Kilosort3 not working for linear probes

[Jialiang-Lu]

It seems that Kilosort3 doesn't consider the situation of linear probes. Naturally, the xcoords in the channel map for a linear probe have the same value, which means that rez.ops.dminx will be 0.

The line

Kilosort/clustering/template_learning.m

Line 34 in d8942c6

xcenter = (min(rez.xc) + dminx-1):(2*dminx):(max(rez.xc)+dminx+1);

will make xcenter an empty array for linear probes and all following computation cannot be done.

I replaced this line with
if dminx>0 xcenter = (min(rez.xc) + dminx-1):(2*dminx):(max(rez.xc)+dminx+1); else xcenter = rez.xc(1); end
and

Kilosort/clustering/template_learning.m

Line 55 in d8942c6

xchan = (abs(ycup - y0) < dmin) & (abs(xcup - x0) < dminx);

with
xchan = (abs(ycup - y0) < dmin) & (abs(xcup - x0) <= dminx);

Same for

Kilosort/clustering/final_clustering.m

Line 56 in d8942c6

xcenter = (min(rez.xc) + dminx-1):(2*dminx):(max(rez.xc)+dminx+1);

and

Kilosort/clustering/final_clustering.m

Line 74 in d8942c6

xchan = (abs(ycup - y0) < dmin) & (abs(xcup - x0) < dminx);

I am not sure if this is the right fix but at least that works for my data collected by a linear probe.

[HiroyukiKato7]

I have the same issue of xcenter becoming blank because of the way xcoords are handled for a linear probe. I'm wondering if there is any update on this.

[shirquinn]

hi @Jialiang-Lu
i had this error using a 32ch linear probe
Index in position 1 is invalid. Array indices must be positive integers or logical values.

Error in getMeWtW (line 30)
iList = int32(gpuArray(isort(iNear, :))); % return the list of pairs for each template

Error in trackAndSort (line 100)
[WtW, iList] = getMeWtW(single(W), single(U), Nnearest);

Error in ksGUI/runSpikesort (line 792)
[obj.rez, st3, tF] = trackAndSort(obj.rez);

Error in ksGUI/runAll (line 628)
obj.runSpikesort;

Error in ksGUI>@(,)obj.runAll() (line 319)
'Callback', @(,)obj.runAll());

Error while evaluating UIControl Callback.

after trying your fix, the sorting was preformed with no errors
i am not an expert on this so i hope this fix will get the approval of the creators
thank you

[marius10p]

Sorry about that, I pushed a fix now. Re-open this issue if you still have problems.