How to add a fluorophore

You can add a new fluorophore in 2 easy steps:

(1) Add the fluorophore excitation/emission spectra

Add the excitation and emission spectra to the data/fluorophore-spectra folder as tabulation-separated files (.tsv). The file name should be the fluorophore name followed by _ex or _em, respectively for excitation and emission spectra. For example, when adding the fluorophore GFP, two files should be added: GFP_ex.tsv and GFP_em.tsv.

Each file should contain two columns (with a header line):

• w is the wavelength in nanometers,
• and ri is the relative intensity in a.u.. Please, note that the relative intensity should be in the 0-1 range.

Check out the examples available in the default installation here.

(2) Updated the main fluorophore table

Update the data/fluorophores.tsv table by adding one line. The table contains 4 tabulation-separated columns:

• name is the fluorophore name,
• wex is the wavelength (in nm) of the excitation peak,
• wem is the wavelength (in nm) of the emission peak,
• and color is either "auto" (in which case the color will be calculated based on wem; if wem is not in the visible range the automatic color will be "black") or an hexadecimal color string of your choice (useful when wem is outside the visible range).

Check out the default fluorophores table here! In the case of EGFP, you would add a line like below:

EGFP 488    509 auto