Manual curation tutorial

This tutorial will guide you through the manual cell-type curation process in CellExplorer.

  1. Launch CellExplorer
    cell_metrics = CellExplorer('metrics',cell_metrics); 
  2. Navigate the cells using the keyboard, the graphical buttons, or by left-clicking the plots.
  3. Assign cell types from the Cell Assignment side menu using your mouse or the numeric keys (not the keypad). You can add new cell types by pressing + Cell-type. You can also do group assignment via the group action menu:
    • Select cell(s) and press space to open the group actions menu.
    • Click the middle mouse button on any of the CellExplorer plots to start drawing a polygon using left mouse button circling the cells you want to select. This can be done from any of the plots. Finish the polygon by pressing the right mouse button. This will show the group action menu.
    • Pressing space without any cells selected will show a cell selection filter dialog. Select a filter and press OK to open the group actions menu.
  4. You can save your progress from the top menu File -> Save classification. This will save your metrics to the original session-wise cell_metrics files, even when working in batch mode.
  5. A dialog will be shown and you can select to update sessions with tracked changes or all of them.

All your classification actions are tracked, shown in the message log, and can be reversed step-wise by pressing ctrl+z. The pre-defined list of cell-types shown in CellExplorer is defined in CellExplorer_Preferences.m. Putative cell-types are stored in cell_metrics.putativeCellType. Cell types present in cell_metrics.putativeCellType will be added to the selection-list in CellExplorer. Default cell-type colors are defined in CellExplorer_Preferences.m. Learn more about preferences and the interface below.

Preferences Graphical interface