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 other 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 inherently co-registered — each DAPI nucleus can be directly checked for GFP signal without image alignment.