Calibration files do not seem to work

[danielpollak]

Hello,

I received Calibration files for some neuropixel probes, but the quality of the signal I am getting is clearly worse than it should be, and I wonder if it would be possible to help me understand where these issues are coming from. Every other channel is severely clipped in the LFP, apparently owing to a too-high gain (see image of LFP band and AP band below). In fact, this is what the signal looked like before it had a calibration file.

For some reason, one half of the probe is very noisy, and the other half is not as noisy, though it is getting somewhat clipped, which is in turn impacting the AP band. I wonder if this is a problem with the calibration file. I have attached the Calibration file, and below are some screenshots of the LFP and AP signal from the Neuropixel PXI tab in the open ephys acquisition software. 18005123662.zip

This signal is from a mouse moving freely in an open arena, sometimes bumping its cap into the side of the wall. We used the Buzsaki microdrive and cap design found here, the ground and reference wires are shorted, and I have a chlorided ground wire in the brain. I would be very grateful for any feedback you might have!

[nsteinme]

Very unlikely to be calibration file; these only change the signal minorly. I think instead you have a broken probe or a poor recording setup.

…

On Tue, May 23, 2023 at 9:49 AM Daniel Pollak ***@***.***> wrote: Hello, I received Calibration files for some neuropixel probes, but the quality of the signal I am getting is clearly worse than it should be, and I wonder if it would be possible to help me understand where these issues are coming from. Every other channel is severely clipped in the LFP, apparently owing to a too-high gain (see image of LFP band and AP band below). In fact, this is what the signal looked like before it had a calibration file. [image: Screenshot 2023-05-23 093122] <https://user-images.githubusercontent.com/15875720/240359900-8c920221-4abf-43ce-91c3-363f048e413a.png> [image: Screenshot 2023-05-23 090627] <https://user-images.githubusercontent.com/15875720/240360060-74f9aba5-cdfd-48b0-b707-a3199d4fd52f.png> For some reason, one half of the probe is very noisy, and the other half is not as noisy, though it is getting somewhat clipped, which is in turn impacting the AP band. I wonder if this is a problem with the calibration file. I have attached the Calibration file, and below are some screenshots of the LFP and AP signal from the Neuropixel PXI tab in the open ephys acquisition software. 18005123662.zip <https://github.com/cortex-lab/neuropixels/files/11546609/18005123662.zip> [image: Screenshot 2023-05-23 090839] <https://user-images.githubusercontent.com/15875720/240363265-8da69db2-059f-4fb9-8800-de9d22ae55eb.png> [image: Screenshot 2023-05-23 090907] <https://user-images.githubusercontent.com/15875720/240363267-05733de9-e28c-4960-be18-8b2aa2c471dd.png> This signal is from a mouse moving freely in an open arena, sometimes bumping its cap into the side of the wall. We used the Buzsaki microdrive and cap design found here <https://elifesciences.org/articles/65859>, the ground and reference wires are shorted, and I have a chlorided ground wire in the brain. I would be very grateful for any feedback you might have! — Reply to this email directly, view it on GitHub <#59>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZ5IP3YO426FBHNFFSQS4DXHTS75ANCNFSM6AAAAAAYMFMNLQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[danielpollak]

Thanks for your reply! I'm a bit confused about why only half of the channels would be bad though- is it possible for the probe to break in a way that disconnects only the left half of the probe? The other channels seem to have reasonable spiking activity.