Synapses (branched structure analysis)

Purpose

 

Synapses analysis can provide a general report for number, density and average diameter of the synapses grouped by branch order (see About branch orders), and/or details reports that provide data for each individual synapse.

Use Punctum analyses for puncta automatically detected in the 3D environment of Neurolucida 360 versions 2020.2.1 and later.

Analysis results

Synapses

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

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

This report is available for synapses detected using AutoSynapse (Neurolucida version 11 or earlier) or 3D automatic detection (Neurolucida 360 versions 2020.1.1 and earlier).

Marker 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.

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

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

Distance 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.

Marker 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 user guide.

Branch diameter: Diameter of the segment at the point closest to the synapse.

Surface Area: Surface area of the synapses calculated based on the detection method below:

• Synapses detected in Neurolucida 360: Apparent (that is, not corrected for residual axial smear) exterior surface area of the synapse in µ².
• Synapses detected with AutoSynapse: Based on the mesh.
• Manually-placed synapses: Modeled as a frustum.

Volume: Volume of the synapses calculated based on the detection method below:

• 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.

Coordinate (X,Y,Z): 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.

Synapse marker details

This report provides details on synapses represented by markers that were placed either manually or using the Synapse markers tool in Neurolucida or Neurolucida 360.

Coordinates (X, Y, Z): Location of the synapse marker.

Distance: Measurement of the area between axon and dendrite surfaces at the synapse-marker location.