.. _visualize-cell-interactions: 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: :term:`neighborhood`, :term:`pair measurements` **Prerequisite:** You must have computed :doc:`neighborhoods ` and enabled **MEASURE PAIRS**. Open the Pair Signal Viewer ~~~~~~~~~~~~~~~~~~~~~~~~~~~ #. Open the **Interactions** section in the control panel. #. Click the :icon:`eye-check,black` 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. Visualizing Pairs ~~~~~~~~~~~~~~~~~ The viewer displays the movie with both cell populations overlaid. 1. **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. 2. **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. 3. **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. Customizing the View ~~~~~~~~~~~~~~~~~~~~ * **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 :ref:`Signal Annotator Shortcuts ` (Space to play, arrows to step).