Multi-shanks trouble on Phy

[mndiguilmi]

Hi

I’m currently use a Neuronexus probe A4x4 (16 ch), 4 shanks with 4 channels each one (https://www.neuronexus.com/files/catalog/2021-Probe-Catalog.pdf; page 34).

Assuming the following distribution of the Neuronexus channels: (from the left to the right: shank 1 -> 4; channels distribution from down to top: 6, 2, 3, 1 (shank 1); 5, 8, 4, 7 (shank 2) 9, 12, 10, 13 (shank 3); 15, 11, 16, 14 (shank 4))

I made the following channel map for Kilosort 2

function ops=make_16_A4x4_MD_channelMap(fpath,connectedOriginal) chanMap = [6 2 3 1 5 8 4 7 9 12 10 13 15 11 16 14]; connected=true(16,1);

for i=1:length(connected) connected(i)=connectedOriginal(chanMap(i)); end

xcoords=[0 0 0 0 125 125 125 125 250 250 250 250 375 375 375 375]; ycoords=[0 50 100 150 0 50 100 150 0 50 100 150 0 50 100 150]; kcoords = [1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 4];

fs = 20000;

ops.fs = fs;

ops.NchanTOT = 16;

ops.Nchan = sum(connected);

save(fullfile(fpath, 'chanMap.mat'), 'chanMap', 'connected', 'xcoords', 'ycoords', 'kcoords', 'fs')

When I open the sorted data on Phy, the ProbeView looks OK however all channels appear on the same shank, sh 0 (see below). I’m not really sure if it’s a real problem or not and if it’s a problem in KS or Phy. On the other hand, I’d like to increase the channels for my recording (32-64 ch) using multiple shanks, but I’d like to fix this trouble before.

Thanks!

Mariano

[kingsEffy]

just to wave in seems the kcoords isnt saved in channel map related npy files but these:' chanMap0ind = int32([1:rez.ops.Nchan]-1); writeNPY(chanMap0ind, fullfile(savePath, 'channel_map.npy')); writeNPY([xcoords ycoords], fullfile(savePath, 'channel_positions.npy')); ', so .. shankid is inaccuarte?

besides I'm having the same issue, also 4 shanks...

[Lorena-J]

Hi! I have a similar issue, i'm trying to do the sorting with a 4-shank probe, all the coordenates are revised and ok, but when i plot the probe view is not the same shape than my probe.

(This is my probe loaded with the jupyter notebook

this is how the probe is seen in kilosort4 Páginas desdeCambridge-NeuroTech-Product-Catalog.pdf and this is my real probe