How to get sync timestamps from spikeglx and open ephys

[gabrielstine]

Hi Guys,

I have a simple question that I'm having trouble finding the answer to in the documentation. I am recording simultaneously from a neuropixels probe (recorded in spikeGLX) and a DBC probe (recorded in open ephys). I'd like to extract the timestamps of the sync events from each stream and save them as .npy files. In open ephys, the sync signal is a ttl pulse fed into digital input 1. I imagine there are straightforward functions for extracting and saving these, but I can't find them!

Thanks!
Gabe

[zm711]

I feel like @alejoe91 is going to need to be the person to comment on this. I don't actually use ephys or any of the event based code in spikeinterface. So just ping this issue if you don't get a response soon!

[alejoe91]

Hi @gabrielstine !

You should be able to read the open ephys events with this function:

events = se.read_openephys_events(openephys_folder)

This will return an Event object, which will allow you to interact with the event data. There can be events from multiple channel ids, which you can retrieve with the events.channel_ids field.
In particular, calling evts = events.get_events(channel_id) will return a structured numpy array with the following field:
dtype([('time', '<f8'), ('duration', '<f8'), ('label', '<U100')]). For open ephys, the label is the channel the event was recorded on, so you can select all events from channel 1 as follows:

evts_1 = evts[evts["label"] == "1"]

Let me know if you have other questions!

[gabrielstine]

Thanks @alejoe91. And is there a way to automatically get the timestamps at which the sync channel went high in the spikeGLX data, or do I need to extract this manually? If not, could be nice to have a built-in function that takes the channel as input and returns timestamps.

[alejoe91]

You can try the event_spikeglx = se.read_spikeglx_events(spikeglx_folder) ;)