness and definition. (B) Edges of cells are computed by the program after setting up the appropriate parameters. The yellow curves are the computed cell edges (coinciding with the cell walls). (C) An image in the middle of the series is defined as the reference image and the cell edges are coloured green. A succeeding or anteceding image (cell edges coloured white) is superimposed. The image does not match the reference image until the green and the white lines coincide. (D) Images are rotated and translated to best match the reference. (E) On the image in the middle of the series, all the cells are filled with green (default colour of the system). Xylem vessels in the reference image to be reconstructed are selected and their lumens are manually filled with different colours. The vessel colour registrations are then propagated to the other aligned images. (F) The background colour, no longer necessary, is removed leaving the selections (vessels) for 3-D-reconstruction and visualization.