|The normal mode, in which only images from the current section (called "layer" in TrakEM2) are shown.
In this example, the top-left image is selected and thus a white frame paints around it.
|The color overlay mode, activated from the "Layers" tab via right-click popup menu, paints the current layer in green, and one or two other arbitrary layers in the red and blue channels.
When scrolling through layers, the relative position of the red and blue layers is preserved. See this video.
|The alpha overlay mode, activated by dragging the sliders of any layer panel in the "Layers" tab, paints all those other layers with the desired degree of transparency over the current layer, the latter always at 100% opacity.
For the alpha overlays to operate, color overlays must be disabled (again from popup menu over the layer panels to the left).