Is connected(n) = 0; still valid in Kilosort2.5?

[JoseGuzman]

I was using the script below to remove some channels of my probes. Is it possible that Kilosort2.5 doesn't blank the channels anymore?

%%========================================================================
%% 64Fx24x47x51
%%========================================================================
fname = '~/SiliconProbes/Kilosort2/configFiles/64Fx24x47x51.mat';
Nchannels = 67; % Total number of channels
connected(24) = 0;
connected(48) = 0;
connected(52) = 0;

connected = true(Nchannels,1); % zero if bad channel 
connected(65:67) = 0; % AUX channels
chanMap = 1:Nchannels;
chanMap0ind = chanMap - 1; % zero-index channel

% xlocation of 10 or 11 electrodes in 6 shanks
xloc_10 = [0 -16.5 0 -16.5 0 -16.5 0 -16.5 0 -16.5 ];
xloc_11 = [0 -16.5 0 -16.5 0 -16.5 0 -16.5 0 -16.5 0];

xlocA = xloc_10 ;
xlocB = xloc_11 ;
xlocC = xloc_11 ;
xlocD = xloc_11 ;
xlocE = xloc_11 ;
xlocF = xloc_10 ;


xlocAUX = [-125 -375 -625];
%xcoords = vertcat(xlocA, xlocB, xlocC, xlocD, xlocE, xlocF, xlocAUX); 
xcoords = horzcat(xlocA, xlocB, xlocC, xlocD, xlocE, xlocF, xlocAUX);

% ylocation of 10 or 11 electrodes shanks

yloc_10 = [  -15 -30 -45 -60 -75 -90 -105 -120 -135 -150];
yloc_11 = [0 -15 -30 -45 -60 -75 -90 -105 -120 -135 -150];


ylocA = yloc_10 - 300;
ylocB = yloc_11 - 600;% - 1500;
ylocC = yloc_11 - 900;% - 3000;
ylocD = yloc_11 - 1200;% - 4500;
ylocE = yloc_11 - 1500;% - 6000;
ylocF = yloc_10 - 1800;% - 7500;
%kcoords = vertcat(ones(10,1), ones(11,1)*2, ones(11,1)*3, ones(11,1)*4, ones(11,1)*5, ones(10,1)*6, zeros(3,1));

% Auxiliary channels far away
ylocAUX = [500 500 500;];
ycoords = horzcat(ylocA, ylocB, ylocC, ylocD, ylocE, ylocF, ylocAUX);

% not used in Kilosort2 
% (see https://github.com/MouseLand/Kilosort2/issues/155)
kcoords = ones(Nchannels,1);

fs = 30000;
save(fname, ...
'chanMap','connected','xcoords','ycoords','kcoords','chanMap0ind','fs')

fprintf('Creating  %s \n', fname)
%%========================================================================

[Hankslab-ABG]

For what it's worth, KS 2.5 recognizes when I label a channel (in this case channel 192 on a Npx 1.0 probe, which is a reference channel that shouldn't be connected) as not connected.

[marius10p]

It should be blanking them, but I'll try to see what happens when I blank some channels and report back.