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Perform custom analysis directly from NeuroScope2

You can add your own custom functions that can be run from NeuroScope2 from the menu called Analysis. You must create a wrapper function for what you want to call outside NeuroScope2. There are a lot of examples included, that you can take inspiration from. The analysis tools are located in the +analysis_tools folder. Please see the wrapper example at the bottom of this page.

Organization of analysis tools and included functions

The analysis menu and underlying +analysis_tools folder are organized according to the underlying data types of CellExplorer. Various functions are already included:

behavior:

  • 2D and
  • 3D plot of behavior

cell_metrics

  • run ProcessCellMetrics
  • open CellExplorer
  • Plot metrics for a subset of cells, including CCGs and other built-in plots from CellExplorer

events

  • detect ripples. Shows a dialog first, allowing for defining input parameters

lfp

  • generate the .lfp file from the raw data

session

  • Plot channel coordinates

spikes

  • Detect monosynaptic connections
  • plot CCGs
  • plot spike-rasters

states

  • Detect brain states using SleepScoreMaster - requires the Buzcode toolbox.
  • Edit brain states in TheStateEditor - requires the Buzcode toolbox.

timeseries

  • open StateExplorer

traces

  • Plot correlation between channels
  • Plot RMS noise across channels
  • Show power spectral density across channels on a linear scale
  • Show power spectral density across channels on a log scale
  • Show temporal offsets between channels

The folder structure is purely for organization but the names are hard-coded in NeuroScope2, so they should not be altered.

Wrapper example provided

The wrapper example is located in the +traces folder (wrapper_example.m), use it to built your own analysis functions.

function out = wrapper_example(varargin)
% This is a wrapper example file for NeuroScope2. 
% Use this wrapper example to make calls from NeuroScope to any other analysis that can be applied to the traces, raw data or any derived data types.
% This function can be called from NeuroScope2 via the menu Analysis 

p = inputParser;

% The inputs are NeuroScope2 variables:
addParameter(p,'UI',[],@isstruct); % UI: struct with UI elements and settings of NeuroScope2
addParameter(p,'ephys',[],@isstruct); % ephys: Struct with ephys data for current shown time interval, e.g. ephys.raw (raw unprocessed data), ephys.traces (processed data)
addParameter(p,'data',[],@isstruct); % data: contains all external data loaded like data.session, data.spikes, data.events, data.states, data.behavior
parse(p,varargin{:})

ephys = p.Results.ephys;
UI = p.Results.UI;  
data = p.Results.data;

out = [];

% % % % % % % % % % % % % % % %
% Function content below
% % % % % % % % % % % % % % % % 

% Your function content should go here