How to visualize cell-cell interactions

This guide shows you how to use the Pair Signal Viewer to inspect the signals of interacting cell pairs.

Reference keys: neighborhood, pair measurements

Prerequisite: You must have computed neighborhoods and enabled MEASURE PAIRS.

Open the Pair Signal Viewer

Open the Interactions section in the control panel.
Click the button next to the MEASURE PAIRS checkbox (or the relevant pair protocol).

Note

The viewer adapts the standard Signal Annotator interface to show both reference and neighbor populations simultaneously.

The viewer displays the movie with both cell populations overlaid.

Select a Reference Cell: Click on a cell from the reference population.
- All other reference cells will be hidden (colored black) to reduce clutter.
- The selected cell remains visible.
- Valid pairs involving this cell are displayed as dynamic segments connecting the reference cell to its neighbors.
Select a Pair: Click on the segment center or directly on the neighbor cell.
- The signal plot panel (left) updates to show traces for this specific pair.
Inspect Signals: The plot canvas displays:
- Reference Signal: The signal of the reference cell.
- Neighbor Signal: The signal of the neighbor cell.
- Pair Signal: Derived pair metrics (e.g., distance, angle) if selected.
You can toggle visibility of each trace using the legend or dropdown menus.

Color Coding: Use the control panel to change the color coding for each population independently (e.g., by “class” or “status”).
Navigation: Use the standard Signal Annotator Shortcuts (Space to play, arrows to step).