Link Search Menu Expand Document

General tutorial

This tutorial shows you the full processing pipeline, from generating the necessary session metadata from the template, running the processing pipeline, opening multiple sessions for manual curation in CellExplorer, and finally using the cell_metrics for filtering cells, by two different criteria. The tutorial is also available as a Matlab script: (tutorials/CellExplorer_Tutorial.m).

  1. Define the basepath of the dataset to run. The dataset should at minimum consist of the raw data basename.dat, and spike sorted data. An optional Neuroscope compatible basename.xml can also be used.
    basepath = '/your/data/path/basename/';
  2. Generate session metadata struct using the template function and display the metadata in a GUI
    session = sessionTemplate(basepath,'showGUI',true);
  3. Run the cell metrics pipeline ProcessCellMetrics using the session struct as input
    cell_metrics = ProcessCellMetrics('session', session);
  4. Visualize the cell metrics in CellExplorer
    cell_metrics = CellExplorer('metrics',cell_metrics); 
  5. Open several session from paths
    basenames = {'Rat08-20130708','Rat08-20130709'};
    basepaths = {'/Volumes/buzsakilab/Buzsakilabspace/Datasets/GirardeauG/Rat08/Rat08-20130708','/Volumes/buzsakilab/Buzsakilabspace/Datasets/GirardeauG/Rat08/Rat08-20130709'};
    cell_metrics = loadCellMetricsBatch('basepaths',basepaths,'basenames',basenames);
    cell_metrics = CellExplorer('metrics',cell_metrics);
  6. Curate your cells and save the metrics
  7. load a subset of units fulfilling multiple criteria
    1. Get cells that are assigned as Interneuron
      cell_metrics_idxs1 = loadCellMetrics('cell_metrics',cell_metrics,'putativeCellType',{'Interneuron'});
    2. Get cells that are has groundTruthClassification as Axoaxonic
      cell_metrics_idxs2 = loadCellMetrics('cell_metrics',cell_metrics,'groundTruthClassification',{'Axoaxonic'});