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Advanced Selection

The Edit menu provides a number of commands for the selection of dendrites and spines. These methods can be used to create selections for further editing or as a way to visually identify objects of a specific type. Below is a summary and description of the available commands. Note that these commands only affect the current selection state of the model objects, but not the actual structure of the model.

Select All Connected

Menu item Edit >> Select All Connected. Given one or more selected dendritic vertices, this command select all other vertices in the same connected component. A connected component is a set of vertices where a path (series of edges) exists from any vertex to every other vertex.

Example:

1) A vertex has been selected. Selecting more than one is also valid.

Advanced Selection Example 1 Image 1

2) The Select All Connected feature has been run. Note that all vertices become selected in this model since it has only one connected component.

Advanced Selection Example 1 Image 2

Select Sub-Trees

Menu item Edit >> Select Sub-Trees. Similar to Select All Connected, except that the selection always halts at any vertices labeled as soma.

Example:

1) A vertex has been selected. Selecting more than one is also valid.

Advanced Selection Example 2 Image 1

2) The Select Sub-Trees feature has been run. In this case only the apical tree (shown in green) becomes selected. The soma (shown in yellow) limits the selection from passing through it.

Advanced Selection Example 2 Image 2

Select by Type / Function

Menu item Edit >> Select by Type / Function. Selects dendritic vertices or spines according to their type or function. The image below shows the sub-menu with all available commands. The first group offers methods to select dendritic vertices according to their topological fuction while the second group can select them by their function. The third group allow for the selection of dendritic spines according to their type.

Select by Type / Function Popup Window

Example:

1) No vertices are selected. Current selections might be lost when the Select by Type / Function feature is run.

Advanced Selection Example 3 Image 1

2) The Select by Type / Function has been run for basal dendrites (shown in brown). All basal dendrites therefore become selected.

Advanced Selection Example 3 Image 2

IMPORTANT: This feature depends on accurate labeling of the tree structure.

Create Neurite Selection Paths

Menu item Edit >> Create Neurite Selection Paths. In many editing operations it is necesary to select all dendritic vertices connecting two or more specified vertices. After selecting the ending vertices of a desired selection, this command can be run to create a selection that also includes all connecting vertices.

Example:

1) A few vertices are selected. However, paths can be created for any number of selected vertices.

Advanced Selection Example 4 Image 1

2) The Create Neurite Selection Paths feature has been run. Note how all vertices in between the original selected vertices also become selected.

Advanced Selection Example 4 Image 2

Select Spine Stems

Menu item Edit >> Select Spine Stems. This command is used to select spines, from a set of already detected spines, that can potentially be considered the stem of another spine. The algorithm used locates the stems by evaluating the shape of the spine as well as its proximity to the attachment vector on nearby spines.

Example:

1) An example of a spine with a clearly defined stem that has been falsely detected as a spine.

Advanced Selection Example 5 Image 1

2) The Select Spine Stems feature has been run. The stem becomes selected. All such stems could now be deleted in a single step. See also spine deletion.

Advanced Selection Example 5 Image 2

Select Spines on Selected Neurites

Menu item Edit >> Select Spines on Selected Neurites. As the name implies, this command selects spines that connects to a specified set of dendritic segments. The segments are specified by first selecting their vertices with any of the vertex selection methods.

Example:

1) A number of vertices have been selected using the neurite tool Neurite Tool. Spine axes are shown in green to help visualize the spines that are attached to these selected vertices.

Advanced Selection Example 6 Image 1

2) The Select Spines on Selected Neurites feature has been run. The spines that are attached to the selected vertices also become selected.

Advanced Selection Example 6 Image 2

Select Spines with Invalid Surface Area

Menu item Edit >> Select Spines with Invalid S.A.. This command select any spines having an Rayburst attachmment area that is greater than its Rayburst Surface area.

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Send questions or comments to: alfredo.rodriguez@mssm.edu