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Added support for cluster_KSLabel.tsv' #11

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Added support for cluster_KSLabel.tsv' #11

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dd1fc1f
Added support for cluster_KSLabel.tsv'
peterzh Apr 1, 2020
fdf55bc
Added some documentation
peterzh Apr 16, 2020
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32 changes: 30 additions & 2 deletions preprocessing/phyHelpers/loadKSdir.m
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Original file line number Diff line number Diff line change
@@ -1,6 +1,30 @@


function spikeStruct = loadKSdir(ksDir, varargin)
% spikeStruct = loadKSdir(ksDir) loads kilosorted ephys data. Input
% argument should be a path to a folder containing the output kilosort.
% The output spikeStruct contains the following data:
%
% -dat_path, n_channels_dat, dtype, offset, sample_rate, hp_filtered: these
% are parameter variables associated with the recording. Most variables are
% self-explanatory.
% -st: vector of all spike event times
% -spikeTemplates: vector of the template identity associated with each
% spike event. [0 indexed]
% -clu: vector of cluster IDs associated with each spike event. This can
% differ from spikeTemplates because spikes from multiple kilosort
% templates can be merged. Or spikes from one template can be split into
% separate clusters.
% cluster (same value in clu).
% -tempScalingAmps: vector of scaling factors associated with each spike
% event. This value reflects how much the kilosort template for the cluster
% was scaled to match the waveform of each spike event.
% -cids: list of cluster IDs
% -xcoords, ycoords: location of each channel on the probe
% -temps: clusterID x time x channel matrix, containing the kilosort
% template for each cluster.
% -winv: whitening matrix used to ensure all channels have the same
% variance.
% -pcFeat: PCA analysis on spike statistics
% -pcFeatInd: PCA analysis on spike statistics

if ~isempty(varargin)
params = varargin{1};
Expand Down Expand Up @@ -39,13 +63,17 @@
pcFeatInd = [];
end

%Load phy annotation labels (cluster_groups.csv or .tsv)
cgsFile = '';
if exist(fullfile(ksDir, 'cluster_groups.csv'))
cgsFile = fullfile(ksDir, 'cluster_groups.csv');
end
if exist(fullfile(ksDir, 'cluster_group.tsv'))
cgsFile = fullfile(ksDir, 'cluster_group.tsv');
end
if exist(fullfile(ksDir, 'cluster_KSLabel.tsv'))
cgsFile = fullfile(ksDir, 'cluster_KSLabel.tsv');
end
if ~isempty(cgsFile)
[cids, cgs] = readClusterGroupsCSV(cgsFile);

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