updating pipelines

eaj_qualityMetrics_pipeline.m

@@ -9,15 +9,15 @@
 %% set paths
 clearvars
 probe = 0;
-sessions = readtable('D:\WT_Sequences\all_sessions.csv');
-for s = 201:height(sessions) %[97,101-200]
+sessions = readtable('Z:\WT_Sequences\2024_winter\Preprocessed_Data\Provenance\all_sessions.csv');
+for s = 1:height(sessions)
     epoch = string(sessions{s,'Epoch'});
     rec_error = string(sessions{s,'Recording_Error'});
-    if strcmp(epoch, 'g1') && strcmp(rec_error, 'FALSE')
+    if strcmp(epoch, 'g0') && strcmp(rec_error, 'FALSE')
         % generate the path to the directory containing the ap.bin file
         base_dir = string(sessions{s,'Base_Directory'});
         base_dir = strrep(base_dir, '/', '\');
-        ecephys_path = strcat(base_dir, '\Preprocessed_Data\Spikes\g1');
+        ecephys_path = strcat(base_dir, '\Preprocessed_Data\Spikes');
 
         rec_file_stem = split(string(sessions{s,'File'}),'/');
         rec_file_stem = convertStringsToChars(rec_file_stem(2));

eaj_qualityMetrics_pipeline_2point0.m

@@ -8,9 +8,8 @@
 
 %% set paths
 clearvars
-%%%sessions = readtable('D:\WT_Sequences\all_sessions.csv');
-sessions = readtable('Z:\WT_Sequences\2023_spring\Preprocessed_Data\Provenance\all_sessions.csv');
-for s = 350
+sessions = readtable('Z:\WT_Sequences\2024_winter\Preprocessed_Data\Provenance\all_sessions.csv');
+for s = 1:height(sessions)
     task = string(sessions{s,'Task'});
     rec_error = string(sessions{s,'Recording_Error'});
     for probe = 0:1

eaj_qualityMetrics_pipeline_WenSorscher2023.m

@@ -0,0 +1,58 @@
+%% ~~ EAJ bombcell pipeline ~~
+% Adjust the paths in the 'set paths' section and the parameters in bc_qualityParamValues
+% This pipeline will run bombcell on your data and save the output
+
+addpath(genpath("C:\Users\Niflheim\Documents\GitHub\External\bombcell"))
+addpath(genpath("C:\Users\Niflheim\Documents\GitHub\External\npy-matlab"))
+addpath(genpath("C:\Users\Niflheim\Documents\GitHub\External\prettify_matlab"))
+
+%% set paths
+clearvars
+sessions = readtable('//oak-smb-giocomo.stanford.edu/groups/giocomo/export/data/Projects/JohnKei_NPH3/WenSorscher2023_revisions/all_sessions.csv');
+    %'Z:\WT_Sequences\2023_spring\Preprocessed_Data\Provenance\all_sessions.csv'
+for s = 29
+    %rec_error = string(sessions{s,'Recording_Error'});
+    for probe = 0
+        % generate the path to the directory containing the ap.bin file
+        base_dir = string(sessions{s,'Base_Directory'});
+        base_dir = strrep(base_dir, '/', '\');
+        ecephys_path = base_dir;
+
+        rec_file_stem = split(string(sessions{s,'File'}),'/');
+        rec_file_stem = convertStringsToChars(rec_file_stem);
+        rec_file_path = sprintf('%s\\%s\\SuperCat\\%s\\supercat_%s\\%s_imec%d',...
+            ecephys_path, string(sessions{s,'Animal'}),...
+            rec_file_stem(1:end-3), rec_file_stem,...
+            rec_file_stem, probe);
+
+        % set variables for BombCell
+        mainDir = rec_file_path;
+        ephysKilosortPath = sprintf('%s/imec%d_ks',rec_file_path,probe);
+        rec_file_base = sprintf('%s/%s_tcat.imec%d.ap',rec_file_path,rec_file_stem, probe);
+        rawFile = [rec_file_base,'.bin'];
+        ephysMetaFile = [rec_file_base,'.meta'];
+
+        saveLocation = mainDir;
+        savePath = fullfile(saveLocation, 'qMetrics');
+
+        % load data
+        [spikeTimes_samples, spikeTemplates, templateWaveforms, templateAmplitudes, pcFeatures, ...
+            pcFeatureIdx, channelPositions] = bc_loadEphysData(ephysKilosortPath);
+
+        % which quality metric parameters to extract and thresholds
+        param = eaj_qualityParamValues(ephysMetaFile, rawFile, ephysKilosortPath);
+        % param = bc_qualityParamValuesForUnitMatch(ephysMetaDir, rawFile) % Run this if you want to use UnitMatch after
+
+        %% compute quality metrics
+        [qMetric, unitType] = bc_runAllQualityMetrics(param, spikeTimes_samples, spikeTemplates, ...
+            templateWaveforms, templateAmplitudes,pcFeatures,pcFeatureIdx,channelPositions, savePath);
+
+        %% save to cluster_group.tsv
+        % overwrite ecephys cluster labels if any units were found to be noise
+        cluster_group_file = [ephysKilosortPath filesep 'cluster_group.tsv'];
+        cluster_group = readtable(cluster_group_file, 'FileType', 'text', 'Delimiter', '\t');
+        cluster_group(unitType==0,'group') = {'noise'};
+        writetable(cluster_group, cluster_group_file, 'FileType', 'text', 'Delimiter', '\t');
+
+    end
+end