Neuropyxels with Open Ephys data

[javierzsm]

Hi,
This is super cool although I can't use it because I'm not using SpikeGL. Is there any chance to have it working with data acquired using Open Ephys?
Best,
Javier

[m-beau]

Hi Javier,

I could actually use your help! Can you send me an example dataset? Are you recording with neuropixels 1.0, the commercial version?

Maxime

[javierzsm]

Sure, you can find a little piece of data here https://owncloud.icm-institute.org/index.php/s/b8i5s4lVV8Dub6C
I put the entire directory with all the sub-folders and files created by Open Ephys during an acquisition session.
It's been acquired with a single neuropixels 1.0 probe using the Open Ephys Neuropixels-PXI plugin.

[m-beau]

Cheers, and which spike-sorter did you use?

[javierzsm]

Kilosort 3, I added a folder with the spike sorting outputs.
Let me know if that works.

[javierzsm]

Hi!
I saw the README was updated and it should also work with Open Ephys recorded data. Yet, the script doesn't seem to find the binary file.
How should the data be organized for it? KS outputs + .dat file in the same folder?
Thanks!

[m-beau]

Hi! I am currently working on it, I edited the readme file a but prematurely - bear with me!

[m-beau]

Hi Javier, almost there - I am trying to work out how to infer the bits to uVolts conversion factor from openephys metadata.

In spikeGLX, the amplification factor can customized and is typically 500. From there, I can compute the conversion factor which is about 2.34: glx_convfactor = Vrange/2**bits_encoding/ampFactor

in the oebin file, I do not find any amplification factor but I find another number per channel: "bit_volts", which must be what I am looking for. Its value is 0.19499999284744262695 on all of your channels.

I assume that this number must be 1/glx_convfactor, but it would mean that you have an amplification factor of ~228.5 which is rather odd. Can you let me know what was your amplification factor?

MAxime

[m-beau]

FYI, I figured it out - the compatibility layer is now written, and updated on github and pip.

The only missing bit is how to format the sync channel in events/Neuropixels-PXI-100.0, for that I need an example of recording with an actual sync signal

[javierzsm]

Hi Maxime, that's amazing! sorry, I had some issues and couldn't record the sample with the TTLs as we agreed, I'm hoping to do it tomorrow if everything goes well. I'll keep you posted. Cheers !

…

On Mon, 25 Oct 2021 at 00:22, Maxime Beau ***@***.***> wrote: FYI, I figured it out - the compatibility layer is now written, and updated on github and pip. The only missing bit is how to format the sync channel in events/Neuropixels-PXI-100.0, for that I need an example of recording with an actual sync signal — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#96 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEJTX4VJFNLZEUZNW6CQW3TUISBLZANCNFSM5FTX2PFA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[javierzsm]

Hello Maxime,
Here is a sample recording of about 180 s during which I gave a 30s TTL train @1Hz.
I also included the KS3 sorting results. Let me know if it's what you needed.
https://owncloud.icm-institute.org/index.php/s/NsvvdgKWsFDrkW5
Cheers,
j

[m-beau]

Hi Javier,

I am not prioritizing this at the moment - you can now use npyx with OpenEphys, simply not load the sync channel through npyx yet. It isn't critical with openephys though as you can simply load the sync signal from 'events/Neuropix-PXI-100.0/TTL_1/timestamps.npy using numpy! Let me know how npyx works for you, don't hesitate to ask if you encounter further issues!

[m-beau]

Hi Javier,

Did it work out for you? Everything should work smoothly on an openEphys dataset, apart from extracting the sync channel which is very easy to do manually (it is pre-extracted in OpenEphys, at 'events/Neuropix-PXI-100.0/TTL_1/timestamps.npy' I reckon)

[m-beau]

Confirmed that it worked orally - closing this issue

[chris-angeloni]

FWIW, there was a recent OpenEphys update that has made most of this code no longer work for data recorded with the new GUI (mostly due to folder name changes). I'm working on updating it!