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A root system is represented as a graph object. A root portion is represented as an edge (e couple of vertices) in the graph and is associated to different types of properties e.g. diameter. Recording the whole architecture necessitates a recursive pathway to be followed throughout the root system, with information about each link and segment being recorded at each stage of the measurment. The connection between two segments of the same root are coded with the symbol <. The link between a mother and a daughter root is noted +. The branching order, o, is then defined as the number of branching to get to the initial root (at the stem base) which branching order is 1. In order to trace the pathway throughout the root system, the following rules have to be applied during the measurements of topology :

1. The measurement is initiated at the base of the tree trunk and followed the direction of root growth.

2. Two types of link are used to connect root segments : < when the segment belongs to the same branch ; + to initiate a daughter branch (Figure 1).

3. The pathway must describe the root of the highest branching order. When a root ends, the pathway is continued where it stops on the mother root.

see Godin et al 1999 for more information

The previous sectin has described how to describe the network of connection between root branches, but acquiring the root geometrical information is also crucial. Particularly, the question of how to obtain the spatial coordinates (x, y, z) at each new axis formation (<). Existing systems using motion tracking systems (Danjon et al. (2000)) have neen developped but can be difficult to apply during field work. The solution implemented by Archiroot is to obtain spatial coordinates from simple grometrical information. The parameters are gathered with a simple compass, inclinometer and calliper. The position of the current measured position is calculated (not directly measured) from the previous position: each new root is described by its length (l) its angle to horizontal (inclination), and its direction in the horizontal plane (azimuth). The position of the root tip can then be calculated from the previous root tip and is recorded for the next measurment. The (xn,yn,zn) position is express simply as a function of the antecedant position (xa,ya,za):

xn = xa + l · cos(inclinaison) · cos(azimuth)

yn = ya + l · cos(inclinaison) · sin(azimuth)

zn = za + l · sin(inclinaison)

The resulting data structure is a list of consecutive nodes, the type of connection they have with the antecedent node of the same branching order and the associated geometrical attributes. Beam elements FEM meshes can be derived from such architectural data, provided further formatting of data be carried out. These elementary topological and spatial information are then completed with additional properties and can be specific to the study that is being carried out: diameters in horizontal and vertical direction, type of root and other descriptions.

There are 5 properties that needs to be given at each measurments:

1. length of the root portion
2. Arimuth of the root axis
3. Inclination of the root with the horizontal plane
4. Diameter in the horizontal plane
5. Diameter in the vertical plane

Custom additional properties can given in the "settings" menu under the "optional parameters" sub menu. Additional parameters can be provided as a list of names, separated by comas. The software need to be resarted for changes to be made.

The data is writen in the table under the "Data" tab and can be accessed and modified at any time.

The resulting measured structure can them be visualized in 3D under the "Visualisation" tab. The visualisation uses currently the Cortona VRML player (http://www.parallelgraphics.com/products/cortona/) for navigating through the architecture, and provides two modes of interaction (Virtual reality and CAD type), and various navigation functions (Fit, goto, rotate etc...).

Short keys can be used to save time during the measurments

RETURN: switch from one field to the other

F1: initiate a new branch (+)

F2: add a new root portion (>)

F3: end the root (END)

Backspace: cancel previous measurment

F11: Refresh visualisation

F12: Screen capture

Ctrl-s: saving the project

Before you use the Archiroot software (or visualize the 3D models on this web site), you need to install a VRML viewer. There are several of them. On windows, the Cortona player is excellent and propose various functionalities.

Cortona player

cortona_install

On Linux, you may want to use Octaga player

Octaga vrml player player

Latest version

Old version