preferences_ProcessCellMetrics.m

function preferences = preferences_ProcessCellMetrics(session)
% Preferences loaded by ProcessCellMetrics
%
% Check the website of CellExplorer for more details: https://cellexplorer.org/

% By Peter Petersen
% Last edited: 10-11-2022

% General
preferences.general.probesVerticalSpacing = 20; % 20um spacing between channels
preferences.general.probesLayout = 'poly2';     % Default probe layout

% Loading spike data
preferences.loadSpikes.labelsToRead = {'good'}; % allows you to load units with various labels, e.g. MUA or a custom label

% Waveform
preferences.waveform.nPull = 600;               % number of spikes to pull out (default: 600)
preferences.waveform.wfWin_sec = 0.004;         % Larger window of the waveform for filtering (to avoid edge effects). Total width in seconds [default 4ms]
preferences.waveform.wfWinKeep = 0.0008;        % half width of the waveform. In seconds [default 0.8ms]
preferences.waveform.trilat_nChannels = 16;     % Maximum number of channels used for trilateration 
preferences.waveform.showWaveforms = true;

% PSTHs / Events / Manipulations (the standard preferences for PSTHs)
preferences.psth.binCount = 100;                     % how many bins (for half the window)
preferences.psth.alignment = 'onset';                % alignment of time ['onset','center','peaks','offset']
preferences.psth.binDistribution = [0.25,0.5,0.25];  % How the bins should be distributed around the events, pre, during, post. Must sum to 1
preferences.psth.intervals = [nan,nan,nan];          % Define specific intervals to be applied. Must be a 1x3 vector [in seconds]
preferences.psth.duration = nan;                     % duration of PSTH (for half the window - used in CCG) [in seconds]
preferences.psth.smoothing = 5;                      % any gaussian smoothing to apply? units of bins.
preferences.psth.percentile = 99;                    % if events does not have the same length, the event duration can be determined from percentile of the distribution of events

% PSTH for ripples (custom preferences for events. below preferences are applied for the PSTHs calculated for ripples)
preferences.psth.ripples.binCount = 150;                    % how many bins (for half the window)
preferences.psth.ripples.alignment = 'peaks';               % alignment of time ['onset','center','peaks','offset']
preferences.psth.ripples.binDistribution = [0.25,0.5,0.25]; % How the bins should be distributed around the events, pre, during, post. Must sum to 1
preferences.psth.ripples.intervals = [nan,nan,nan];         % Define specific intervals to be applied. Must be a 1x3 vector [in seconds]
preferences.psth.ripples.duration = 0.150;                  % duration of PSTH (for half the window - used in CCG) [in seconds]
preferences.psth.ripples.smoothing = 5;                     % any gaussian smoothing to apply? units of bins.
preferences.psth.ripples.percentile = 99;                   % if events does not have the same length, the event duration can be determined from percentile of the distribution of events

% ACG metrics
preferences.acg_metrics.population_modIndex = true;

% Other
preferences.other.firingRateAcrossTime_binsize = 3*60;      % 180 seconds default bin_size

% PutativeCellType
% Default classification schema:
preferences.putativeCellType.classification_schema = 'standard'; % You may select and define your own schema. The classification schemas are loaded from +celltype_classification

% By default cells are reassigned as interneurons by below criteria
% 1. narrow interneurons are assigned if troughToPeak <= 0.425ms
preferences.putativeCellType.troughToPeak_boundary = 0.425; % 
% 2. the remaining cells are assigned as wide interneurons if acg_tau_rise > 6ms:
preferences.putativeCellType.acg_tau_rise_boundary = 6;
% Remaining cells are classified as pyramidal cells

% PCA

% ACG

% monoSynaptic_connections

% Spatial

% % % % % % % % % % % % % % % % % % % %
% Hippocampal preferences
% % % % % % % % % % % % % % % % % % % %
% Deep superficial 
preferences.deepSuperficial.ripples_durations = [20 150]; % in ms
preferences.deepSuperficial.ripples_passband = [80 240]; % in Hz

% Theta oscillation metrics
preferences.theta.bins = [-1:0.05:1]*pi; % theta bins from -pi to pi
preferences.theta.speed_threshold = 10;  % behavioral running speed (cm/s)
preferences.theta.min_spikes = 500;      % only calculated if the unit has above 500 spikes

% % % % % % % % % % % % % % % % % % % %
% User preferences 
% % % % % % % % % % % % % % % % % % % % 
% You may edit above preferences or provide your own preferences in a separate file.
% Provide the path to your preferences as an analysis tag in the session struct: 
% session.analysisTags.preferences_ProcessCellMetrics = 'user_preferences.my_preferences'; % loads the my_preference.m file from the folder +user_preferences

if exist('session','var') && isfield(session,'analysisTags') && isfield(session.analysisTags,'preferences_ProcessCellMetrics') && ~isempty(which(session.analysisTags.preferences_ProcessCellMetrics))
    preferences = feval(session.analysisTags.preferences_ProcessCellMetrics,preferences,session);
end