Link Search Menu Expand Document

Ground truth data tutorial

CellExplorer contains a select set of ground truth data located in +groundTruthData/. This tutorial will guide you through using the ground truth data included with CellExplorer.

  1. Launch CellExplorer
  2. From the top menu Ground truth, select Define ground truth data. This will display the dialog below with a list of ground truth cells from the +groundTruthData/ folder. The data is orgazied by sessions, where each session contains at least one tagged cell but can contain more.
  3. Select the cells you would like to load as ground truth data, press OK and the data will be loaded.
  4. From the Ground truth menu, you can select how to display the ground truth data: as scatter points, as a density map (image), or double histograms.
  5. You can select which of the ground truth cell types to display in the Display Settings tab group GroundTruth at the bottom of the right panel in CellExplorer.

Once a selection has been made, you can skip step 2 and 3. If you have data that you are interested in sharing please contact us. See the opto-tagging tutorial for how to analyse and add your own data to the ground truth selection. The ground truth cells are labeled in cell_metrics.groundTruthClassification. The video below shows the above steps in CellExplorer: