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| Why PubSpectraPubSpectra fills an unmet need in the biomedical fields of light microscopy, flow cytometry, histochemistry and pathology, plus cytomics, tissomics, etc (the ultimate 'omic is whyomics = science), for absorption, fluorescence, transmission and reflectance spectral data. The spectra I work with are sometimes called UV-VIS-NIR, and span the wavelength range of 200-1200 nm. Most of the spectra are concerned with what we can see by eye, approximately 380-750 nm. Note that short (<400 nm) and long (>700 nm) wavelength light that is bright enough to see by eye may be more than bright enough to damage your eyesight. To quote a well known physics sign: "Caution! Do not look into laser with remaining eye" (finding a good sign on the 'Net is not so easy, one was here). Data OrganizationPubSpectra (this page) contains links to seven files that are scattered over several websites. The Spectral Data Links section contains a downloadable Excel file that is the index to three downloadable zip files containing dye/protein, filters and light sources/other spectra. A table listing the data sources is below the links. We published a paper in Cytometry:
McNamara G, Gupta A, Reynaert J, Coates TD, Boswell C: Spectral imaging microscopy web sites and data. Cytometry. 69A: 863-871 (2006). PubMed Abstract. Link.
The Non-Spectral Data Links section contains links to three downloadable Excel files (and one Excel file) containing, respectively, information on over 5000 dyes, over 1000 fluorescent proteins, and a specifications on hundreds of objective lenses. We have a manuscript in press for the 1000+ fluorescent protein dataset:
McNamara G, Boswell C (2007) A Thousand Proteins of Light: 15 Years of Advances in Fluorescent Proteins. Modern Research and Educational Topics in Microscopy (volume 3), in press. http://www.formatex.org/microscopy3/ Downloads: Word Doc Draft Data
Readers can also find a plethora of information about light microscopy and fluorescent methods and reagents at George McNamara's Multi-Probe Microscopy document (1500 pages), downloadable from http://home.earthlink.net/~mpmicro/mpmicro.zip.
Who are We PubSpectra and Fluorescent Spectra: An Interactive Exploratory Database ("Fluorescent Spectra Graphing Site") have been developed in a collaboration between George McNamara and Carl Boswell. The sites are an extension of an earlier graphing site that Carl put together. George, at the instigation of his supervisor, Prof. Thomas D. Coates, started collecting spectra to serve the needs to the Childrens Hospital Los Angeles Cellular Imaging Core. George contacted Carl and a collaboration was born. Carl convinced the University of Arizona's web development center to devote considerable resources to assembling the Graphing site. I encourage researchers and spectral companies to repost the data files on their own web sites. Please cite McNamara et al 2006, include links to here (http://home.earthlink.net/~pubspectra), and to Fluorescent Spectra graphing site organized by Carl Boswell, http://www.mcb.arizona.edu/ipc/fret/default.htm,
A manuscript about these sites has been accepted by Cytometry and is scheduled for a special issue on spectral imaging that should appear in August 2006 as Cytometry Volume 69A issue 8 (click here for the index of all Cytometry issues). Spectra are also available on the PUCL Cytometry CD 9 / Microscopy CD4 joint CD (http://www.cyto.purdue.edu/flowcyt/cdseries.htm) distributed at the 2006 ISAC (Quebec City) and Microscopy Society of America meetings (note: this web site is more up to date). Torsten Mayr (torsten.mayr@tugraz.at)
has set up
Spectral Data LinksThe web links for the data files are scattered over several of my personal web sites because of the way my Internet service provider partitions my "free" web space (8 accounts of 10 Mb each, with a 1 Gb/month download limit). The location of the ZIP and Excel files change as I need to relocate files across the accounts, so please use the PubSpectra web page to find current versions. Current versions uploaded May 15, 2006. See this paper by Carl Boswell and I for details about PubSpectra;
McNamara G, Gupta A, Reynaert J, Coates TD, Boswell C: Spectral imaging microscopy web sites and data. Cytometry. 69A: 863-871 (2006). PubMed Abstract. Link.
Index file for the whole dataset: McNamara_Boswell_000_2006_Index_Dyes_FPs_Filters_Lamps_Other_Spectra.xls
Fluorescent dyes and fluorescent proteins spectra: McNamara_Boswell_Spectra_Dyes_FPs.zip
Filters spectra: McNamara_Boswell_Spectra_Filters.zip
Light sources and other spectra: McNamara_Boswell_Spectra_Lamps_other.zip
Non-Spectral Data Links
McNamara 2007 Fluorophore Data Tables (>5000 dye entries, 3.2 Mb)
McNamara G, Boswell C (2007) A Thousand Proteins of Light: 15 Years of Advances in Fluorescent Proteins. Modern Research and Educational Topics in Microscopy (volume 3), in press. http://www.formatex.org/microscopy3/ Downloads: Word Doc Draft Data [Excel Data file is current version of what used to be "McNamara 2006 Fluorescent Proteins Data" Excel file]
McNamara 2005 Objective Lens Tables (Leica, Nikon, Olympus, Zeiss biomedical microscope lenses) The three web links above are to three Microsoft Excel files that I've posted on the Internet. These three files have data about fluorescent proteins, dyes, or lenses, respectively.
Janos Szollosi and Horvath Gabor sent me an Excel FRET calculator, that I have modified slightly:
PubSpectra Zip file contents:
The spectra above were assembled for the Fluorescent Spectra web site project that Carl Boswell and I put together (hopefully a manuscript will appear in the Paddock 2.0 confocal microscopy book). Carl did great work getting the site together. My thanks to Carl for his patience with me. See: http://www.mcb.arizona.edu/ipc/fret/default.htm Invitrogen, Zeiss (formerly Bio-Rad), and BC Biosciences have interactive spectra web graphing sites. See http://home.earthlink.net/~geomcnamara/spectra_links.htm for links.
Janos Szollosi and Horvath Gabor were kind enough to send me their FRET calculator Excel file. I've made minor additions, such as a Kappa2 vs. refractive index table for displaying Ro values. If you use the spreadsheet, please acknowledge them. See also the FRET calculation capability of PhotoChemCAD (Windows application) at http://www.photochemcad.com (Jonathan Lindsey, NCSU). Multiphoton excitation fluorescence spectra weblinks PubSpectra does not (yet) have multiphoton excitation data. Several researchers have published papers and/or posted graphs, including:
In particular, Zipfel and Webb have reproduced many publication graphs on their website, including: Fluorophores: http://www.drbio.cornell.edu/Infrastructure/FluorescentProbes_WWW/CommerciallyAvailable.htm http://www.drbio.cornell.edu/Infrastructure/FluorescentProbes_WWW/crosssections.htm http://www.drbio.cornell.edu/MPE/mpe2.html
(see website for more
Stowers Institute has a table, a few spectra graph, and web links at http://research.stowers-institute.org/wiw/external/Technology/NLO/index.htm
An additional multiphoton resource is Steve Potter's website http://www.neuro.gatech.edu/groups/potter/2photon.html
Zeiss objective lens transmissions are at https://www.micro-shop.zeiss.com/us/us_en/czshop.php?cp_sid=641133a98ce&cp_tpl=main (Olympus also has some spectra online). The Zeiss spectra graph server is at https://www.micro-shop.zeiss.com/us/us_en/spektral.php?cp_sid=&f=db
Spectral file format If I knew at the start that I'd be releasing 2000+ spectra on the Internet, I might have spent a few more seconds organizing the header section. I didn't. Deal with it. I did have the inspired notion to have Microsoft Excel file worksheets rows 200 to 1200 be the spectra in nanometers. Rows 1-199 are header information (rows 100-199 being empty in most worksheets, or some attempts at getting the extinction coefficients and quantum yields for each dye into the absorption, excitation and emission columns). Column A's rows 200-1200 also have the wavelength in nanometers.
More spectra
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