rSync aligner

[margo-tje]

Hi,
I have been trying to use random pulses to synchronize my licking data (collected with Arduino) with my pyphotometry data.

The pulse I am generating (on Arduino) are randomly drawn from intervals 250 - 1500 ms and have a pulse length of 250 ms.

I receive the Licking data in ~50 Hz with a column 'rSync' being 0 and 1s to indicate the pulses.
In PyPhotometry, the pulses are also displayed as 0s and 1s with a sampling rate of 86 (3ex2em).

I am a bit confused how to work with Rsync_aligner(). I keep getting the error: 'RsyncError: No match found between inter-pulse interval sequences.' I have tried 'auto' units, and also 1000/86 or 1000/50 units respectively.

• What are the pulses inputs supposed to be? The random times between the pulses, or the data as 000111's with its corresponding sampling rate?
• The total length of my two data streams are not equal as I start one after the other; does that matter?
• As an alternative method, does it make sense to just look at the times of each pulse and sync on that?

Happy to hear your thoughts.

[ThomasAkam]

Hi @margo-tje,

The Rsync_aligner expects the pulse_times_A and pulse_times_B inputs used to set up the aligment to be the times of the pulses, not either the inter pulse intervals or a stream on 0s and 1s indicating the value of an input sample by sample. The times can be in units of seconds or ms, or they can be in units of samples since the start of a recording, as will be the case for your data.

For example, when we are synchonising pyControl data with pyPhotometry signals, we use the times of the pulses generated by the pyControl system (in units of seconds since the start of the pyControl session) and the pyPhotometry sample numbers when the sync pulse input went high at the start of each pulse (so in units of samples since the start of the pyPhotometry recording). When setup this way the Rsync_aligner can be used to convert between pyControl times and pyPhotometry sample numbers. For an example of this see this ipython notebook.

In your case you will need to compute the sample numbers on each system (licking data and pyPhotometry) when the sync pulses went high and use these as the pulse times for setting up the aligner. The aligner will then let you convert sample numbers from one system into those on the other system or vice versa.

Thomas

[margo-tje]

Hi Thomas,
Thank you. I have updated my Arduino code to get less variation in the resulting sampling rate and that seems to have solved the issue.

Best,
Margo