The most common PanoBrain configuration captures two channels per section:
- Channel 1 (DAPI): Labels all nuclei, providing the reference for cell detection and total cell counts
- Channel 2 (GFP or another reporter): Labels the population of interest (transduced neurons, transgenic cells, activity-dependent expression)
Because both channels are captured at the same tile positions, they are co-registered by construction. Each DAPI nucleus can be checked directly for GFP signal without aligning the images.