Paths

BioVis3D includes a tool designed to easily draw paths to reconstruct tree-like structures.

This is done using the Path Tool. A path in BioVis3D is a set of nodes that can be connected with each other or not. Once rendered in 3D, the path will appear as a tubular structure that resembles a tree that traverses all the connected nodes.

These nodes can be distributed within the same slice or in different slices, thus allowing the path to span multiple slices along the Z axis.

Each node defines its diameter which in turn defines the section of the path at that given point. This property is specified in the Properties panel for each selected node in the 2D view.

The color of the path is determined by the color of the object it belongs to.

Any given object can contain only one path.

 

Drawing Paths

To draw a new path, open one of the slices, go to the Object Explorer and right-click on the object will contain the new path and choose New Path.

Select the Contour tool and click where the nodes should be located.

Once clicked on the slice a new Node will appear. You can then adjust the Diameter of this node in the Properties section. The diameter of the node determines the thickness of the path at that point. Each Node can have a different diameter.

The color of the nodes is defined to match the color of the object it belongs to. The color of the connections in the 2D view is set to the opposite of the node’s making it easy to see. Once rendered in 3D, the color of the path will be the color of the nodes.

Paths are drawn in the 2D view automatically connecting the nodes within the same slice in the order they are clicked.

The following image shows a slice with a portion of a path comprised of 4 nodes. The bold red node labeled “Current Node” corresponds to the last Node clicked, also known as “Selected Node”. If a new node is created it will be automatically connected to this one and the new one will become the Selected Node.

It is also possible to create bifurcations.

To do so, just select the node where the bifurcation should begin and then create a new Node.

For instance we can click on the second Node to make it active as shown in the image.

Then when a new Node is created it will be automatically connected to that previously selected Node.

Nodes can also be added without any connection to the rest of the path. This provides an easy way to place the Nodes throughout the slice and then connect them at a later stage.

These Isolated Nodes can be added by clicking on the slice while holding the SHIFT key.

It is also possible to add nodes using a context menu accessible through right-click as shown in the image.

Deleting a Node

Any Node can be easily deleted. To do so, just select it and hit the DELETE Key.

Optionally, you can right-click on the node and choose the Delete option in the context menu.

Deleting Connections

Nodes can be disconnected at any time to make minor corrections to the paths.

Disconnecting a Node is a two step process.

Suppose you want to remove the connection shown in the image.

First you would need to select one of the Nodes that define the connection to make it the Selected Node.

Then you have to right-click on the other end and choose to Disconnect from Selected.

In our example you can select Node 1 by simply clicking on it.

Then you can right-click on Node 2 and choose Disconnect from Selected from the popup menu.

The result would be as follows.

Connecting Nodes

Nodes are normally connected to the previous ones as they are created. However it is also possible to manually add connections to existing nodes.

Adding new connections is also a two-step process, just like deleting a connection.

First you need to select one of the Nodes that you want to connect.

Then you need to right-click on the other Node to connect and select the Connect Node with Selected option.

Extending the path to the next slice

Normally, a path spans multiple slices.

To continue drawing the path in the following slice, right-click on the Node that will be the connection point to the next slice and select the “Connect Node at Next Slice” option.

This will open the next slice where you can click the location of the next Node that will be automatically connected to the Node in the previous slice.

By default, during the edition of a path, both the nodes in the current slice and the slice beneath it are shown.

Nodes in the current slice are shown with a red border, while nodes in the slice underneath are shown with a blue border.

Connections between nodes of different slices are shown as dotted lines.

To switch to the next slice you can alternatively just right-click anywhere in the current slice and choose the Open Next Slice option.

The Open Next Slice and Open Previous Slice options provide an easy way to move back and forward along the stack of images thus helping identify where the Nodes should be located.

Slices may take a while to open the first time, but as they remain open in the background, they show up faster the next time that you access them.

Paths in 3D

The 3D model of a path is built from tubular structures along the connecting lines between the Nodes.

The thickness of the tubes is determined by the diameter of the Nodes in each connection.

Just like any other 3D structure paths can be shown and hidden using the actions in the Object explorer called Show/Hide Object and Show/Hide Path.

           

Refer to The 3D model view for further details.