Synapse markers (2D)

Overview

The synapse markers tool evaluates traced neurons to identify where dendrites converge onto axons then places markers at putative synapse sites.

Before you start

In order to use the tool, open or create a data file with neuron trees traced and their types identified.

• Trace at least one axon and dendrite in either the 2D or 3D environment.

Placing synapse markers

1. You must be in Neuron mode; get there by clicking the Neuron button in the Trace ribbon of the 2D window.

2. Click the Synapse markers button.

3. In the Putative Synapses window, choose a marker and settings for detection of putative synpases:

   • Click the marker that you want to use.

   • In the open field, enter the maximum distance between dendrite and axon for putative synapses.

     Neurolucida 360 software will consider placing markers where traced dendrites and axons are within this distance from each other.

   • Choose spine and varicosity requirements. You can limit putative synapse detection by checking the boxes to consider the presence of spines and or varicosities in addition to dendrite-axon distance:

     • Click Spine required on dendrite to place markers only when there is a spine on the dendrite.

     • Click Varicosity required on axon to place markers only when there is a varicosity on the axon.

   • Click OK and Neurolucida 360 software places markers as per the settings you've identified.
4. (optional) Repeat step 3, but using a different marker and different settings.

In Neurolucida Explorer, you can view the Synapse Marker Details report to obtain the coordinates of the synapse markers and the distance between axon and dendrite surfaces at the marker location.