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
).
- 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 compatiblebasename.xml
can also be used.basepath = '/your/data/path/basename/'; cd(basepath)
- Generate session metadata struct using the template function and display the metadata in a GUI
session = sessionTemplate(basepath,'showGUI',true);
- Run the cell metrics pipeline
ProcessCellMetrics
using the session struct as inputcell_metrics = ProcessCellMetrics('session', session);
- Visualize the cell metrics in CellExplorer
cell_metrics = CellExplorer('metrics',cell_metrics);
- 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);
- Curate your cells and save the metrics
- load a subset of units fulfilling multiple criteria
- Get cells that are assigned as Interneuron
cell_metrics_idxs1 = loadCellMetrics('cell_metrics',cell_metrics,'putativeCellType',{'Interneuron'});
- Get cells that are has groundTruthClassification as Axoaxonic
cell_metrics_idxs2 = loadCellMetrics('cell_metrics',cell_metrics,'groundTruthClassification',{'Axoaxonic'});
- Get cells that are assigned as Interneuron