Fluorescence Spectra Viewers
Posted On: Wednesday, February 11, 2015
It is useful to know the excitation and emission spectra of fluorophores to help in selecting lights and filters for fluorescence. Some web sites provide tabulations of excitation and emission maxima but we find it more helpful to be able to view full spectra, and ideally to overlay light source and filter characteristics. There are a number of sites that offer interactive graphical viewers – you can select fluorophores to plot their excitation/emission spectra, overlay light sources and filters, download data and plots, upload your own data, and more. Not all of the sites offer the same options. We have prepared the list below with summaries of capabilities to help you compare spectra viewers. If you know of any good viewers that we have missed please let us know by email or by leaving a comment.
Fluorofinder
Fluorophores: their own dyes, plus a good library
Light sources: no
Filters: no
Download data: no
Upload data: No
Notes:
– Tools for microscopy, flow cytometry, spectral analyzer
– Customization if open (free) account
– Can add laser lines and filter overlays to spectra for assessment
Tocris/Biotechne
Fluorophores: > 1,200
Light sources: Can add laser lines
Filters: Can add to graphs manually
Download data: Not currently
Upload data: No
Notes:
–
FPbase
Fluorophores: solid collection of ~165 fluorescent proteins and probes
Light sources: Yes, including lasers, LEDs, lamps
Filters: Yes – many
Download data: Not currently
Upload data: Can send new spectra for inclusion
Notes:
– Very convenient graphical interface
– Multiple tables and input formats available that can help in choosing solutions
– Extensive supplementary notes on fluorophores, including extinction coefficient, quantum yield, and brightness
Semrock SearchLight
Fluorophores: Large database of fluorophores – based on University of Arizona data set
Light sources: Yes, including lasers, LEDs, lamps
Filters: Semrock filter sets and individual filters
Download data: Yes, individual spectra or bulk download all currently displayed spectra in txt format in zip file
Upload data: Yes, into personal database that can be overlaid on existing data
Notes:
– Extensive plot editing tools
– Create account to save and share sessions
– Calculators to evaluate absolute and relative signals (i.e., brightness or system throughput) and signal-to-noise ratios (contrast) for combinations of filters, fluorophores, light sources, and detectors
University of Arizona
Fluorophores: >800 spectra
Light sources: Yes, including lasers, LEDs, lamps
Filters: Yes, including dichroic mirrors
Download data: Yes, csv format
Upload data: With password
Notes:
– Easy to overlay multiple spectra
– Can bulk download all displayed data
– Supplementary notes on fluorophores, light sources, filters, etc. where available
Site: Fluorophores.org
Fluorophores: >800 spectra
Light sources: No
Filters: No
Download data: Yes, csv format
Upload data: Yes (data reviewed before being added to the list, then publicly available)
Notes:
– Fluorophores searchable by Application, Dye Class, Excitation max, Emission max, Quantum Yield, Lifetime. Multiple spectra
– Supplementary data on fluorophores, including references
– A bit awkward to overlay data compared to other sites
Fluorescence SpectraViewer – ThermoFisher
Fluorophores: >800 spectra
Light sources: Yes, including lasers, mercury and xenon lamps
Filters: Excitation and emission, limited number
Download data: Yes, fluorophore data csv format, current graph as png
Upload data: No
Notes:
– Easy to overlay multiple spectra
Evrogen Spectra Viewer
Fluorophores: Evrogen’s line of fluorescent proteins
Light sources: No
Filters: No
Download data: No
Upload data: No
Notes:
– Choose laser or wide-field excitation
– Normalized and non-normalized to compare efficiencies
Chroma Spectra Viewer
Fluorophores: ~150 fluorophores
Light sources: No
Filters: Chroma filter sets and individual filters
Download data: Individual spectra in txt format, current graph as png
Upload data: No
Notes:
– Good plot controls to turn individual spectra on and off
BioLegend Fluorescence Spectra Analyzer
Fluorophores: ~80 fluorophores
Light sources: Yes, lasers
Filters: Yes, specify center wavelength and bandpass
Download data: Current graph as png
Upload data: No
Notes:
– Good plot controls to turn individual spectra on and off
– Oriented to flow cytometry
Fluorophores: ~150
Light sources: No
Filters: Yes, Omega filter sets
Download data: No
Upload data: No
Notes:
– When you select and graph a filter set a window appears that lists the compatible fluorophores
– When you select and graph a fluorophore a window appears that lists the compatible filter sets
Fluorophores: ~250
Light sources: Yes – lasers, LEDs, lamps
Filters: Yes, Zeiss filter sets
Download data: No
Upload data: No
Notes:
– Tabulated lists of fluorophores and filter sets. When you select a fluorophore you see a plot and a list of compatible filter sets. When you select a filter set you see a plot and a list of compatible fluorophores.
– Interactive fluorescence dye and filter database
Hi,
Leica Microsystems has an online fluorescence spectra viewer (FluoScout™), accessible at http://www.leica-microsystems.com/fluoscout/.
Omega Optical has an online fluorescence spectra viewer as well (Curvomatic), accessible at http://www.omegafilters.com/curvomatic/.
Thanks Shiraz. We have added those to the list.
two very useful visualizations of almost all fluorescent proteins & photoswitchable fluorescent proteins have been developed by Talley Lambert and Kurt Thorn (UCSF):
http://nic.ucsf.edu/FPvisualization/ and http://nic.ucsf.edu/FPvisualization/PSFP.html
George McNamara, MD Anderson Cancer Center, submitted a lengthy comment loaded with valuable information. He has long been a leader in advocating for public access to spectral data and aggregating data to make it available. We felt that his comments deserved to be a post of their own – you can find that at https://nightsea.com/sfa-sharing/george-mcnamara-spectra-viewers/
BD Biosciences has a viewer that I use for fluorophores traditionally used in flow cytometry:
http://www.bdbiosciences.com/in/research/multicolor/spectrum_viewer/index.jsp
Thanks Esteban. We saw that one and did not include it since we are more microscopy- than cytometry-oriented. We may change that, but for now people can find that in your comment. Thanks for sharing that.
the FPbase spectra viewer now how as extensive selection of fluorescent protein spectra, as well as common organic dyes, commercial filters, light sources, and camera QEs.
http://fpbase.org/spectra
Talley, thank you for submitting this new spectra viewer that you created. It looks very powerful and convenient and I think will be of great value to the community.