Synapses (branched structure)

Only available when AutoSynapse (Neurolucida 11 or before) or 3D automatic detection (Neurolucida 360) was used to detect the synapses.

If the synapses were identified manually with markers, see Branched Structure Analysis: Individual Marker, Branched Structure Analysis: Marker Totals or Marker and Region Analysis.

Results

Synapses report

Provides data grouped by branch order.

ClosedDensity

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

Closed Average diameter

Average diameter of the synapses on the segment.

For the analyses, each synapse is associated with a marker shaped as a circle (even when synapses are represented as solids). The synapse diameter is extracted from the circle diameter to approximate the synapse size.

This value is the average of the "marker diameter" values included in the Synapse Details report.

Synapse Details report

Provides data such as area, volume, and distance from tree.

ClosedMarker to branch

Distance from the synapse center to the closest point along the dendritic segment.

For the analyses, each synapse is associated with a marker shaped as a circle (even when synapses are represented as solids). The synapse center corresponds to the circle center.

ClosedDistance along branch

Distance from the start of the segment to the point on the segment closest to the synapse.

ClosedDistance from root

Distance from the origin of the tree, along the tree, to the point closest to the synapse.

ClosedDistance to previous

Distance along the tree to the previous synapse. If the synapse is not placed on the tree, Neurolucida Explorer provides the distance to the point on the tree that the synapse is associated with, instead of the distance to the synapse.

ClosedMarker diameter

Refers to the intrinsic size of the marker which is set when markers are placed in Neurolucida. The size of the circular crosshair used for the marker is considered to be the diameter of the marker. See Using Markers in Neurolucida.

ClosedBranch diameter

Diameter of the segment at the point closest to the synapse.

ClosedSurface Area
  • Synapses detected in Neurolucida 360: Apparent (that is, not corrected for residual axial smear) exterior surface area of the synapse in ยต2.
  • Synapses detected with AutoSynapse: Based on the mesh.
  • Manually-placed synapses: Modeled as a frustum
ClosedVolume
  • Synapses detected in Neurolucida 360: Measured by the number of voxels that make up the synapse object multiplied by the volume of a single voxel. The volume of a single voxel is: X resolution * Y resolution * Z resolution.
  • Synapses detected with AutoSynapse: Based on the mesh.
  • Manually-placed synapses: Modeled as a frustum
ClosedCoordinate

3D coordinate of the point where the synapse is attached to the segment. The center point used is the center of mass, with no weighting.