Synapses

Visualization

Synapses are visualized as balls in the 3D window with different colors to distinguish pre-synaptic elements (TBars) and post-synaptic elements (PSDs).

Synapse Visualization in 3D

We can adjust synapse visualization in the control panel.

Object Panel (Named Puncta) for Synapses

Visualization Settings for Synapses

In the Original Point Color color mode, which is the default option, you can change the color of selected synapses

Change Color of Selected Puncta

Synapse Selection

You can select synapses with certain connections by specifying the connection patterns.

Input format:

Selecting TBars from body_id_1 connecting to body_id_2: body_id_1 -> body_id_2

Selecting PSDs from body_id_1 receiving inputs from body_id_2: body_id_1 <- body_id_2

Together with the color changing function, you can colorize specific connections more conveniently than before.

To certain selections only, you can hide all synapses first, and then use Add Puncta Selection to select the synapses you want to see. Once the selection is issued, you can use Show Selected Puncta in the context menu to bring back selected puncta only.

Show Selected Puncta