Mesh Labeler3 – User Manual

Author: Tai-Hsien Wu

This project is powered by SOVE Inc. and is mainly developed based on Visualization Toolkit (VTK) and, especially, vedo.

This program is originally developed to conveniently label/annotate dental mesh model. It can also work on any other type of mesh model.

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Current version: 3.3

• changed the underlying method for spline selection.
• fixed the bug that saving the selection as additional label.
• made the default of colormap to contain wisdom teeth.
• removed the wireframe of mesh when rendering

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1. Download installer from https://app.box.com/s/f2x3xmbykt5vb6cov94lf55920acvz0g (click "Download" on top-right without sign-in).

2. Execute Mesh_Labeler3_Setup.exe to install the program. You can find the shortcut of Mesh Labeler in Windows Start menu.

3. Once the program is launched, you will see the user interface, as shown below.

4. Use the bottom-right button Load to open a mesh file. Currently, the program supports VTP (with a cell array named Label) and STL, OBJ, and PLY files. There are four examples (Example_01.vtp, Example_02.stl, Example_03.obj, and Example_04.ply) that you can download via my github.

Note: For those files that do not contain the cell array "Label" (e.g., STL, OBJ, PLY), the program will initially generate a cell scalar array called "Label" and assign 0 (i.e., all background) to the array for each cell (i.e., for each triangle) after loading them. The screenshot after loading a VTP with the cell array "Label" will look like below.

5. From Version 2, users can define the number of labels, label color, and label description by themselves. To do it, please modify the colormap.csv in the installed folder of Mesh_Labeler (e.g., C:\Program Files\Mesh Labeler), which is a CSV file containing five columns: Label, R, G, B, Descriptions. Please keep the headers as the default file. Each row corresponds to a label.

6. The view on the scene can be changed by using various mouse actions, as follows:

• Rotating the mouse wheel upwards will zoom in, and downwards will zoom out.

• Holding the middle mouse button down and dragging will pan the scene or translate the object.

• Holding the left mouse button down and dragging will rotate the camera/actor in the direction moved.

7. There are two methods to annotate a mesh. Users can go for each method by selecting the corresponding tab. Different methods have different input(s) under their tabs.

   (1) Spline Method: Change label by selecting cells (triangles) The simplest way to select cells is to right-click on a cell. The selected cells are highlighted by grey color. Right-click on a selected cell can cancel its selection. An advanced way to select cells is to press "s" to enter "Spline model" (you can look at the status bar to check whether the Spline model is on or off). In Spline model, you can add points by left click on the mesh. Once the number of selected points > 2, you can decide to use these points to generate a spline by pressing "Enter". All cells within this spline will be highlighted. Press "c" if you would like to clean the current selection. Before you execute the change, please make sure the active label is what you plan to apply. The default active label is 0. You can change it through the spinBox under the Spline tab. Once you satisfy the selection, press "e" to execute the change which will assign the value of active label on those selected cells. Please follow the colormap to assign/fix the label of each cell for the mesh. Note that there are certain probabilities that Spline Method doesn't work well (e.g., the uncontinuous selected area), particularly for an aggregative selection . Based on my understanding, it's a potential problem in VTK and hard to fix by myself. However, this method is still useful for selecting a large area, followed by manaully fixed with the right-click selection.

   (2) One-Way Swap Method: Change all cells with a specific label one-shot In this way, we can entirely change cells from one label to another label. There are two spinBoxs (i.e., Original label and New label) under the One-Way Swap tab. Once they are all set, click Change! button; then, all cells with the original label will be changed to be the new label.

8. Once everything is done, you can save the result by using the Save button. The default extension file is VTP, which will save the result in the VTP format with the cell array Label. If the extension file is STL or OBJ, Mesh Labeler will save each label to an individual STL or OBJ file. For example, a 15-class mesh model will output 15 STL files.

9. Version 3 adds a new function for identifying landmarks on mesh data. To do that, please select "landmarking" tab on the top of the program.

• Landmarking Method: Annotate landmarks on the loaded mesh Note that a mesh must be loaded before doing any actions in landmarking mode. Users can load a list of landmarks from a fcsv-format file (fiducials file exported from 3D Slicer) by clicking Load FCSV or create a new list of landmarks by clicking Add (default position is the origin for a new landmark). All landmarks are shown as red spheres in the view, and the name and position of landmarks can be found in the table under this tab. User can select a landmark by clicking the corresponding column of landmark in table. The selected landmark will be represented by a blue sphere, as shown below. A selected landmark can be renamed by pressing Rename button. A new window will pop up to ask the new name for the landmark. A selected landmark can also be relocated by pressing Relocate button. After that, please left-click on the mesh for the new location of the landmark. To unselect a landmark, please right-click mouse. The list of landmarks can be exported as fcsv-format by clicking Save FCSV. For the format of FCSV file, please refer to the example (Example_01_UR1.fcsv) in the repository or portable folder.

Hotkey Table

VTK hotkeys	Function
Keypress j / Keypress t	toggle between joystick (position sensitive) and trackball (motion sensitive) styles. In joystick style, motion occurs continuously as long as a mouse button is pressed. In trackball style, motion occurs when the mouse button is pressed and the mouse pointer moves.
Keypress a	toggle actor modes. In actor mode, mouse events affect the actor that is under the mouse pointer.
Keypress 1	unknown. (Don't press)
Keypress 2	unknown. (Don't press)
Keypress 3	toggle the render window into and out of stereo mode.
Keypress f	fly to the picked point
Keypress p	perform a pick operation. (Don't press)
Keypress w	modify the representation of all actors so that they are wireframe.
Mesh Labeler Spline Mode	Function
Keypress s	toggle splien mode & modify the representation of all actors so that they are surfaces.
Keypress e	execute the change in spline mode
Keypress Enter	generate a spline based on the given points
Keypress c	clean the current selection including existing spline and points

Reference

If you think Mesh Labeler is useful for your research project, please cite:

• Wu TH. et al. (2021) Machine (Deep) Learning for Orthodontic CAD/CAM Technologies. In: Ko CC., Shen D., Wang L. (eds) Machine Learning in Dentistry. Springer, Cham. https://doi.org/10.1007/978-3-030-71881-7_10

Problems?

If you have any questions about using Mesh Labeler, please feel free to open an issue or email me (tai-hsien.wu@soveortho.com)..