A fluorescence spectra viewer lets you overlay the excitation and emission spectra of fluorophores so you can design a flow cytometry or microscopy panel, match dyes to your laser and filter set, and avoid spectral overlap. Below are the best current viewers and a guide to using them well.
Fluorescence spectra viewers
- BD Spectrum Viewer — overlay excitation/emission curves, lasers and filters; strong for flow cytometry panel design.
- Thermo Fisher SpectraViewer — large dye library with laser/filter overlays and panel tools.
- FPbase Spectra Viewer — open, comprehensive, especially good for fluorescent proteins and microscopy.
What to check when choosing fluorophores
- Excitation vs your laser lines. A dye should be efficiently excited by a laser your instrument actually has (e.g. 488, 561, 640 nm).
- Emission vs your filters. The emission peak should fall within a detector’s bandpass filter.
- Spectral overlap (spillover). When emission curves of two dyes overlap, signal bleeds between channels and needs compensation. Pick dyes with well-separated emission where possible.
- Brightness for low-abundance targets; reserve the brightest dyes for the dimmest markers.
How to use a spectra viewer
- Add each fluorophore in your planned panel.
- Turn on your instrument’s laser lines and filter sets (most viewers let you select a configuration).
- Look for emission overlaps between dyes detected on adjacent channels — minimise them or plan compensation.
- Confirm each dye is excited by an available laser and detected by an available filter.
Frequently asked questions
What is a fluorescence spectra viewer for?
To visualise excitation and emission spectra of fluorophores so you can build a panel that matches your instrument’s lasers and filters and minimises spectral overlap.
How do I avoid spectral overlap?
Choose dyes whose emission peaks are well separated and detected on different channels; where overlap is unavoidable, plan compensation (or use spectral cytometry).
Which viewer should I use?
Any of the three above works; use BD or Thermo for flow cytometry dye libraries, and FPbase for fluorescent proteins and microscopy.
