Mismatch between channel and cluster IDs?

Hi Cyrille,

1. How does Phy2 determine the channel number of a given cluster displayed under ClusterView? I thought that the correct way was to determine the channel which had the biggest template amplitude for each cluster. This seemed to be working in Phy1 but not in Phy2. An adaptation of my matlab code goes below.

2. Under clusterView, the best channel for a given cluster seems to be mismatched. In the attached picture, you can see that even though channel 2 wasn’t include in this analysis, clusters 3, 4 and 5 indicate it as the best one.

Thanks!

% Load kilosort2 results
results_dir = 'D:\DataAnalysis\Kilosort2\monkey\ephys_2018_03_05_1452\Results';
channel_map = double(readNPY(fullfile(results_dir,'channel_map.npy')));
templates = double(readNPY(fullfile(results_dir,'templates.npy')));
spike_templates = double(readNPY(fullfile(results_dir,'spike_templates.npy')));

% Preallocate clusters_n_channels array
[n_clusters, ~, n_channels] = size(templates);
clusters_n_channels = nan(n_clusters,2);

% Determine cluster Ids
unique_spike_templates = unique(spike_templates);
clusters_n_channels(unique_spike_templates + 1, 1) = unique_spike_templates;

% Choose the channel which has the biggest template amplitude for each cluster
for i_clusters = 1 : n_clusters
    max_amplitude_channel_ind = 1;
    max_amplitude_template = max(templates(i_clusters, :, max_amplitude_channel_ind)) - min(templates(i_clusters, :, max_amplitude_channel_ind));
    for i_channels = 2 : n_channels
        temp_max_amplitude_template = max(templates(i_clusters, :, i_channels)) - min(templates(i_clusters, :, i_channels));
        if temp_max_amplitude_template > max_amplitude_template
            max_amplitude_template = temp_max_amplitude_template;
            max_amplitude_channel_ind = i_channels;
        end
    end
    clusters_n_channels(i_clusters, 2) = channel_map(max_amplitude_channel_ind);
end

[rossant]

closing, please reopen if new issues arise

[JoseGuzman]

I will have to reopen the issue for a minor detail. The TraceView channel ordering will not work if phy is called when >1 probes are analyzed simultaneously. This is after using spyking-circus sorted (latest developmental version).

Attached you can find a screenshot with the most updated developmental version of phy. Channels must be 1-64 ordered in traceView. Note that WaveformView and ProbeView shows the right numeration