Velocity detection for optogenetic manipulation

FishQian

Dear Josh,

I've been using bpod system for a while , and it's been working great.
Briefly, my experiment involves water restricted head fixed animals running on a treadmill with water reward delivered at a given location. Currently I'm trying to add an LED stimulation option for my experiment at a specific location, which can be easily controlled by the RotaryEncoder Module. To avoid over-stimulating the brain, i.e., if an animal stops running inside the given LED stimulation zone, I would like to stop the LED stimulation, and restart stimulation once the animal starts to run. I wonder if there is an easy way of doing this in Bpod and want to hear your opinions.

Here are two simple scenarios:
1) reward inside the LED stimulation zone, which covers a certain distance. Generally animal would stop and lick the water reward, I can simply stop the LED stimulation for a few seconds before starting again.
2) I can either turn off the LED using Bpod console directly, or set up a timing for the LED so that it automatically goes to standing state, that can transition back to the LED state manually.

The first scenario might not generalize very well across conditions, as it depends on a hard coded number of time, that only deals with a certain stereotypical behavior pattern. The second scenario requires the experimenter to deal with speed information in real time, which is a little challenging too.

What's your suggestions? Are there ways of detecting the running speed as External Trigger?
Thanks
Fish

Josh

Hello Fish,

Unfortunately speed is not currently computed by the rotary encoder module firmware.

Here are two ideas that may work for your application depending on the precision you need:

Up to 8 thresholds are supported by the rotary encoder module. You can set all 8 to evenly span your stimulation zone. When the animal crosses each threshold, start a global timer to measure the maximum amount of time to move to the next threshold. Handle the timer-elapse event by stopping stimulation, and start it again on the next threshold crossing. After handling the timer, you can step back to the previous state if necessary with the >back command.
Mod the RotaryEncoderModule class. getUSBStream() beginning on line 809 is the section that is called periodically to read new position data when USB streaming is enabled. You can have the PC compute speed and call SendBpodSoftCode() to prompt the state machine to stop stimulation. This approach will have some latency and jitter because speed is computed on the PC.

-Josh