search

open-ephys / Bonsai.ONIX

Bonsai library for Open Neuro Interface Compliant hardware with a focus on the ONIX System
https://open-ephys.github.io/onix-docs/index.html#
MIT License
1 stars 3 forks source link

Neuropixels channel locations #16

Open ikharitonov opened 1 year ago

ikharitonov commented 1 year ago

Hi, Working with Neuropixels, is there a way to access channel information (particularly channel locations) similarly to settings.xml from Neuropixels PXI plugin for OE GUI? The exported configuration file from NeuropixelsV1Device interface seems to only contain gain correction information. Is there documentation explaining how to parse it? Thanks.

jonnew commented 1 year ago

Hi,

Good question. In the exported file JSON or XML file, there is a field called "ElectrodeNumber". This has a well defined location on every neuropixel device. However, this is quite annoying to figure out and given the fact that we create a drawing of the probe for display purposes, it seems like XY position meta data would be a good idea.

We are in the process of completely overhauling this library, including its GUI elements. This is a good feature to add during that process. I will put an issue on the refactor indicating this feature request.

Jon

ikharitonov commented 1 year ago

Thanks Jon, is there any publicly available reference relating "ElectrodeNumber" to the probe? If not, I guess to find other ways to estimate the channel map.

jonnew commented 1 year ago

Im asking around on the OE discord (https://discord.gg/kZY5uCcr). Also the neurpixels slack channel might be a good place to ask.

On Tue, Oct 31, 2023 at 5:59 AM ikharitonov @.***> wrote:

Thanks Jon, is there any publicly available reference relating "ElectrodeNumber" to the probe? If not, I guess to find other ways to estimate the channel map.

— Reply to this email directly, view it on GitHub https://github.com/open-ephys/Bonsai.ONIX/issues/16#issuecomment-1786884720, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAK47YY2XSMYLP7XLMHIWH3YCDDYBAVCNFSM6AAAAAA6WE4OKOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOBWHA4DINZSGA . You are receiving this because you commented.Message ID: @.***>

jonnew commented 1 year ago

Here we go:

https://github.com/open-ephys-plugins/neuropixels-pxi/blob/main/Source/Probes/Geometry.cpp

nhp.json np2_1.json np2_4.json np1.json

ikharitonov commented 1 year ago

Thank you!