We have the following filters available for fluorescent scanning in the Pannoramic 250 and Zeiss Axio z.1 scanners:
| Filter set | Excitation filter | Dichroic mirror | Emission filter |
| DAPI cube (Zeiss Filter Set 02) | G365 | FT395 | LP420 |
| FITC cube (Zeiss Filter Set 38 HE) | BP470/40 (HE) | FT495 (HE) | BP525/50 (HE) |
| Cy3 cube (Chroma Technology Corp 49004 ET CY3/R) | ET545/25x | T565lpxr | ET605/70m |
| Cy5 cube (Chroma Technology Corp 49006 ET CY5) | ET620/60x | T660lpxr | ET700/75m |
| Cy7 cube (Chroma Technology Corp 49007 ET CY7) | ET710/75x | T760lpxr | ET810/90m |