This Graphical User Interface is intended for visualizing results from the following paper:

TopoRoot: A method for computing hierarchy and fine-grained traits of maize roots from X-ray CT images

The paper can be found in here: https://rdcu.be/cC9Ng

The tool can be directly used by opening the exe file in the release package. In case for any need for customization, the source code is also included in this repository. The steps are the following:

• All dependencies except QT is pre-shipped in the folder third-party. Thus, please download qt5.11.0, which can be found here: https://download.qt.io/new_archive/qt/5.11/5.11.0/
• After installation, to run the exe file, Go to This PC -> system settings -> advanced system settings -> advanced -> environment variables, and add bin file to the path variable. E.g: D:\Qt\Qt5.11.0\5.11.0\msvc2017_64\bin.
• To configure and build the code, define the environment variable QTDIR that points to the root dir of your QT. This way VS can pick up the QT headers and libs.
• After these steps are completed, the VS .sln file should build, and the exe file can be run smoothly.
• Again, you do not need to build to use the tool. The release package has a ready-to-go file which is ready to run.

1. Navigate to the RootGUI/release package/ directory, and double click on the root_mesh_viewer.exe application. This will open the user interface. Click on select .ply and select .txt to load the outputs of TopoRoot.

2. Switch to the Mesh tab, and click Select .off . Select the .off file with the same name as the .ply file (the name of your sample).

After clicking open, the surrounding shape (the result of topological simplification) will be loaded in.

Mouse controls:

• Rotate: drag left mouse button
• Translate: drag right mouse button
• Zoom: Click down on middle scroll of the mouse, and drag up and down.

3. To view the radius level of the skeleton, change the "Skeleton Color" option from Normal Coloring(Black) to Color by Radius. Cooler colors (dark blue) represent lower radius levels (thinner roots), while warmer colors (green, yellow, red, etc.) represent higher radius levels (thicker roots which are closer to the stem).

4. To view the hierarchy level, change the "Skeleton Color" option from Normal Coloring(Black) to Color by Hierarchy. Cooler colors (dark blue) represent lower hierarchy levels (starting from the stem), while warmer colors (green, yellow, red, etc.) represent higher hierarchy levels (higher-order lateral roots).

5. To filter the view of the hierarchy, toggle the checkboxes in the left panel of the Skeleton tab. For example to only view the stem path uncheck the other boxes.

6. After loading in the annotation file, the GUI can visualize the locations of the soil pland and whorls. These can be toggled at the skeleton tab. The

6.1 Soil Plane Visualization

Roots above and below the plane: (red represents information above the soil plane, and blue represents info below the plane.)

6.2 Whorl Visualization (red represents information above the soil plane, and blue represents info below the plane.)

Nodal roots colored by their originated whorl: (Each whorl colors its nodal roots by a unique color)

7. Editing: the GUI provides a way to edit the incorrect root traits generated by the algorithm. All the editing happens in the Edit tab.

7.1 Hierarchy Editing:

The hierarchy error here labels a nodal root pointing at an incorrect direction. The green represents the nodal roots, and the red represents the lateral roots. By identifying the next junctions on two paths that you wish to swap, the GUI can help to edit the growing direction of this nodal root.

The editing is done by identifing the juntion where its children's hierarchy levels are incorrectly assigned and enter its index. Then, enter the junction index of its correct child and press "Swap".

7.2 Whorl Editing:

The whorl error could be an extra or missing whorl labeled. The red box from the GUI represents the location of the whorl and its associated junctions. Note that those junctions are only from the stem path. The GUI provides addition and deletion of whorls.

The deletion can be down by enter the whorl index labeled on top of each whorl. Whorls above are labelled using lower-case alphabets, and whorls below are labelled using upper-case alphabets. The addition of whorls is based on the starting and ending junction on the stem path. After identifying their index, enter in the box and press "Add Whorl".

7.3 Soil Plane Editing:

The soil plane can be edited by toggling the horizontal plane upwards or downwards at the slide bar on the Edit tab. By shifting the soil plane, the labels of nodal roots and whorls will change correspondingly.

Contact:

• Dan Zeng ([email protected])
• Yiwen Ju ([email protected])
• Tina Wang ([email protected])