How to compare collapsed measurements across conditions

This guide explains how to aggregate single-cell track data (e.g., computing the time-average of a signal) and compare it across different experimental conditions using Boxplots and Stripplots.

Prerequisites

  • You have tracked cells and generated measurement tables.

  • Your experiment has conditions (e.g., different treatments per well) loaded as columns (e.g., derived from [Labels] in config.ini).

Step 1: Open the Table Explorer

  1. Select your experiment or specific position.

  2. Open the Analysis tab.

  3. Click Table Explorer (or access it via the Measurement results).

Step 2: Collapse Tracks

Transform the data from “one row per timepoint” to “one row per track”.

  1. Press Ctrl+G or select File > Collapse tracks….

  2. In the dialog: * Operation: Select mean (for time-average), max, or another statistic.

  3. Click OK. * Result: The table updates. Rows now represent individual cells (Tracks). New columns like mean_mean_intensity appear. Columns that are constant per track (like well_id or treatment) are preserved.

Step 3: Plot by Condition

  1. Select the Condition Column first (Categorical, e.g., well_name).

  2. Hold Ctrl and select the Measurement Column (Numerical, e.g., mean_mean_intensity). * Note: The order of selection often determines X and Y axes. Condition (X) vs Measurement (Y).

  3. Press Ctrl+P or select File > Plot….

Step 4: Configure the Visualization

  1. The plotting window opens.

  2. In the Plot Type dropdown, select Box Plot.

  3. To show individual data points, check the Stripplot option (or select Strip Plot to view it alone).

  4. (Optional) Use the Hue dropdown to subdivide the boxplots by another category (e.g., replicate).

  5. Check Show stats if you wish to display statistical comparisons (e.g., p-values between boxes).

Step 5: Export

  • Click the Save Icon in the plot window to export the figure.

  • Or press Ctrl+S in the Table Explorer to save the collapsed data table to CSV.