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interneuron classification for full cohort
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,39 +1,65 @@ | ||
| %% set session | ||
| animal = 'BaggySweatpants'; | ||
| session_name = '20220214_BaggySweatpants_DY01'; | ||
| basepath = ['Z:\WT_Sequences\2022_winter\Preprocessed_Data\Spikes\g1\',animal,'\Ecephys\',... | ||
| session_name,'\catgt_',session_name,'_g1\',session_name,'_g1_imec0']; | ||
| cd(basepath) | ||
| addpath(genpath("C:\Users\Niflheim\Documents\GitHub\External\CellExplorer")) | ||
|
|
||
| %% calculate | ||
| tic | ||
| % % set params | ||
| session = sessionTemplate(basepath); | ||
| session.extracellular.fileName = [session_name,'_g1_tcat.imec0.ap.bin']; | ||
| session.extracellular.srLfp = 2500; | ||
| % session = gui_session(session); | ||
| % validateSessionStruct(session); | ||
| % set session | ||
| sessions = readtable('D:\WT_Sequences\all_sessions.csv'); | ||
| start_gate = 1; | ||
| probe = 0; | ||
| for s = 1:height(sessions) | ||
| task = string(sessions{s,'Task'}); | ||
| rec_error = string(sessions{s,'Recording_Error'}); | ||
| if strcmp(task, 'X Maze') && strcmp(rec_error, 'FALSE') | ||
|
|
||
| % generate metrics file | ||
| cell_metrics = ProcessCellMetrics('session', session,... | ||
| 'metrics',{'monoSynaptic_connections'},... | ||
| 'includeInhibitoryConnections',true,... | ||
| 'manualAdjustMonoSyn',false,... | ||
| 'getWaveformsFromDat',false,... | ||
| 'showWaveforms',false,... | ||
| 'sessionSummaryFigure',false,... | ||
| 'showGUI',false); | ||
| toc | ||
| % generate the path to the directory containing the ap.bin file | ||
| base_dir = string(sessions{s,'Base_Directory'}); | ||
| % base_dir = strrep(base_dir, 'Z', 'D'); %while running off local drive | ||
| base_dir = strrep(base_dir, '/', '\'); | ||
| ecephys_path = strcat(base_dir, '\Preprocessed_Data\Spikes\g1'); | ||
|
|
||
| rec_file_stem = split(string(sessions{s,'File'}),'/'); | ||
| rec_file_stem = rec_file_stem(2); | ||
| rec_file_stem = convertStringsToChars(rec_file_stem); | ||
| rec_file_stem = rec_file_stem(1:end-3); | ||
| rec_file_path = sprintf('%s\\%s\\Ecephys\\%s\\catgt_%s_g%d\\%s_g%d_imec%d',... | ||
| ecephys_path, string(sessions{s,'Animal'}),... | ||
| rec_file_stem, rec_file_stem, start_gate,... | ||
| rec_file_stem, start_gate, probe); | ||
| cd(rec_file_path) | ||
|
|
||
| % set params | ||
| tic | ||
| session = sessionTemplate(rec_file_path); | ||
| % pass the ap.bin file name (not the path) | ||
| session.extracellular.fileName = sprintf('%s_g%d_tcat.imec%d.ap.bin', rec_file_stem, start_gate, probe); | ||
|
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||
| % generate metrics file | ||
| % session.extracellular.srLfp = 2500; %only necessary if running LFP metrics | ||
|
|
||
| % %% view | ||
| % cell_metrics = CellExplorer('metrics',cell_metrics); | ||
| % | ||
| % %% view from file | ||
| % animal = 'BaggySweatpants'; | ||
| % session_name = '20220214_BaggySweatpants_DY01'; | ||
| % basepath = ['Z:\WT_Sequences\2022_winter\Preprocessed_Data\Spikes\g1\',animal,'\Ecephys\',... | ||
| % session_name,'\catgt_',session_name,'_g1\',session_name,'_g1_imec0']; | ||
| % cd(basepath) | ||
| % monosynaptic connections only (fast) | ||
| % cell_metrics = ProcessCellMetrics('session', session,... | ||
| % 'metrics',{'monoSynaptic_connections'},... | ||
| % 'includeInhibitoryConnections',true,... | ||
| % 'manualAdjustMonoSyn',false,... | ||
| % 'getWaveformsFromDat',false,... | ||
| % 'showWaveforms',false,... | ||
| % 'sessionSummaryFigure',false,... | ||
| % 'showGUI',false); | ||
| % all interneuron metrics (slow_ | ||
| cell_metrics = ProcessCellMetrics('session', session,... | ||
| 'metrics',{'monoSynaptic_connections','waveform_metrics','acg_metrics'},... | ||
| 'includeInhibitoryConnections',true,... | ||
| 'manualAdjustMonoSyn',false,... | ||
| 'showWaveforms',false,... | ||
| 'sessionSummaryFigure',false,... | ||
| 'showGUI',false, ... | ||
| 'keepCellClassification',false); | ||
| % display GUI | ||
| % cell_metrics = CellExplorer('metrics',cell_metrics); | ||
| toc | ||
| end | ||
| end | ||
|
|
||
| %% view from file | ||
| % cd(rec_file_path) | ||
| % session = loadSession; | ||
| % cell_metrics = loadCellMetrics; | ||
| % cell_metrics = CellExplorer('metrics',cell_metrics); |