How to measure edge intensity

This guide shows you how to measure intensity features within specific contour bands relative to the cell boundary (e.g., peripheral or peri-cellular intensity).

Reference keys: contour, single-cell measurement

Prerequisite: You must have segmented the cells. Tracking is recommended but not required.

Enable contour measurements

  1. Open the Measure tab for your population of interest.

  2. In the measurement settings, locate the Contour section.

  3. Check the Contour option.

Configure the contour band

  1. Channel: Select the intensity channel to measure.

  2. Distance \(d\) (pixels): define the offset from the mask edge.

    • Positive values (\(d > 0\)) measure inside the cell (erosion from the boundary).

    • Negative values (\(d < 0\)) measure outside the cell (dilation beyond the boundary).

  3. Range (min, max): define a specific ring band using distance transforms. For example, (0, 5) measures a 5-pixel-wide ring at the cell edge.

Run the measurements

  1. Click Set to save the configuration.

  2. In the control panel, check the MEASURE box and click Submit.

The contour intensity features (e.g., intensity_mean, intensity_max) for the selected band will be appended to your measurement table with a suffix indicating the contour distance.

Tip

Combine a positive and negative distance to measure both inside and outside the cell boundary, which is useful for quantifying membrane-associated signals.