LFP data of Visual Behavior - Neuropixels July 2022 and Probe Missmatch

Technical
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Hi! :wave: ,
Just some quick questions…

Extracting LFP data in Visual Behavior - Neuropixels July 2022

I wanted to extract LFP data from the new dataset (Visual Behavior - Neuropixels July 2022) but I can’t find any related method.
According to the tutorial from the previous version (Visual Coding - Neuropixels October 2019), we can use .get_lfp(probe_id) but there is no such method in the brand new dataset.
_I tried to open the NWB session file with HDF view and as far as I searched, I could not find any LFP time series data
Well, is there any method to use LFP data?

Mismatch in probe data

Also, I guess there is a bug in the new dataset while extracting probe descriptions (IMGAE attached) :
output description about probes is different between cache.get_probe_table() and session.probes

1446×653 74.5 KB

Is there any white paper or a released paper about the new dataset?

thanks! :sweat_smile:

2

Hi Mostafa,

The first release of this data doesn’t include LFP data. LFP data will come in a release later this year, at which point the LFP columns for the session object will be populated. Sorry for the confusion there.

You’re a little ahead of the game (the data is public for testing purposes, but hasn’t been officially ‘released’ with the accompanying public announcement and documentation). There will be a technical white paper released in the next week.

Cheers,
Corbett

3

oh got it, thanks!
recently I saw a tweet about its official release, so are LFP data accessible now?

best,
M

4

Hey Mostafa,

We plan on releasing the LFP data by the end of this year. We still have some packaging and validation to do before it’s ready to go.

-Corbett

5

Hello! Has the LFP data been released yet?
Thanks!
Chris

6

Yes! The LFP data has been released. Right now this is a soft release, so tutorials to demonstrate how to access this data are forthcoming and should be available here in the next week or so. If you’re eager to get going, you should find that this data is formatted very similarly to the Visual Coding Neuropixels LFP data, a tutorial for which can be found here.

To access the LFP data, you’ll need to be use allensdk version 2.14.1 and the 0.4.0 manifest for the Visual Behavior Neuropixels data cache.

Cheers,
Corbett

7

I’m using the LFP from the visual behaviour dataset but I’ve found that not all the channels described in the metadata are available in the LFP object.

Also my colleague said we need to scale the LFP data by 0.195, is this still true?

8

Hi,

I’m sorry for the delay in this response. The LFP is downsampled in space such that only every 4th channel is represented in the LFP xarray (check out the tutorial here: visual_behavior_neuropixels_LFP_analysis). Does this account for the discrepancy you’re encountering?

The xarray units are already volts, and you do not need to scale the data. Please note however that we recently fixed a bug in the scaling (see the changelog here: GETTING STARTED — Allen SDK dev documentation). Using the latest version of the sdk (2.16.2) and data manifest (visual-behavior-neuropixels_project_manifest_v0.5.0.json) should resolve this issue but will require you to re-download the nwb files into a fresh cache.

Cheers,
Corbett

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