Mesh Contour Editor

The Mesh Contour Editor is a tool for manually creating and editing 3D mesh surfaces, including dendrite meshes. 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 (1) of eight (8) tools found in the 3D Tools tab in the Analysis Panel. Go to 3D View to show the 3D Tools tab. Click on the 3D Tools tab and then on the Mesh Contour Editor icon (outlined with a blue box near the upper-left corner of the figure below) to launch the tool. The Mesh Contour Editor interface, with all advanced sections expanded, is shown in the figure below. The interface has four (4) main sections, which 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) or dendrite(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.

Open

Mesh Contour Editor GUI with a colored box around each section

On this page:

Input Options section

The Input Options, pertaining to whether or not a mesh/dendrite 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 or dendrite for editing. The channel to use for prediction may be selected from the Input Channel menu.

Painting Tools and Options section

The Painting Tools and Options section is outlined in purple in the figure above. The Enable Painting button allows/restricts painting operations. Options for manual painting and erasing are described in the table below.

Name	Icon	Description

Name	Icon	Description
Paint Brush	Open	Toggles the Paint Brush tool, with which you can click and drag the mouse on an image slice to paint; use the Size slider to change the brush size
Eraser		Toggles the Eraser tool, with which you can click and drag the mouse to remove painting data; use the Size slider to change the eraser size
Floodfill Brush		Toggles the Floodfill Brush tool, with which you can click in regions that are enclosed by painted borders to fill them
Remove Data from Slice		Removes all painting data for the mesh surface or dendrite that is being created or edited from the current image slice
Remove All Drawn Data		Removes all painting data for the mesh surface or dendrite that is being created or edited from all image slices

Advanced painting options

To access the advanced painting options, click on the caret next to Advanced in the Painting Tools and Options section. By default, Auto Floodfill, Auto Step, Auto Draw, and Clipping Caps 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 section

The Slice-Traversal Controls section is outlined in 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 figure above).

Advanced slice-traversal options

To access the advanced slice-traversal options, click on the caret 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 section

The buttons and menus for choosing when/where to output the created/edited mesh surface(s) or dendrite(s) as well as how to post-process the created/edited mesh surface(s) or dendrite(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 objects. The Output To menus allow you to select whether to output a standard Mesh Feature or a Dendrite mesh as well as to specify the output object group; choose the <Create Object Group> option to output the mesh(es) to their own, new object group. The Complete Mesh button finishes generating the mesh surface(s) or dendrite(s) and adds it/them to the specified object group. 

Hotkeys

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

Ortho-plane hotkeys

Keyboard shortcuts for adjusting the position of the ortho plane are often useful when using the Mesh Contour Editor and 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/dendrite 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. When a dendrite mesh is edited, the centerline/trace is not modified.

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 ortho-plane hotkeys can be used to position the ortho plane.

You may also configure the ortho plane using the options and controls in the Clipping Planes & Ortho Planes panel.

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 (or press 1, 2, or 3 on your keyboard respectively) to select the corresponding painting tool. When using the Paint Brush, the cursor will appear as a circle that is the same color as the Clipping Caps (blue by default). 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 Shift while scrolling with the mouse wheel to change the brush size, which applies to both the Paint Brush and Eraser tools. With the Floodfill Brush, click inside the border of an enclosed region to fill the region. You may hold down Ctrl 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 Ctrl + J 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 or press Esc. Remove what is painted on all slices by clicking the Remove All Drawn Data icon or pressing Delete.

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 Shift + S and Shift + W keys on your keyboard (for Step Down and Step Up respectively), or the ortho-plane position controls in the Clipping Planes & Ortho Planes panel, among other ortho-plane controls.

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 box 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 group

In the Output Options section, use the first menu to specify whether to create a Mesh Feature or a Dendrite. To select the object group to add the created/edited mesh surface to, expand the second menu and choose the desired object group from the options provided. Only object groups of the appropriate type will appear as options in the menu—dendrites must be output to neuron object groups. Select <Create Object Group> to add the edited/created mesh or dendrite to a new object group.

Complete mesh surfaces

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

When a dendrite mesh is first created, a centerline/trace for the dendrite is generated during mesh creation; you may edit this trace using the Neuron Composer. When a dendrite mesh is edited, the centerline/trace is not changed when the mesh edit is completed.

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