Using RootReader3D

The Main GUI

When RootReader3D opens, you will be greeted by the main GUI, which consists of 9 menus and 24 buttons (see Fig. 1).

Figure 1. The main GUI for RootReader3D as displayed on Mac OS X.

Loading Images

To begin manual mode, first load your image sequence by clicking on 'Load Image Sequence' from the File menu (see Fig. 2).

Figure 2. Loading your image sequence from the File menu.

You will be prompted to navigate to a directory on your computer where your image sequence (i.e, pre-processed binary TIFF files) is located. You can view the progress of this in the action log, which can be opened by checking the box next to 'Show action history log' in the View menu. Once your images have been loaded into RootReader3D, the sequence image stack window will appear with your image sequence (see Fig. 3). Place your mouse pointer over the sequence image stack and use the scroll wheel to rotate your root system.

Figure 3. Original image sequence read into RootReader3D. The action history log shows the operations taken during image loading. The sequence image stack shows a preview of the images.

Use the keyboard command Alt+= to zoom into the sequence image stack, Alt+- to zoom out and Alt+r to reset the zoom. When zoomed, press and hold the right-click (or control+click in Mac OS X) and drag to recenter the image within the sequence image stack window.

Root System Reconstruction

The root system reconstruction utilizes a calibrated perspective reconstruction algorithm developed by Clark et al. (2011). The calibrated perspective reconstruction algorithm requires the following parameters:

Parameter Prida Value Units Description
Degrees per rotation -- deg 360º divided by the number of images in your sequence
Translation Yt pixels Horizontal shift of the axis of rotation
Roll θ deg Roll of axis of rotation (counter/clockwise)
Pitch ψ deg Pitch of axis of rotation (up/down)
Distance to AOR zt m Distance between the camera and axis of rotation
Pixel size Ir mm/pixel Image resolution

The calibration parameters must be calculated before reconstruction can be performed. The calibration utilizes the axis of rotation (AOR) technique (Clark et al., 2011), whereby the roll, pitch and translation are calculated from a sequence of 2D images taken of an indexed calibration rod. The calibration rod images are taken in addition to the plant root system. The Prida software (see https://bitbucket.org/usda-ars/prida_one/) includes the processing steps for calculating these parameters (see Fig. 4).

Figure 4. The axis-of-rotation calibration technique for an indexed calibration rod executed by the Prida software.

Enter the above calibration values into RootReader3D's Reconstruction Parameters window by clicking on 'Set reconstruction parameters' in the Settings menu (see Fig. 5).

Figure 5. The Reconstruction Parameters input window accessed through the Settings menu.

Note that the 'Degrees per Rotation' field is automatically populated based on the number of images that were imported (i.e., 360º divided by the number of images).

Once the reconstruction parameters are entered, click on 'Reconstruct Root System' in the Filters menu (see Fig. 6).

Figure 6. Beginning root system reconstruction from the Filters menu.

You can view the reconstruction progress in the Processing Log. When reconstruction finishes, the Reconstruction Volume Stack window appears. Use your mouse wheel to scroll through the horizontal slices. Open the Information Window to see the current slice information (see Fig. 7).

Figure 7.