Recording external TTL pulse events across trials + outputting a square wave

malda

Hi, I am planning to run a behavioral task through Bpod with photometry. For synchronization purposes, the photometry computer sends a TTL pulse. While my task is going to have a trial structure, the photometry and the pulse will be continuous. My plan is to record the pulse with Bpod and align it with behavioral events. My questions are:

Can Bpod do this, even across trials?
Also can it output a 20_40Hz square waveform of 5V amplitude?
If so, up to what current can it output?

Thank you!

Josh

Hello Malda,

If your task protocol is written using BpodTrialManager, the inter-trial interval is only approx. 150 microseconds, so you should capture all of the pulses that arrive from the photometry computer during your session.

You can set up a looping global timer (as in this example) to output a 5V square waveform from a state machine BNC output channel in parallel with your trial's state flow. The output is driven by Analog Devices ADUM6200, an isolated logic driver IC. The two channels can supply up to 40mA.

-Josh

malda

Hi Josh,

Thank you for your reply. Do you have any sample code, where you record an external pulse signal? Also for outputting the square waves, I'm thinking of outputting it at the time of a behavior event such as an auditory cue produced by Bpod. Do you have an example code for this too?

malda

Also, will it be possible to record the timing of the beginning of each trial and the timings of the external sync pulse (or at least the timing of the first rising edge of it), say as measured from the beginning of the session? Again a sample code would be super helpful here.

malda

By the way, how would Bpod record an external sync pulse (it will be a 5V square wave of a certain fixed frequency)? Will it just record the timings of the rising or falling edges of it? Or will it record whether the sync pulse channel is in the up (5V) or down (0V) state in each sampled timepoint with a certain sampling frequency? If a rising edge occurred during the 150 us down time, will Bpod detect and record the rising edge in the next available sampled timepoint (which would cause 150us delay, which is perhaps okay)?

Josh

Hi Malda,

Incoming TTL pulses will be automatically recorded (with timestamps), so long as a behavior session is running.

To set one of the BNC output lines high in a state, simply add {'BNC1', 1} to the 'output actions' section of your state declaration, e.g.

sma = AddState(sma, 'Name', 'MyState', ... 'Timer', 1,... 'StateChangeConditions', {'Tup', '>exit'},... 'OutputActions', {'BNC1', 1});

You'd use {'BNC2', 1} to set channel 2 high. The channel will remain high for the duration of the state.

Both rising and falling edges will be recorded as events with timestamps. The state machine updates at 10kHz, but does not stream out the state of the lines between edges (at each sample). An edge that occured during the inter-trial time would be registered on the first update of the next trial.

I hope this helps,

Josh

malda

Thank you! I have a couple more follow-up questions.

When you say when behavior session is running, What exactly do you mean? Ideally, I want to record the first rising edge in both the photometry system and Bpod. And our system is set up such that the sync pulse is generated when photometry recording starts, and the freq of the pulse can be set to an arbitrary value. If I start photometry recording before I start a Bpod protocol, then I would likely miss the first rising edge (unless I use a small freq and start Bpod immediately after photometry begins). So what I think I should do is to first start Bpod session and then start photometry recording. But in this case, because Bpod session begins before photometry, the very beginning of the session may not be recorded by photometry. How do I solve this problem? If the recording on the Bpod side begins when I press the play button for the protocol and continues even if I pause the protocol, I think this could work because I can start the protocol and have pause command in the protocol script so that the protocol immediately pauses. Then I can start photometry recording, and once it's running, I can manually restart the protocol. This way, I will be able to record the first rising edge and also not lose any part of the session in the photometry recording. Is this possible?
Relatedly, you said the incoming TTL pulses will be automatically recorded. Are they timestamped relative to the time when the protocol begins? Does Bpod also record the beginning of each trial in the same manner? So I can align trials with photometry?
You comment about {'BNC1', 1} refers to outputting a 5V square waveform, right? What I need is something a bit more specific. For example, I want a square wave of a certain frequency like 40 Hz of 500 ms duration to be output by Bpod if a certain behavior event, like when I output an auditory cue, happens. How can I do this?

malda

Hi Josh, following up on this in case you missed my previous replies. Thank you!

Josh

Hello Malda,

In reply to your item 1:

The behavior session is "running" between the time you click the "Start" button in the launch manager, and the time you click the "stop" button on the Bpod Console GUI to end the session.

You're correct that you would miss the first logic edge if you start photometry before the Bpod session.

I'd solve the problem by creating an extra state on the first trial of your session (or a special trial consisting of a single state):

sma = AddState(sma, 'Name', 'WaitForPhotometry', ... 'Timer', 1,... 'StateChangeConditions', {'BNC1High', 'myNextState'},... 'OutputActions', {});

During the WaitForPhotometry state, you'd start the photometry system. That way you capture your first edge, but the photometry system is running prior to the first actual trial.

The pause button on the GUI does not pause mid-trial. To keep the trials consistent, it schedules a pause for the next break between trials. Events are not captured during a pause.

In reply to your item 2:

All events (including incoming TTL pulses) are timestamped with respect to trial start time. Each trial start time (with respect to session start time) is separately included in the data. If your photometry system has a TTL interface with 10kHz sampling or better, you can set up any free digital output channel as a "sync" channel so that trial start and end times are also timestamped on the photometry system clock. You'd set that up from the settings menu (wrench icon on the Bpod console GUI) and then the "sync" icon.

In reply to your item 3:

To output a square or pulse waveform on trigger, you can set up a looping global timer as shown in this example.

Please let me know if this was the info you were looking for.

Thanks,
Josh

malda

Regarding "reply to your item 2":
So that means I can stitch together rising edge times across trials relative to the session start time?

Regarding "reply to your item 3":
It's not clear from the example (I am not familiar with the global timer syntax) whether I have the enough flexibility to generate a 40Hz 50% duty cycle square wave of 5V for 500ms duration. Also, in the example, it seems like I can generate some (infinite duration) pulse triggered by some event, but it seems like it needs to be stopped by some event. Can I generate pulses that lasts for a specific duration triggered by some event, without needing another event that stops it?

Josh

Hello Malda,

Yes, rising edge times on the sync channel indicate each trial-start and trial-end times relative to session start.

In the example, the 'Duration' and 'LoopInterval' parameters set the logic high and low periods of the waveform respectively. To make a 50% duty cycle square wave at 40Hz, you'd set both Duration and LoopInterval to 0.0125.

The 'Loop' argument indicates how many times to loop the waveform following the trigger, as shown in this example. Since each period of the waveform is 0.025s long, you'd need 20 repetitions to span 0.5s.

Josh