The Mesh Contour Editor is a tool for manually creating and editing 3D mesh surfaces. While there are options to manually paint, fill, and erase, there are also predictive modes for speeding up the workflow. You may use the Mesh Contour Editor to edit objects that were generated by recipes, to create/edit mesh surfaces in order to obtain measurements for 3D objects, or to create/edit mesh surfaces to use as regions of interest (ROIs), among other purposes. 

Interface

The Mesh Contour Editor is one of eight tools found in the 3D Tools tab in the Analysis Panel. Go to 3D View or 3D Plane View to show the 3D Tools tab. Click on the 3D Tools tab and then on the Mesh Contour Editor icon to launch the tool. The Mesh Contour Editor interface, with all advanced sections expanded, is shown in the figure below. The interface has four main sections that are divided by horizontal white lines:

• The Input Options let you specify whether you will be creating or editing as well as which image channel will be used. 
• The Painting Tools and Options section provides different painting options, including predictive modes.
• The Slice-Traversal Controls allow you to step through image slices as well as copy and paste painted regions between slices.
• The Output Options allow you to specify where the created/edited mesh surface(s) will be output to and which post-processing steps will be applied.

When the Mesh Contour Editor is launched, an ortho plane is shown and any existing clipping planes are hidden. The tool is designed for painting slice by slice on 3D images.

Input Options

The Input Options, pertaining to whether or not a mesh will be created from scratch and to which image channel is used for predictive painting, are outlined in red in the figure above. The Start New button removes any existing painted regions, allowing you to start with a clean slate, and enables painting. The Edit Existing button prepares a selected mesh surface for editing. The channel to use for prediction may be selected from the Input Channel menu.

Painting Tools and Options

The Painting Tools and Options section is outlined in purple in the "Mesh Contour Editor GUI with a colored box around each section" figure above. The Enable Painting button allows/restricts painting operations. Options for manual painting and erasing are described in the following table:

Advanced painting options

To access the advanced painting options, click on the Expand icon next to Advanced in the Painting Tools and Options section. By default, Auto Floodfill, Auto Step, and Auto Draw are on, while EM AI Prediction, Replace Existing, Hide Surface, and Expert Mode are off. Descriptions of the advanced painting options are in the table below:

Slice-Traversal Controls

The Slice-Traversal Controls section is outlined in lime green in the "Mesh Contour Editor GUI with a colored box around each section" figure and includes buttons that control the ortho-plane/slice position within the image volume. The Step to Bottom button  and Step to Top button  move the ortho plane to the bottom and top faces (relative to the image origin) of the image respectively. The Step Down button  and Step Up button  move the ortho plane to the next slice in the downward and upward directions respectively.

While Auto Step mode is used, the stepping direction is indicated by a gray box around the Step Down button or Step Up button (see below).

 Advanced slice-traversal options

To access the advanced slice-traversal options, click on the Expand icon next to Advanced in the Slice-Traversal Controls section. The Copy Slice button copies the painting data that is on the current slice, and the Paste Slice button pastes previously copied painting data onto the current image slice.

Output Options

The buttons and menus for choosing when/where to output the created/edited mesh surface(s) as well as how to post-process the created/edited mesh surface(s) are outlined in blue in the "Mesh Contour Editor GUI with a colored box around each section" figure. The Smooth icon  may be used to toggle smoothing of the created mesh surface(s). The Generate Multiple Surfaces icon  may be used to toggle whether or not painted surfaces that do not touch will be created as multiple mesh surfaces. The Output To menu allows you to select the object set that the newly created mesh surface(s) will be output to, and the Complete Mesh button finishes generating the mesh surface(s) and adds it/them to the specified object set.

Hot keys

Keyboard shortcuts for the Mesh Contour Editor are described in the table below:

Using the Mesh Contour Editor

To launch the Mesh Contour Editor, click on the 3D Tools tab in the Analysis Panel in Aivia and then on the Mesh Contour Editor icon in the 3D Tools toolbar. This will open the Mesh Contour Editor interface, show an ortho plane in the Image Viewer, and hide any existing clipping planes 

Start new mesh surfaces

If nothing has yet been painted using the Mesh Contour Editor, toggle on Enable Painting to start creating a new mesh surface. If there are existing painted regions that have not been completed and output to an object set, click the Start New button to discard the existing painted regions and start fresh.

Edit a mesh surface

To edit an existing mesh, select the mesh in the Image Viewer and then click on the Edit Existing button. A pop-up window will show the progress Aivia has made in preparing the mesh for editing. Once the existing mesh is ready for editing, you may paint, erase, etc. as you would when creating a new mesh surface.

Configure the ortho plane

You may have to move the ortho plane so that it intersects the region where you would like to create a mesh surface, and you may also wish to position the ortho plane at the edge of the region of interest so that you can step through image slices in one direction as you paint the mesh surface. The Step buttons in the Slice-Traversal Controls section as well as the S and W keys on your keyboard (for Step Down and Step Up respectively) can be used to position the ortho plane.

The Adjust Plane Position bar and Position textbox for the ortho plane, found in the Clipping Planes & Ortho Planes panel, can also be used to change the ortho plane position. (Note that you may rotate the ortho plane using the Plane Orientation control  in the Clipping Planes & Ortho Planes panel or use the control widget for the ortho plane.) You can click on the Toggle Volume Clipping icon  and Toggle Mesh Clipping icon  for the ortho plane to change how much of the image and its shown mesh surfaces are displayed; it is easiest, in general, to create/edit mesh surfaces while both volume clipping and mesh clipping are toggled on.

Paint, erase, and floodfill

The Paint Brush, Eraser, and Floodfill Brush tools are only enabled when Enable Painting is toggled on in the Painting Tools and Options section. Click on the Paint Brush icon , Eraser icon , or Floodfill Brush icon  to select the corresponding painting tool. (You may also press E on your keyboard to switch between the Paint Brush and Eraser or press F to toggle the Floodfill Brush.) When using the Paint Brush, the cursor will appear as a blue square. Click and drag the cursor across the image to paint. The Eraser is also used by clicking and dragging the mouse, but the cursor is red when the Eraser is toggled on. Use the Change Brush Size slider (or hold down Ctrl and Shift while scrolling with the mouse wheel) to change the brush size, which applies to both the Paint Brush and Eraser tools. Click inside the border of an enclosed region to fill it with the Floodfill Brush. You may hold down Shift on your keyboard to temporarily disable a painting tool while you adjust the camera angle, move the image in the Image Viewer, etc.

Click on Hide Surface (or press H on your keyboard) to hide/show the mesh surface that is being created/edited. If you would like to remove everything that is painted on the current slice, click the Remove Data from Slice icon . Remove what is painted on all slices by clicking the Remove All Drawn Data icon .

To continue painting on other image slices, you may manually advance to another slice using the Step buttons in the Slice-Traversal Controls section, the S and W keys on your keyboard (for Step Down and Step Up respectively), the ortho plane position controls in the Clipping Planes & Ortho Planes panel, or the ortho plane's control widget.

Copy and paste painted regions

To copy the painting data from one slice to another, first navigate to the slice with the painting data to be copied, and then click on Copy Slice in the Advanced section of the Slice-Traversal Controls section. Navigate to the slice where you would like to paste the painting data, and click on Paste Slice. The position and rotation angle of copied/pasted painting data is relative to the angle of the ortho plane as well as the position of its control widget.

Use predictive modes

The predictive mode options are in the Advanced section of the Painting Tools and Options section. By default, Auto Floodfill, Auto Step, and Auto Draw are on; with these options, if you paint around the edge of the region that you would like to create a mesh surface for, the two ends of the brushstroke are automatically connected, the region is automatically filled, the ortho plane is automatically advanced to the next slice, and a suggested painted region is shown on the next slice. Any combination of the Auto Floodfill, Auto Step, and Auto Draw modes is permissible, and you may toggle all of them off to disable any automatic predictions.

Auto Floodfill

With Auto Floodfill on, the endpoints of brushstrokes are automatically connected and enclosed regions are automatically filled. 

Auto Step

With Auto Step on, the Mesh Contour Editor automatically advances the ortho plane to the next slice of the image once there is a successful floodfill on the current slice. The direction in which Auto Step moves between slices is indicated by a gray outline around either the Step Up icon (if Auto Step advances in the upward direction) or Step Down icon (if Auto Step advances in the downward direction) in the Slice-Traversal Controls section. You may click on the Step Up icon  or Step Down icon  to change the Auto Step direction.

Auto Draw

With Auto Draw on, predictions that are based on painted data on the previous slice as well as data from the image channel specified as input are displayed. These predictions can be edited, if needed. Change the input image channel by expanding the Input Channel menu and choosing the desired image channel. Also, with Auto Draw on, you may toggle the Replace Existing option; when Replace Existing is toggled on, Auto Draw replaces existing painting data.

Toggle on the EM AI Prediction option, which is in beta, to use a prediction method that is designed for EM images.

Choose post-processing options

To smooth created/edited meshes upon completion and addition to an object set, toggle on Smooth in the Output Options section. Smoothing lengthens the final process of completing mesh surfaces. The other available post-processing option is to generate multiple surfaces when there are painted regions that do not touch; to turn on/off this option, click on the Generate Multiple Surfaces icon . The Generate Multiple Surfaces option does not affect the shapes of the mesh surfaces but rather whether they can be selected, measured, and used individually. Having Generate Multiple Surfaces on also prolongs the final process of completing mesh surfaces.

Choose an output set

To select the object set to add the created/edited mesh surface to, expand the Output To menu and choose the desired object set from the options provided. Only object sets of the appropriate type (neither neuron object sets nor outline sets) will appear as options in the menu. Select <Create Object Group> to add the edited/created mesh to a new object group.

Complete mesh surfaces

Click on the Complete Mesh button (or press C on your keyboard) to convert the painting data into mesh-surface data, perform any smoothing or generation of multiple surfaces as necessary, and add the resulting mesh surface(s) to the specified output set. A pop-up window will show a progress bar for the mesh-completion process.

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