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PubSpectra - Open Data Access Fluorescence Spectra
  • George McNamara

The Internet is enabling greater access to spectral imaging publications, spectral graphs, and data than that was available a generation ago. The spectral imaging systems discussed in this issue of Cytometry work because reagent and hardware spectra are reproducible, reusable, and provide input to spectral unmixing and spectral components recognition algorithms. These spectra need to be readily available in order to determine what to purchase, how to use it, and what the output means. We refer to several commercially sponsored and academic spectral web sites and discuss our spectral graphing and data sites. Sites include fluorescent dye graph servers from Invitrogen/Molecular Probes, BD Biosciences, Zeiss/Bio-Rad Cell Sciences, and filter set servers from Chroma Technology and Omega Optical. Several of these sites include data download capabilities. Recently, two microscope manufacturers have published on their web sites transmission curves for select objective lenses-crucial data for anyone doing multiphoton excitation microscopy. Notable among the academic sites, PhotoChemCAD 2.0 has over 200 dyes and a downloadable database/graphing program, and the USC-A Chemistry UV-vis Database displays absorption spectra of many dyes and indicators used in clinical histology and pathology. Our Fluorescent Spectra graphing/calculator site presents dyes, filters, and illumination data from many of these and additional sources. PubSpectra is our free download site which uses Microsoft Excel files as standardized human/machine readable format with over 2,000 biomedical spectra. The principle that data is not subject to copyright provides a framework in which all scientific data should be made freely accessible.

The above abstract is from:

McNamara G, Gupta A, Reynaert J, Coates TD, Boswell C 2006 Spectral imaging microscopy web sites and data. Cytometry A 69(8): 863-871. PubMed PMID: 16969821. DOI: 10.1002/cyto.a.20304 (full text freely available at this web site) and McNamara et al 2006 is available in the file here.

The here is from mid-2009. I plan on updating the PubSpectra XLSX (Microsoft Excel 2007 file format, based on XML) when I have a lot more data.

The PubSpectra data set is part of the data underlying:

Spectra Database hosted at the University of Arizona

and the Zeiss ZEN software Smart Setup and spectra viewer.

I welcome everyone to use the PubSpectra dataset.

  • PubSpectra,
  • open data access,
  • fluorophores,
  • chromophores,
  • fluorescent dyes,
  • fluorescent proteins,
  • quantum dots,
  • interference filter,
  • dichroic beamsplitter,
  • exciter filter,
  • emission filter,
  • light source,
  • fluorescence microscopy,
  • flow cytometry,
  • fluorescence activated cell sorter
Publication Date
Winter February 11, 2012
The PubSpectra data set is DATA - Data are facts, facts cannot be copyrighted (see the Discussion of McNamara et al). Therefore the PubSpectra.xlsx contents as well as the "FPaa.xls' file are CC0 = CC Zero - see for explanation.
Citation Information
George McNamara. "PubSpectra - Open Data Access Fluorescence Spectra" (2012)
Available at: