Can IronClust support A4x4-tet design?

[kouichi-c-nakamura]

A quick YES or NO question.

I don't find any *.prb file in the prb folder that matches the design below, but can this design be supported by manually editing a .prb file?

A4x4-tet-5mm-150-200-121

http://neuronexus.com/electrode-array/a4x4-tet-5mm-150-200-121/

[bapungiri]

Yes you can customize the .prb files according to your probe's electrode position.

[jamesjun]

Of course Kouichi, I will define each tetrode as its own shank such that each tetrode group gets processed separately.

For example, if chan 1,2,3,4 belong to tetrode 1 and chan 5,6,7,8 belong to tetrode 2, define

channels = [1,2,3,4,5,6,7,8]. % mapping between channel ID to site ID, sorted by the site ID (uses 1-base array indexing) shank = [1,1,1,1,2,2,2,2]; % shank ID corresponding to each site geometry = … % [nSites x 2 matrix, col1: x coordinates, col2: y coordinates

Please refer to the probe file from here: https://github.com/JaneliaSciComp/JRCLUST/wiki/Probe-file https://github.com/JaneliaSciComp/JRCLUST/wiki/Probe-file

On Jul 17, 2019, at 9:42 AM, Kouichi C. Nakamura notifications@github.com wrote:

A quick YES or NO question.

I don't find any *.prb file in the prb folder that matches the design below, but can this design be supported by manually editing a .prb file?

A4x4-tet-5mm-150-200-121

http://neuronexus.com/electrode-array/a4x4-tet-5mm-150-200-121/ http://neuronexus.com/electrode-array/a4x4-tet-5mm-150-200-121/ — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/jamesjun/ironclust/issues/27?email_source=notifications&email_token=ACEHBOCN2XAPIFWBZGZ4FOTP74OTZA5CNFSM4IEQQKX2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4G7XOFXA, or mute the thread https://github.com/notifications/unsubscribe-auth/ACEHBOCV7GVEVKULHQLACU3P74OTZANCNFSM4IEQQKXQ.

[kouichi-c-nakamura]

Thanks, guys! Because we're planning to order it, it's important to know if there is a tool that can handle it.

[jamesjun]

I think it might work well in Basal Ganglia. I just added the probe file in the repository (a4x4nn.prb). Here is the content of the probe file below. You may need to update the channels variable with the correct channel map from NeuroNexus.

% Order of the probe sites in the recording file channels = 1:64; % assuming linear mapping between sites to channels. Refer to the NeuroNexus documentation for correct channel mapping.

% Site location in micrometers (x and y) fh_col = @(x)x(:); geometry = repmat([0, -17.6777, 17.6777, 0; 0, 17.6777, 17.6777, 35.3554]',[16,1]); geometry(:,1) = geometry(:,1) + fh_col(repmat([0,200,400,600],[16,1])); geometry(:,2) = geometry(:,2) + repmat(fh_col(repmat([0,150,300,450],[4,1])),[4,1]);

% Recording contact pad size in micrometers. Height x width pad = [11 11];

% Shanks shank = fh_col(repmat(1:16,[4,1]))';

% Micrometers per center-to-center vertical site spacing um_per_pix = 17.6777;

---

irc probe a4x4nn.prb % running this command will generate a plot below

On Jul 17, 2019, at 9:54 AM, Kouichi C. Nakamura notifications@github.com wrote:

Thanks, guys! Because we're planning to order it, it's important to know if there is a tool that can handle it.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/jamesjun/ironclust/issues/27?email_source=notifications&email_token=ACEHBOCTAU3RMQDQHALMNBLP74QC7A5CNFSM4IEQQKX2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2EIVKI#issuecomment-512264873, or mute the thread https://github.com/notifications/unsubscribe-auth/ACEHBOGWVPVV32VTJWJ5QIDP74QC7ANCNFSM4IEQQKXQ.

[kouichi-c-nakamura]

Thanks a lot!