Optogenetics with the Tower

The optogenetics panel in the new Tower electronics (aka the Pizza Box) is nearly the same as its predecessor.

The main difference is that synchronization and timing of stimulation is done internally and does not require any external electronics. The parameters at the bottom specify the width of the LED, GATE pulses and the number of consecutive frames COUNT that will be generated upon a trigger. The LED and GATE values are in milliseconds (and GATE>LED) (these can be floating point values). Note that, depending on the gated PMT you are using, there are additional limits on pulse width. The GATE signal is routed internally to all PMTs in the system, so no additional connections are required. The LED ENABLE signal is available on PSoC2:DOUT0.

Stimulation is synchronized the the start of a frame. Thus, if a trigger command arrives in the middle of a frame, the system will wait until the next frame to stimulate. Triggering can happen in one of three ways while the pull-down menu is in the “Pulse” state. Users can manually trigger the system by using the Trigger button in the optogenetics panel. An external trigger can be generated by the rising edge of a TTL signal going into PSoC2:DIN0 as long as the checkbox in the GUI is enabled. A network command consisting of a single character ‘e’ will also generate a stimulus.

Note that a trigger command will not have any immediate effect if the system is not scanning. However the command will nevertheless be queued and, as soon as the system starts scanning, the stimulus pulse will be triggered.

Note that for the optogenetics panel to work properly you should have both Master and Slave firmware installed in the dual PSoC tower. To find out the version currently installed, just type the following in the Matlab command window:

>> scanbox_config
>> sb_open
>> sb_version

COM7: v1.11.0 (Master)
COM9: v2.11.0 (Slave)

In this example, we see a Master with version 11.0 on COM7 and a Slave with version 11.0 on COM9. Version should be 11.0 or higher. If you have an earlier version, or one PSoC is active, you need to update the system to enable this feature.