Branched Structure Analysis: Spines

Each tree selected for the analysis is assigned a unique number starting at 1.

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.

Shortest distance from the center of the head layer diameter to the surface of the dendrite.

Uses the centrifugal branch order.

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.

Shortest distance from the center of the head layer diameter to the center of the dendrite.

Refers to the classification used in Neurolucida 360 to mark the spines.

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.

Based on Rayburst diameters calculated in the XY plane after the automatic detection process.

Auto: Refers to the type automatically assigned when you use Classify All.

Manual: Refers to the type you assigned via the Edit Spines panel.

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.

3D coordinates of the center of the head of the spine measured in microns from the reference point.

Shortest distance from the furthest identified voxel to the surface of the dendrite.

To determine the radius of the dendrite, subtract Total extent from Total extent to center.

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.

Shortest distance from the center of the neck layer diameter to the surface of the dendrite.

Shortest distance from the furthest identified voxel to the center of the dendrite.

3D coordinate of the point where the spine is attached to the dendrite.

Shortest distance from the center of the neck layer diameter to the center of the dendrite.

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.

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.

Based on Rayburst diameters calculated in the XY plane after the automatic detection process.

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.

Each tree selected for the analysis is assigned a unique number starting at 1.

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.

Shortest distance from the center of the head layer diameter to the surface of the dendrite.

Uses the centrifugal branch order.

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.

Shortest distance from the center of the head layer diameter to the center of the dendrite.

Refers to the classification used in Neurolucida 360 to mark the spines.

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.

Based on Rayburst diameters calculated in the XY plane after the automatic detection process.

Auto: Refers to the type automatically assigned when you use Classify All.

Manual: Refers to the type you assigned via the Edit Spines panel.

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.

3D coordinates of the center of the head of the spine measured in microns from the reference point.

Backbone length to center minus distance between dendritic surface and insertion point on the center line.

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.

Shortest distance from the center of the neck layer diameter to the surface of the dendrite.

Tortuous path from furthest voxel along the path of the backbone to the insertion point on the center line.

3D coordinate of the point where the spine is attached to the dendrite.

Shortest distance from the center of the neck layer diameter to the center of the dendrite.

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.

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.

Based on Rayburst diameters calculated in the XY plane after the automatic detection process.

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.