Where to find channel of units in phy-output

[reinderdorman]

Hi all,
I've recently started to use spike Interface, and so far it's been working great.

However, I'm having trouble in finding the channel (or the channel with highest amplitude) in the phy configutation. All the .npy files I have checked don't seem to have this information. I have access to other info just fine (waveforms, spike times, quality metrics, etc ...)

I'm not going to preten i'm fluent in this entire library, but it appears there are some functions here and there about finding channels for units, but I can't figure out where to find this in either the phy-output, or the spike-sorter specific output (in my case with Tridesclous).

Any help is greatly appreciated!

[h-mayorquin]

@zm711 maybe you know?

[zm711]

I'm trying to understand the question. @reinderdorman are you hoping to get the channel with the highest amplitude like it demonstrates in the phy gui? Because that is calculated on the fly in phy so it is not stored in the files itself, but calculated. Spikeinterface has functions to get that type of information, but before I start sharing functions I want to make sure I know what you are hoping to obtain. Honestly when dealing with Phy it is usually best to just post a picture and circle what you want.

[reinderdorman]

@zm711 that's indeed my question. I just spoke to a co-worker this morning and I now have access to this information after manually curating with the template-gui, after which a few extra files are stored from which the highest-amplitude channel is written.

I'm still interested in the function from SpikeInterface, so if you could mentioned those that would be appreciated. But other than that, this issue is (for me at least) solved by looking at the saved info after curating in the template-gui.

[zm711]

Hey @reinderdorman, yep so there are a couple of things you can do!

So if you truly only want the peak channel then we have a function you can import like

from spikeinterface.core import get_template_extremum_channel
# we need a sorting analyzer:
channel_ids = get_template_extremum_channel(sorting_analyzer, outputs='id')

You can read more about the arguments to that function here

If you'd prefer instead to have estimated/calculated "true" spike locations you can use the SortingAnalyzer.compute() function which can calculate `"spike_locations" using a variety of computational methods, e.g. based on center of mass or using monopolar triangulation.

To do this you would do

# we have our sorting analyzer
sorting_analyzer.compute(['random_spikes', 'waveforms', 'templates', 'spike_locations'])
# then to get the data
spike_locations = sorting_analyzer.get_extension('spike_locations').get_data()

You can read more about that in the docs or the source code.

does that sound good?

[zm711]

I'm going to close this discussion since the spikeinterface answer is included and phy based questions are better for the phy repo.