Spines (branched structure analysis)

Purpose

Spines analysis can be generated by going to Analyze > Structure > Branched Structure Analysis > Spines.

In the Spine Analysis dialog, check the boxes to indicate which reports you want to generate.

You can choose to analyze specific types of spines with the following reports:
- Axon spines
- Dendrite spines
- Apical dendrite spines
The Spine details report includes comprehensive data about spines (see below).
- More metrics are available for spines that were detected or placed in the Neurolucida 360 3D environment, compared to spines that were placed in the 2D window using Neurolucida or Neurolucida 360.
The Terminal spine density report lists the density and quantity of spines that are a certain distance from the tree termini. Enter the desired Distance from the terminus.

If you used regular markers for the spines, you need to use the Individual Marker or Marker Totals analyses instead.

Analysis results

Axon spines, Dendrite spines, or Apical dendrite spines: Reports the quantity, density, and average diameter of each spine class by centrifugal branch order.

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Type (spine class)

Spine class assigned in Neurolucida or Neurolucida 360.

Density

[Quantity of spines on the segment]/[Length of the segment]

Average diameter

Average diameter of the spines on the segment.

If you selected additional branch orders for your analyses, additional data is displayed below the rows of data relative to the centrifugal branch orders. To select additional branch orders, go to Preferences in the File menu and select Ordering.

Spine details - automatic: Metrics describing spines that were detected or placed in the Neurolucida 360 3D environment.

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Assigned type	Auto: Refers to the type automatically assigned when you use Classify all. Manual: Refers to the type you assigned via the Edit Spines panel.
Anchor radius	Refers to the radius of the dendrite at the point where the spine attaches. This radius is calculated with the assumption that the dendrite is modeled as having an elliptical cross section. For a spine with a length L and an anchor radius AR, the maximum distance to the center line is: L + AR.
Attached?	Yes: The spine head appears connected to the dendrite. No: The spine head is connected by a neck that is too dim to be identified by the image segmentation used to extract the spine shape. As a result, the spine head appears disconnected from the dendrite. To detect such a spine, you may increase the detector sensitivity and manually re-detect the spine to allow the neck to be modeled.
Backbone length	Backbone length to center minus distance between dendritic surface and insertion point on the center line.
Backbone length to center	Tortuous path from furthest voxel along the path of the backbone to the insertion point on the center line.
Base coordinate	3D coordinate of the point where the spine is attached to the dendrite.
Branch order	Uses the centrifugal branch order. See About branch orders.
Contact area	Apparent (that is, not corrected for residual axial smear) cross-sectional area of the base of the spine (area of the dendritic model covered by the spine). N/A: Spine is too small to determine contact area. Note that when there is no correction for residual axial smear, objects typically appear elongated along the optical axis because the microscope's axial resolution is much lower than its lateral resolution.
Distance	Sum of the lengths of the branch segments from the base of the spine to the beginning of the tree the spine is attached to.
exM neck diameter	The exM neck diameter is the average of the Rayburst diameters from the center of all layers below the spine head. The top of the neck is one radius from the center of the head.
Head diameter	Based on Rayburst diameters calculated in the XY plane after the automatic detection process.
Head backbone length	Head backbone length = [1] +[2] + [3] - [anchor radius]
Head backbone length to center	Head backbone length to center = [1] +[2] + [3]
Head position	3D coordinates of the center of the head of the spine measured in microns from the reference point.
Neck backbone length	Neck backbone length = [1] +[2] + [3] - [head radius] -[anchor radius]
Neck backbone length to center	Neck backbone to center = [1] +[2] + [3] - [head radius]
Neck diameter	Based on Rayburst diameters calculated in the XY plane after the automatic detection process.
Plane angle	Refers to the radius of the spine attachment vector with respect to the optical plane. Zero means that the spine axis is parallel to the optical plane. 90 (+/-) means that the axis is perpendicular to the optical plane. This is useful for discriminating between spines that are clearly visible on the side of the dendrite and spines that are detected over or under the dendritic segment when viewed in the direction of the optical axis.
Segment ID	Segment IDs indicate the tree and the segment of the tree to which the spine is attached. Data are reported in the format Tree ID - Segment ID. For example, segment 2 on dendrite 3 would have a segment ID of Dendrite 3 - 2.
Spine type	Refers to the classification used in Neurolucida 360 to mark the spines.
Surface area	Apparent (that is, not corrected for residual axial smear) exterior surface area of the spine in µ². N/A: Spine is too small to determine surface area or spine was not detected in 3D. Note that when there is no correction for residual axial smear, objects typically appear elongated along the optical axis because the microscope's axial resolution is much lower than its lateral resolution.
Tree	Each tree selected for the analysis is assigned a unique number starting at 1.
Volume	Measured by the number of voxels that make up the spine object multiplied by the volume of a single voxel. The volume of a single voxel is: X resolution * Y resolution * Z resolution.
Voxel count	Total number of voxels that constitute the spine. Based on voxel processing and used to evaluate the spine size. It is determined by the image scaling

Spine details - manual: Metrics describing spines that were placed in the 2D window using Neurolucida or Neurolucida 360.

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Tree	Each tree selected for the analysis is assigned a unique number starting at 1.
Branch order	Uses the centrifugal branch order. See About branch orders.
Spine class	Refers to the class(es) used in Neurolucida to mark the spines.
Length to center	Shortest path distance from the center of the spine head to the center of the dendrite.
Length	Shortest path distance from the center of the spine head to the surface of the dendrite. To determine the radius of the dendrite, subtract Length to Center and Length values.
Diameter	Diameter of the spine head.
Distance	Sum of the lengths of the branch segments from the base of the spine to the beginning of the tree the spine is attached to.
Surface area	Modeled as a frustum for manually-placed spines; based on the mesh for detected spines.
Volume	Modeled as a frustum for manually-placed spines; based on the mesh for detected spines.
Base coordinate	3D coordinates of the point where the spine is attached to the segment.

Terminal spine density: Metrics describing spines that are the indicated distance from the terminus of the tree.

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Tree	Each tree selected for the analysis is assigned a unique number starting at 1.
Terminal Spine Density (1/µm)	[Quantity of spines on the segment]/[Length of the segment]
Spine Qty	The number of spines in the terminal segment.
Length Window (µm)	The distance from tree terminus evaluated (users specify this value in the Spine Analysis window, where you select the reports you want to run).