Spectra viewer



Filters, mirrors and light sources


Custom spectra

Use csv files with two or four columns (wavelength, value) and withouth header for data upload. Four columns will be interpreted as a combination of excitation and emission spectra.

Solid lines indicate missing scaling information in 'absolute' mode. Normalized data are shown.

This viewer provides a number of ways to explore and visualize properties of fluorescent molecules and optical elements (such as different types of filters and mirrors).

Selection tools

The left panel provides selection tools for three types of elements (top to bottom): Fluorophores, filters and custom elements. For the first two, dropdown menus ('Selection list') contain all the relevant items from the underlying database, which can be sorted/filtered using the 'Search' and 'Type' fields. Under 'Custom spectra', simple filters can be defined using center and bandwidth values; laser lines can be added; and spectra can be uploaded in form of csv-files.

New elements can be added to the corresponding tables using the '+' button. Table elements can be temporarily hidden by de-selecting them (mouse click on table row).

1D viewer

The '1D viewer' provides the standard view of excitation and emission spectra (excitation and emission values as a function of wavelength). Plots can be shown using either linear or logarithmic y-scale and with normalized or absolute values. For absolute values, the extinction coefficient, quantum yield and 2p action cross-section values are used for 1p excitation, emission and 2p excitation values respectively.

2D viewer

The '2D viewer' combines the excitation and emission data in form of 2D contour plots. This is particularly useful when comparing a large number of fluorophores, since it reduces the number of displayed elements and by making the pairing of related excitation and emission spectra implicit.

Filter spectra are omitted in this view, but 'Custom spectra' are displayed (uploaded spectra only if the file contains four columns which are interpreted as excitation and emission spectra).

Fluorophore browser

The 'Fluorophore browser' lists all available fluorophores together with their most relevant properties in table form. The table allows sorting and filtering each column using the sort / text field on top of each column. Fluorophores can be added from this table to the selection panel on the left.

A second table (below the fluorophore table) lists additional properties of the currently selected entry, such as information about the sources of the spectral data.

Scatter plot

The 'Scatter plot' enables display of up to four (scalar) fluorophore properties, as selected with the respective dropdown menues (x, y, size, color). Using this plot, in particular in combination with the filtering option of the Fluorophore browser makes it easy to identify fluorophores with specific combinations of properties (e.g. large stokes shift, short lifetime, emission around 600 nm, high quantum yield).

Spectra viewer by the Imaging facility at the MPI for Brain Research Frankfurt. Implemented by Stephan Junek.


Many thanks to Georgi Tushev and Friedrich Kretschmer for their help with setting up this app.

A large number of spectra in our database originated from the large collection of fluorescence spectra from George McNamara (George McNamara, Amit Gupta, James Reynaert, Thomas D Coates, Carl Boswell 2006 Spectral imaging microscopy web sites and data. Cytometry A 698 :863-871. doi: 10.1002/cyto.a.20304), which are publicly available. Many thanks for this fantastic resource!

Thanks to Urs Utzinger (University of Arizona) for providing his database (itself largely based on George's collection), as a starting point for our database. You can visit his new viewer here.

Thanks to Mikhail Drobizhev for providing 2p cross-section data for various fluorescent proteins (see also Drobizhev et al, Nat Methods 8, 2011). Data were created with support from the NIH grant U24 NS109107.

Thanks to Ronak Patel for providing spectral data for various Janelia fluorophores and Ca2+-indicators developed at Janelia farm

Additional data were added from various sources. Source information and references can be found in the Fluorophore properties table of the Fluorophore browser tab.


If you would like to contribute to the app or database (bug reports, additional spectra or meta-data, feature requests) please contact us at stephan.junek [at] brain.mpg.de