Sorting single channel plexon data

[AamnaLawrence]

I have recorded spike activity using a tungsten electrode using plexon recording system. I converted the .plx to .mat file and then the .mat file to a .dat file using the following piece of code

aa=fopen("nameoffile.dat","w");
fwrite(aa,x,"int16");
fclose(aa);

x has the dimension 1 by number of time points.
I tried to make a single channel probe however, it does not seem to work.

Can kilosort2 sort single channel data?

I also made a dummy channel dataset having 16 channels in which all contained random data and one of them had the spike data. I used the linear 16x1 probe layout but I could not even see my spike data in the "Data view". What am I missing here?

[marius10p]

It cannot sort single-channel data, but the way you wrote the binary file seems right. If you want to add dummy channels, make sure they are 0s. There could be a data scaling issue in the Data view, and possibly when you write your channels to int16. You would need to convert to the range that int16 expects, so -2^15 to 2^15.

[AamnaLawrence]

Thank for your help. Now I can see the traces

However, when I click on Run All, I get the error "Error running kilosort. Undefined function or variable 'W'
Error saving data for Phy!'

[marius10p]

The GUI errors are not informative... can you please look in the Matlab command line to and paste the entire output?

[AamnaLawrence]

Sure!

Getting channel whitening matrix...
Channel-whitening matrix computed.
Time 4s. Loading raw data and applying filters...
Time 4s. Finished preprocessing 19 batches.
Time 0s. Determining good channels..
found 132 threshold crossings in 40.22 seconds of data
found 15 bad channels
Time 1s. Computing whitening matrix..
Getting channel whitening matrix...
Channel-whitening matrix computed.
Time 1s. Loading raw data and applying filters...
Time 2s. Finished preprocessing 19 batches.
Obtained 7 PC waveforms in 0.27 seconds
Warning: data batch #1 only had 0 spikes

In clusterSingleBatches (line 95)
In ksGUI/runSpikesort (line 782)
In ksGUI/runAll (line 628)
In ksGUI>@(,)obj.runAll() (line 319)
time 0.02, pre clustered 1 / 19 batches
Warning: data batch #2 only had 0 spikes

In clusterSingleBatches (line 95)
In ksGUI/runSpikesort (line 782)
In ksGUI/runAll (line 628)
In ksGUI>@(,)obj.runAll() (line 319)
Warning: data batch #3 only had 0 spikes

In clusterSingleBatches (line 95)
In ksGUI/runSpikesort (line 782)
In ksGUI/runAll (line 628)
In ksGUI>@(,)obj.runAll() (line 319)
Warning: data batch #4 only had 0 spikes

In clusterSingleBatches (line 95)
In ksGUI/runSpikesort (line 782)
In ksGUI/runAll (line 628)
In ksGUI>@(,)obj.runAll() (line 319)
Warning: data batch #5 only had 0 spikes

In clusterSingleBatches (line 95)
In ksGUI/runSpikesort (line 782)
In ksGUI/runAll (line 628)
In ksGUI>@(,)obj.runAll() (line 319)
Warning: data batch #6 only had 0 spikes

In clusterSingleBatches (line 95)
In ksGUI/runSpikesort (line 782)
In ksGUI/runAll (line 628)
In ksGUI>@(,)obj.runAll() (line 319)
Warning: data batch #7 only had 0 spikes

In clusterSingleBatches (line 95)
In ksGUI/runSpikesort (line 782)
In ksGUI/runAll (line 628)
In ksGUI>@(,)obj.runAll() (line 319)
Warning: data batch #8 only had 0 spikes

In clusterSingleBatches (line 95)
In ksGUI/runSpikesort (line 782)
In ksGUI/runAll (line 628)
In ksGUI>@(,)obj.runAll() (line 319)
Warning: data batch #9 only had 0 spikes

In clusterSingleBatches (line 95)
In ksGUI/runSpikesort (line 782)
In ksGUI/runAll (line 628)
In ksGUI>@(,)obj.runAll() (line 319)
Warning: data batch #10 only had 0 spikes

In clusterSingleBatches (line 95)
In ksGUI/runSpikesort (line 782)
In ksGUI/runAll (line 628)
In ksGUI>@(,)obj.runAll() (line 319)
Warning: data batch #11 only had 0 spikes

In clusterSingleBatches (line 95)
In ksGUI/runSpikesort (line 782)
In ksGUI/runAll (line 628)
In ksGUI>@(,)obj.runAll() (line 319)
Warning: data batch #12 only had 0 spikes

In clusterSingleBatches (line 95)
In ksGUI/runSpikesort (line 782)
In ksGUI/runAll (line 628)
In ksGUI>@(,)obj.runAll() (line 319)
Warning: data batch #13 only had 0 spikes

In clusterSingleBatches (line 95)
In ksGUI/runSpikesort (line 782)
In ksGUI/runAll (line 628)
In ksGUI>@(,)obj.runAll() (line 319)
Warning: data batch #14 only had 0 spikes

In clusterSingleBatches (line 95)
In ksGUI/runSpikesort (line 782)
In ksGUI/runAll (line 628)
In ksGUI>@(,)obj.runAll() (line 319)
Warning: data batch #15 only had 0 spikes

In clusterSingleBatches (line 95)
In ksGUI/runSpikesort (line 782)
In ksGUI/runAll (line 628)
In ksGUI>@(,)obj.runAll() (line 319)
Warning: data batch #16 only had 0 spikes

In clusterSingleBatches (line 95)
In ksGUI/runSpikesort (line 782)
In ksGUI/runAll (line 628)
In ksGUI>@(,)obj.runAll() (line 319)
Warning: data batch #17 only had 0 spikes

In clusterSingleBatches (line 95)
In ksGUI/runSpikesort (line 782)
In ksGUI/runAll (line 628)
In ksGUI>@(,)obj.runAll() (line 319)
Warning: data batch #18 only had 0 spikes

In clusterSingleBatches (line 95)
In ksGUI/runSpikesort (line 782)
In ksGUI/runAll (line 628)
In ksGUI>@(,)obj.runAll() (line 319)
Warning: data batch #19 only had 0 spikes

[marius10p]

Looks like it wasn't able to find any spikes. I recommend a few things, try these one by one:

1. use much longer recording
2. increase batch size by 10x or 100x
3. set ops.minfr_goodchannels = 0 so it doesn't drop channels
4. try the latest Kilosort2.5.

[GoktugAlkan]

Hello @marius10p @AamnaLawrence ,

I am currently struggling with running KS 2.5 with a single-channel recording. The data is approximately 10 minutes long and there are spikes inside. KS 1.0 was able to detect those.

As in KS 1.0 I am inserting the data into a format with 3 dummy channels (zero signals). The fourth channel has the actual data. This described procedure is the same as in KS 1.0, which delivered good results. Since we assume that the template-matching might have improved, we want to switch to KS 2.5. However, adding the dummy channels leads to problems in KS 2.5. The error message that I get is below:

Error using matlab.internal.math.interp1
The sample points must be finite.

Error in interp1 (line 188)
        VqLite = matlab.internal.math.interp1(X,V,method,method,Xqcol);

Error in shift_batch_on_disk2 (line 14)
    shifts = interp1(ysamp, shifts, rez.yc, 'makima', 'extrap');

Error in datashift2 (line 138)
        dprev = shift_batch_on_disk2(rez, ibatch, dshift(ibatch, :), yblk, sig, dprev);

Error in testKS25 (line 130)
rez = datashift2(rez, 1); % last input is for shifting data

Do you have any ideas? Many thanks!