PubSpectra 2012 – Tattletales

October 23, 2012 update to PubSpectra

In September 2012 I invented a fusion of 20 years of fluorescent proteins and microscopy/nanoscopy into the novel concept of Tattletales.

The “Tattletales – Multiplexing biosensors and gene reporters in live cells” poster below, which I am posting online on October 23, 2012, is my public disclosure.

Below the “Tattletales” poster is a second poster on two image analysis topics: Temporal Area Maps (TAM) and Tattletales. In the future I look forward to having TAM or its 3D version, Temporal Volume Maps (TVM) and Tattletales in the same cells. Tattletales is public domain, so I don’t have any patents to license or enforce – and neither should anyone else (at least any broad patents). I am happy to accept and cash any thank you checks anyone would like to send me.

PubSpectra logo - no border.jpg

Tattletales poster (jpg image file, originally formatted for a 44x47 inch poster – use a zoom tool to read online or better, download to your computer).


Temporal Area Maps (TAM) and Tattletales image analysis poster (jpg image file, originally formatted for a 44x47 inch poster – use a zoom tool to read online or better, download to your computer).



Most of my web content is now at

PubSpectra contents are available for download at

I am a contributor to the Confocal listserv community -

Below is the old (and somewhat stale) PubSpectra content.

Graphing Web Sites

2012 U Arizona Spectra web site – Please use

organized by Prof. Urs Utzinger, who took over UA spectra website management/development from my collaborator Carl Boswell, on Carl’s retirement. The older site (also referenced below) still works:

Why PubSpectra

PubSpectra 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 Organization

PubSpectra (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.      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


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 (, and to Fluorescent Spectra graphing site organized by Carl Boswell,,

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 ( distributed at the 2006 ISAC (Quebec City) and Microscopy Society of America meetings (note: this web site is more up to date).

Torsten Mayr ( has set up you can use as an upload site for data intended for Pubspectra and the UA Fluorescent Spectra graphing site. Currently both and http://www/ point to  An example of what Torsten has is his Fluorescein page.


Spectral Data Links

The 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:



Fluorescent dyes and fluorescent proteins spectra:


Filters spectra: 


Light sources and other spectra: 


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.     

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: 20050709 FRET Janos Szollosi Horvath Gabor FRET calculator.xls    


PubSpectra Zip file contents:



McNamara & Boswell Fluorescence Spectra Index

2379 total spectra




1314 dye spectra

Fluorescent Dyes & Fluorescent Proteins



McNamara Boswell 001 20050621U MPI 2003 spectra.xls


McNamara Boswell 002 20050621U MPI 2004 spectra.xls


McNamara Boswell 003 20050621U PhotoChemCAD 1998 Lindsey Spectra.xls


McNamara Boswell 004 20050621U Amersham spectra.xls


McNamara Boswell 005 20050621U ATTO-TEC 2004 spectra.xls


McNamara Boswell 006 20050621U Dyomics spectra.xls


McNamara Boswell 007 20050621U Martek 2004 spectra.xls


McNamara Boswell 008 20050621U Vysis 2004 spectra.xls


McNamara Boswell 009 20050621U Aryeh Weiss 2003 spectra.xls


McNamara Boswell 010 20050621U Patterson 2002 spectra.xls


McNamara Boswell 011 20050621U Fluorescent Proteins 2003 Spectra.xls


McNamara Boswell 012 20050621U Miscellaneous 2004 spectra.xls


McNamara Boswell 013 20050621U Adams 2003 Spectra.xls


McNamara Boswell 014 20050621U Tung 2003 Spectra.xls


McNamara Boswell 015 20050621U QDC 2003 spectra.xls


McNamara Boswell 016 20050621U Evident Technologies 2004 Spectra.xls


McNamara Boswell 017 20050621U miscellaneous Spectra.xls


McNamara Boswell 018 20050621U Goldsmith 2004 Spectra.xls


McNamara Boswell 019 20050622W miscellaneous 200503.xls


McNamara Boswell 020 20050622W ASI 1998 dye spectra.xls


McNamara Boswell 021 20051127S Miscellaneous dyes.xls


McNamara Boswell 022 20051218S Miscellaneous dyes.xls





 966 filter, lamps, etc spectra




McNamara Boswell 201 20050622W Chroma 2004 filters.xls


McNamara Boswell 202 20050622W Omega 2004 Microscopy Filters Spectra.xls


McNamara Boswell 203r1 20051113 Semrock 2005 filter spectra.xls


McNamara Boswell 204 20050622W Schott 2004 Filter Spectra.xls


McNamara Boswell 205 20060417M Chroma ET filters.xls


McNamara Boswell 206 20060514S Nikon filter spectra.xls




99 lamps, others spectra

Lamps and Other Spectra

lamps others 


McNamara Boswell 300 20050622W Lamps others 2004 Spectra.xls


McNamara Boswell 301 20050622W Busko lamps 2004 spectra.xls


McNamara Boswell 302 20060514S Lamps spectra Exfo Metal-halide vs Xe vs Hg.xls






Suppliers of Spectra Data Used in This Collection

Dye Spectra

Jonathan S. Lindsey (NCSU)

PhotoChemCAD 2.0 (Jonathan S. Lindsey) 

Please download the PhotoChemCAD 2.0 software from the PhotoChemCAD web site (I've found it works better at 1280x1024 pixel display mode than at 1024x768 pixels).

Invitrogen / Molecular Probes, Inc. (interactive) (web list, most entries have downloadable text spectra) 

Aryeh Weiss (Martin Wessendorf data)

Yuval Garini (Vysis dyes)

Jack Goldsmith (USCA)  

Ching H. Tung (Center for Molecular Imaging Research, Mass. General Hospital)

Robert E. Campbell (U. Alberta)

Roger Y. Tsien (UCSD)

Quantum Dot Corp

Evident Technologies


Dyomics GmbH

Martek Biosciences Corp

GE Healthcare (Amersham Biosciences)

Applied Spectral Imaging (34 chromogen spectra) 

Filter Spectra

Chroma Technology

Omega Optical


Schott Glass Technologies

Nikon USA

Filter spectra digitized with Un-Scan-It 6.0 (Silk Scientific) from the Molecular Expressions hosted Nikon MicroscopyU web pictures. Technical Instruments (San Francisco Bay area Nikon microscope dealer) has a nice PDF of the filter spectra, but over smaller wavelength ranges than the MicroscopyU pictures.

Lamp spectra


Aqua-Botanic (Busko) 






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:

Invitrogen, Zeiss (formerly Bio-Rad), and BC Biosciences have interactive spectra web graphing sites. See  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. 20050709 FRET Janos Szollosi Horvath Gabor FRET calculator.xls     

See also the FRET calculation capability of PhotoChemCAD (Windows application) at (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:






Speiss and Bestvater


In particular, Zipfel and Webb have reproduced many publication graphs on their website, including:


   (see website for more

objective lens transmission curves:  (Olympus and Zeiss have some nicer curves, and possibly some data, on their web sites).

if you are using a PMT based system, quantum efficiency curves for different types are at 


Stowers Institute has a table, a few spectra graph, and web links at


An additional multiphoton resource is Steve Potter's website


Zeiss objective lens transmissions are at (Olympus also has some spectra online). The Zeiss spectra graph server is at


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

The spectra web sites below may be of interest to some readers, but are not likely to by digitized into PubSpectra anytime soon

Torsten Mayr

University of Joensuu Spectra Databases - Finland

(update of )


Munsell colors matt (AOTF measured) (13)


Munsell colors matt (Spectrofotometer measured) (13)


Munsell colors glossy (Spectrofotometer measured) (1)


Munsell colors glossy (all) (Spectrofotometer measured)


Natural colors (3)


Forest colors (11)


Paper spectra (7)


Candy colors (1)


Lumber spectra (3)


Agfa IT8.7/2 set (3)


Daylight spectra (1)

See also


Epolin (infrared and laser absorbing dyes)

University of Rochester - Munsell Color Science Laboratory - Lippmann2000 spectral imaging database

Pigmentum project (catalog historical pigments

the society of dyers and colourists

Colour Experience

Colour Index (web subscription)

Colour Index Heritage Edition, DVD (£500)

Ushio America (bulbs)



More Data

I have a day job, but am willing to work with researchers and companies to get their data into my "standard" Microsoft Excel format. If you have data that I can post here, tell me what you plan to send to me by sending an email to me at Please include PubSpectra at the start of the subject line so that my junk email filters and I don't delete your email. Please do not send me unsolicited attachments - they will be discarded unless I have established an e-relationship with you by preliminary email exchange.   


Illumination spectra (arc lamps, metal halide lamps, lasers ... tunable laser power curves, such as the Coherent Chameleon and Chameleon XR power tuning curves here)


Illumination power stability (over several ranges: seconds, minutes, hours, day-to-day)


Parfocality curves of microscope condensers and objective lenses


Lenses do not focus all wavelengths of light to the same place! Terms like achromat, and apo-chromat, refer to the number of wavelengths that those types of lenses are corrected for (1 and 3, respectively). For apo-chromats, the wavelengths between the three corrected points are close to, but not quite the same as, the corrected points. In the UV and NIR, all bets are off. Not including parfocality data with inexpensive lenses makes a certain amount of sense, but for the price of the best lenses ($6,000 to $10,000 each), we ought to be able to obtain from the manufacturer their performance specification (if they do not have specifications - let me know so I can stop buying their products). 


Transmission efficiency of every optic - especially microscope condensers and objective lenses. 


For example, the published multiphoton absorption spectra (Zipfel


, Dickinson, Lakowicz, Periasamy, Speiss and Bestvater) are of little practical use without the transmission spectra of the users own optics. Zeiss and Leica charge $800,000 for a multiphoton excitation confocal microscope but have to date been unwilling to make objective lens %T curves available to customers. Memo to Leica, and Zeiss: if an objective lens costs $6,000 to $10,000, either include the %T and Parfocality curves with the lens or quote us a (reasonable) price to have you perform the test & send us the data on our objectives. If you do not have test equipment, tell us so we can buy all our future microscopes, optics and data from Nikon and Olympus. 


November 2005 update:


Eric Zeiss (an Olympus dealer) sent me information that Zeiss has some objective lens transmission curves listed through their Micro-Shop web site (  - requires registration). For example, Objective "C-Apochromat" 63x/1.20 W corr UV-VIS-IR M27


Reflection/Transmission curves of filter sets.


The major manufacturers of biomedical optical filters, Chroma Technology and Omega Optical, have done an excellent job posting spectra on their websites and providing data to customers such as me. Schott Glass, Semrock, and Bookham/New Focus, have also posted some data. Olympus and Nikon have low resolution filter set spectra on their Molecular Expressions sub-sites and on their own sites. See:


Molecular Expressions page on interference filters is


Nikon at Mol Exp


Nikon at Mol Exp (compare dyes to Nikon filter sets)


Nikon - filters for fluorescence microscopy


Olympus at Mol Exp (see Java tutorial)


Nikon fluorescence filter blocks


Olympus PDF of filter sets


Additional web pages are:


Leica - Leica Microsystems Fluorescence Microscopy (download area) with the range of filter cubes (0,03 MB) (list of Leica filters) and correlation of fluorochromes and filter cubes (list of dyes and filters).


Zeiss - Zeiss filtersets web list ... clock on the filter number, i.e. 00 to see a spectral graph and then click on to download a PDF of the filter set transmission curve (slightly nicer quality than the web graphic).


Dye Spectra


Molecular Probes Inc set an excellent example by making spectra available for many of their dyes, and Invitrogen has continued that practice since purchasing MPI. See Table 1 at for web links to MPI and other spectra incorporated into the downloadable files above. 


I am keen on obtaining more spectra of histology dyes. My "34 chromogens" dataset was a start. Gurr (our of print) and Green (the Sigma-Aldrich Handbook of Stains, Dyes and Indicators - soon to be out of print) have published spectra of many dyes in solution. It would be useful to get these digitized and into standard format (I'm thinking about it). It would be even more useful to get more spectra from specimens. 


Detector quantum efficiency (photomultiplier tubes, CCD cameras)


The detector companies (Hamamatsu, Roper Scientific/Photometrics/Princeton Instruments, Ardor Technology, etc) often publish graphs, but have not made performance data available in spreadsheet data form. This is especially problematic for PMT QE curves published on log scale. Please post the data! 

Spectra in Education?

Suggestion to professors and teachers: If you have a spectrophotometer or spectrofluorometer in your lab, instead of just have each student collect a spectrum of caffeine, file in their lab report, and forget about it, how about running some interesting reagents, organizing it in Carl and my standard format, and post it on the Internet. Just about any liquid that has color, or not for that matter (if you have UV or IR capability), will yield spectra. Here are some suggestions:


Kitchen/cafeteria: food colorings ... Gatorade (now in many colors), sodas, those little tubes of food colorings in the cake mix section of your local market, vanilla vs. chocolate milk, green vs black vs orange vs other teas. Burger grease. Ketchup vs mustard. M&M coatings (no peeking at the label!). 


Beer and wine (a great use for the lab supplies budget): The Director of the Munsell Color Science Laboratory ( has a webpage ( about the Lovibond Tintometer ( and other links about beer color (such as Not to leave wine out, a Google search turned up (on graph paper, not numeric data). the blogger did cite a scientific article on one of the continuation pages and calculated wine Warmth and Brightness indices at this page). Some companies, such as ETS Labs,  even do wine analysis on a fee for service (drink for data?).


Office/lab supplies: Sharpie marker extract (Sharpie's are from Sanford), "highlighter" extract (fluorescent!), pen ink extract (I use Uni-ball 0.3 mm pens from Sanford), red ink (from your grading pen - we don't need to know what Enron used), Time label tape extracts (Sharpie's and this type of tape are crucial to biology labs). Crayola crayons (try to find something non-toxic to solubilize the dye, or be clever in getting a sample into your 'ometer, such as scribbling onto a microscope slide or coverglass and sticking that in the 'ometer - or find yourself a spectral imaging microscope). 


Stuff from students ... while I do not recommend extracting dyes from clothing (the dyes are usually designed to be color fast), you could try to get some hair from students (and from the instructor, if they have any to spare). 


In other words, "spectra of everyday things".

If you do not have access to an 'ometer, you can have the students look through online free back issues of journals, such as Journal of Biological Chemistry ( - lots of spectra) or Journal of Histochemistry and Cytochemistry ( for spectra. Personally, I use Un-Scan-It (, though you could probably extract the numbers using ImageJ

More on Light Microscopy

I have written a 1500 page manuscript on Multi-Probe Microscopy. You can download it from ( 


This site was inspired by NIH's PubMed (Public Medline), one of the web sites I use often. While I am unable to be as uncluttered as Google and Google Scholar, I will leave the spectral clutter to other web pages, such as 

Putting this PubSpectra webpage online was inspired by the NIH PubChem project, specifically, the stupid complaints the American Chemical Society made about PubChem infringing on ACS's CAS subscription service. Memo to ACS: "data wants to be free". 


Dr. McNamara thanks the biomedical community for making spectra available. Detailed acknowledgements can be found at and in Multi-Probe Microscopy ( 

Dr. McNamara offers special thanks to Carl Boswell, University of Arizona, and Thomas Coates, CHLA, during the gestation of the Fluorescent Spectra website and collection and organization of this data. 


George McNamara, Ph.D.

Some of the data collection and organization was done while Dr. McNamara was Support Scientist at City of Hope National Medical Center (CoH), as well as a consultant, through CoH, to Childrens Hospital Los Angeles (CHLA) Congressman Julian Dixon Cellular Imaging Core ("Image Core"). From 2007-2012 Dr. McNamara has been Image Core Manager at the University of Miami, Miller School of Medicine, Miami, FL.

Much of the data collection for PubSpectra was performed under the direction of CHLA Image Core Director Thomas D. Coates while the author held the position of Imaging Scientist at CHLA. The "34 chromogens" spectra was collected while the author held the position of Applications Scientist at Applied Spectral Imaging, Inc. 

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