George McNamara

Spectra links

mpmicro (zipfile)

Temporal Area Map & Histogram For Analysis of Cell Motility and Chemotaxis (TAM webpage)

Crusade for better micrographs


Boswell-McNamara Fluorescence Spectra Web Site (introduction page)

Tiki God

Tiki Goddess

See also the tiki_goddess website

Geo's favorite places

Geo's EXE's (zip collection)

NIH Biosketch




Spectra links 20050709 

(July 9, 2005)

If you have site(s) related to biomedical absorption, fluorescence, filters, laser/lamps, microscope optics, flow cytometry instruments, please send them to me at (use a subject line that my email filter and I are likely to recognize as ok). 

Please see (University of Arizona) for Carl Boswell & George McNamara's interactive fluorescence spectra web site (you interact with data, not Carl and I). 

McNamara & Boswell Fluorescence Spectra Data (July 9, 2005)         (1.5 Mb)                     (5.4 Mb)     (5.0 Mb) 20050709 FRET Janos Szollosi Horvath Gabor FRET calculator.xls  (0.8 Mb Excel file with FRET calculator)

Note: file sizes and names may change occasionally. 
Spectra Excel file size  McNamara & Boswell Fluorescence Spectra Index
2137 1.5 Mb 
Fluorescent Dyes & Fluorescent Proteins
1282 5.4 Mb 
349 3,683,840 McNamara Boswell 001 20050621U MPI 2003 spectra = index 349 fluor entries.xls
18 184,320 McNamara Boswell 002 20050621U MPI 2004 spectra = index 18 fluor entries.xls
223 2,750,464 McNamara Boswell 003 20050621U PhotoChemCAD 1998 Lindsey Spectra = 223 fluor entries.xls
30 293,888 McNamara Boswell 004 20050621U Amersham spectra = 30 fluor entries.xls
35 621,568 McNamara Boswell 005 20050621U ATTO-TEC 2004 spectra = 35 fluor entries.xls
82 1,192,448 McNamara Boswell 006 20050621U Dyomics spectra = 82 fluor entries.xls
24 261,120 McNamara Boswell 007 20050621U Martek 2004 spectra = 24 fluor entries.xls
20 235,520 McNamara Boswell 008 20050621U Vysis 2004 Spectra = 20 fluor entries.xls
32 226,816 McNamara Boswell 009 20050621U Aryeh Weiss 2003 spectra = 32 fluor entries.xls
6 109,568 McNamara Boswell 010 20050621U Patterson 2002 spectra = 6 fluor entries.xls
70 723,968 McNamara Boswell 011 20050621U Fluorescent Proteins 2003 Spectra = 70 fluor entries.xls
71 665,600 McNamara Boswell 012 20050621U Miscellaneous 2004 spectra = 61 fluor entries.xls
8 154,624 McNamara Boswell 013 20050621U Adams 2003 Spectra = 8 fluor entries - Griffin Tsien CHOxAsH FlAsH ReAsH
18 4,474,368 McNamara Boswell 014 20050621U Tung 2003 Spectra = 18 fluor entries - Lin NIRF SNIRF Dyes.xls
10 150,016 McNamara Boswell 015 20050621U QDC 2003 spectra = 10 fluor entries - Quantum Dot Corp QDots spectra.xls
23 275,456 McNamara Boswell 016 20050621U ET 2004 Spectra = 23 fluor entries - Evident Technologies Evidots.xls
112 938,496 McNamara Boswell 017 20050621U miscellaneous 200501 Spectra 112 fluor entries - DDAOG DDAO SYTO H33258 C
58 1,583,616 McNamara Boswell 018 20050621U Goldsmith 2004 Spectra = 58 dye entries - Jack Goldsmith U South Carolin
59 413,184 McNamara Boswell 019 20050622W miscelleaneous 200503 spectra 59 entries - updated from 0050327S spectra
34 435,712 McNamara Boswell 020 20050622W ASI 1998 dye spectra = 34 entries - 34 chromogen spectra.xls
19,374,592 bytes (unzipped Excel files)
Filters and Lamps
855 5.1 Mb 
450 8,005,632 McNamara Boswell 201 20050622W Chroma 2004 filters = 450 filter entries - 20040606S.xls
230 3,788,800 McNamara Boswell 202 20050622W Omega 2004 Microscopy Filters Spectra = 230 filter entries - 20040529A.x
24 487,936 McNamara Boswell 203 20050622W Semrock 2004 filter spectra = 24 filter entries - 20040229S.xls
66 1,193,472 McNamara Boswell 204 20050622W Schott 2004 Filter Spectra = 66 filter entries - 20040403A.xls
26 410,112 McNamara Boswell 300 20050622W Lamps others 2004 Spectra = 26 entries - 20040405M.xls
59 443,392 McNamara Boswell 301 20050622W Busko lamps 2004 spectra = 59 entries - Aqua botanic 20040403A.xls
14,329,344 bytes (unzipped Excel files)


Fluorescent Spectra Websites

Below are tables related to various web sites that are of use for displaying/using fluorescent spectra. Of special note are:  - Boswell/McNamara University of Arizona site (graphing page). - Invitrogen/Molecular Probes Java based Spectra Viewer - the “old’ list of Invitrogen/Molecular Probes dyes with spectra data - Jonathan Lindsey’s PhotoChemCAD 2.0 site (downloadable database.

The tables below were originally assembled for a manuscript of Carl and mine. The manuscript was sent off (for Paddock 2.0) before the Invitrogen/Molecular Probes Java based web site went online. The version below is from Appendix 30 of Multi-Probe Microscopy (see 

Appendix 30 Table 1: Spectra Data Server Web Sites

Fluorescent Spectra Web Site (this work)

Graphing page / Calculation page

Fluorescent Dyes (ex, em data download)

Multi-Probe Microscopy (doc download [zip])

Carl Boswell, University of Arizona

Invitrogen/Molecular Probes, Inc. (old - list) (new)

Aryeh Weiss (Martin Wessendorf data)

PhotoChemCAD 2.0 (Jonathan S. Lindsey)

Jack Goldsmith (USCA)

BD Biosciences

Zeiss (formerly Bio-Rad)

Zeiss (formerly Bio-Rad) multiphoton

Scott Prahl

OMLCs web based optical calculators

Chroma Technology

Omega Optical


Appendix 30 Table 2 Filter Manufacturers

Chroma Technology

Omega Optical

Semrock, Inc.

Bookham New Focus

Schott Glass Technologies

Newport (Spectra-Physics, Oriel)

Melles Griot

CVI Laser

Edmund Industrial Optics


Appendix 30 Table 3 Spectral Imaging Software Companies

Applied Spectral Imaging, Inc


Kairos Scientific

Lightform Inc


Optical Insights, LLC

Till Photonics (Polychrome V monochromator (light source), future spectral imager)

Confocal Microscope Manufacturers

Leica Microsystems

Nikon Inc

Olympus Microscopes

Zeiss Microscopes


Appendix 30 Table 4: Software Used At Various Times By McNamara

Un-Scan-It 6.0 (Silk Scientific)

Office (Excel and Access) (Microsoft)

Origin / Origin Pro (OriginLab)

Spekwin32 (F. Menges)

SWizard (S.I. Gorelsky)

Lispix (David Bright, NIST)

NMRPipe (F. Delaglio, NIH)

MMSpectra (Data Optics, Inc)

ACD/SpecManager (ACD Labs)

GRAMS Spectroscopy Software (Thermo)

MatLab (Mathworks)


XlXtrFun™ (Extra functions for Microsoft Excel … interpolation, spline …)

(see also 

Appendix 30 Table 6: Academic Spectral Imaging Microscopy Sites/Publications

Michael Sinclair

Sandia National Laboratory

Sandia News (2002)

M. Lovell (2004) Understanding genes. Tech Com 2: 16-17.

D.M. Haaland, M.B. Sinclair, J.A. Timlin, H.D.T. Jones (2005) New 3-D Hyperspectral Confocal Microscope for in vivo Imaging of Cells.  DOE Genomes2Life 4/2005.

Timlin JA, Haaland DM, Sinclair MB, Aragon AD, Martinez MJ, Werner-Washburne M (2005) Hyperspectral microarray scanning: impact on the accuracy and reliability of gene expression data. BMC Genomics 6: 72. PMID: 15888208.

Sinclair MB, Timlin JA, Haaland DM, Werner-Washburne M. (2004) Design, construction, characterization, and application of a hyperspectral microarray scanner. Appl Opt 43: 2079-2088. PMID: 15074416.

Colin MacAulay

British Columbia Cancer Research Centre

MacKinnon N, Stange U, Lane P, MacAulay C, Quatrevalet M. (2005) Spectrally programmable light engine for in vitro or in vivo molecular imaging and spectroscopy. Appl Opt 44: 2033-2040. PMID: 15835352.

H.R. Garner

Center for Biomedical Inventions, University of Texas Southwestern Medical Center


Huebschman ML, Schultz RA, Garner HR (2002) Characteristics and capabilities of the hyperspectral imaging microscope. IEEE Eng Med Biol Mag 21: 104-117. PMID: 12222107.

Schultz RA, Nielsen T, Zavaleta JR, Ruch R, Wyatt R, Garner HR (2001) Hyperspectral imaging: a novel approach for microscopic analysis. Cytometry 43: 239-247. PMID: 11260591.

Kevin Eliceiri

Laboratory for Optical and Computational Instrumentation (LOCI)

University of Wisconsin-Madison

Development of a combination spectral/lifetime detector

See also:

Eliceiri KW, Rueden C (2005) Tools for visualizing multidimensional images from living specimens. Photochem Photobiol (preprint) PMID: 15807634. [Abstract] [Print Version].

Thomas M. Jovin

Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Gottingen, Germany

Grecco HE, Lidke KA, Heintzmann R, Lidke DS, Spagnuolo C, Martinez OE, Jares-Erijman EA, Jovin TM (2004) Ensemble and single particle photophysical properties (two-photon excitation, anisotropy, FRET, lifetime, spectral conversion) of commercial quantum dots in solution and in live cells. Microsc Res Tech 65: 169-179. PMID: 15630694.

Hanley QS, Verveer PJ, Arndt-Jovin DJ, Jovin TM (2000) Three-dimensional spectral imaging by hadamard transform spectroscopy in a programmable array microscope. J Microsc 197: 5-14. PMID: 10620143.

Vereb G, Jares-Erijman E, Selvin PR, Jovin TM (1998) Temporally and spectrally resolved imaging microscopy of lanthanide chelates. Biophys J 74: 2210-2222. PMID: 9591648.

See also

Jares-Erijman EA, Jovin TM (2003) FRET imaging. Nat Biotechnol 21: 1387-1395. PMID: 14595367.

M. Descour, R.M. Lynch,

Optical Sciences Center, University of Arizona

Scholl JF, Dereniak EL, Descour MR, Tebow CP, Volin CE (2003) Phase grating design for a dual-band snapshot imaging spectrometer. Appl Opt 42: 18-29. PMID: 12518819.

Ford BK, Volin CE, Murphy SM, Lynch RM, Descour MR (2001) Computed tomography-based spectral imaging for fluorescence microscopy. Biophys J 80: 986-993. PMID: 11159465.

Martinez-Zaguilan R, Gurule MW, Lynch RM (1996) Simultaneous measurement of intracellular pH and Ca2+ in insulin-secreting cells by spectral imaging microscopy. Am J Physiol 270: C1438-C1446. PMID: 8967445.

M.R. Descour, Dereniak (1995) computed-tomography imaging spectrometer (CTIS). Appl Opt 34: 4817-4826.

H. Matsuoka

Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology


Matsuoka H, Kosai Y, Saito M, Takeyama N, Suto H (2002) Single-cell viability assessment with a novel spectro-imaging system. J Biotechnol 94: 299-308. PMID: 11861088.

X. Michalet & S. Weiss

Michalet X, Kapanidis AN, Laurence T, Pinaud F, Doose S, Pflughoefft M, Weiss S  (2003) The power and prospects of fluorescence microscopies and spectroscopies. Annu Rev Biophys Biomol Struct 32: 161-182. PMID: 12598370.

Daniel L. Farkas

Minimally Invasive Surgical Technologies Institute, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California

Chung A, Wachsmann-Hogiu S, Zhao T, Xiong Y, Joseph A, Farkas DL (2005) Advanced optical imaging requiring no contrast agents--a new armamentarium for medicine and surgery. Curr Surg 62: 365-270. PMID: 15890230.

Wachman ES, Niu W, Farkas DL (1997) AOTF microscope for imaging with increased speed and spectral versatility. Biophys J 73: 1215-1222. PMID: 9284289.

The following publication used the Applied Spectral Imaging (“SKY”) system

H. Tsurui

Department of Pathology, Juntendo University School of Medicine, Tokyo, Japan

Tsurui H, Nishimura H, Hattori S, Hirose S, Okumura K, Shirai T (2000) Seven-color fluorescence imaging of tissue samples based on Fourier spectroscopy and singular value decomposition. J Histochem Cytochem 48: 653-662.
PMID: 10769049.

The following publications used flow cytometers, not imaging. Perfetto et al was published in a review journal. Whether 17 color flow cytometry (plus forward scatter and side scatter) is used daily in the Roederer lab is unclear.

M. Roederer

ImmunoTechnology Section, Vaccine Research Center, National Institute of Allergy and Infectious Disease, National Institutes of Health

Perfetto SP, Chattopadhyay PK, Roederer M (2004) Seventeen-colour flow cytometry: unravelling the immune system. Nat Rev Immunol 4: 648-655. PMID: 15286731.

De Rosa SC, Brenchley JM, Roederer M (2003) Beyond six colors: a new era in flow cytometry. Nat Med 9: 112-117. PMID: 12514723.


Spectral Acknowledgements

We (Carl Boswell and George McNamara) thank all those from whom spectral data has been obtained. Special thanks to Iain Johnson, Mike Ignatius, Rosaria Haugland, Jeff Silk, Paul Millman, Michael Stanley, Jason Cross, Chris Baumann, Roy Kinoshita, Carolyn Whyland, Jonathan Lindsey, Jack Goldsmith, Scott Prahl, Robert Campbell, Roger Tsien, Atsushi Miyawaki, Ching Tung, Patricia Whaley, Andy Watson, Marcel Bruchez, Richard Ornberg, Lisa Seeber, Sarah Eby, Aryeh Weiss, Martin Wessendorf, Jeremy Lerner, Robert Zucker, Horváth Gábor, Janos Szollosi, Matthias Wenzel, Robert Leif, Kolja Wawrowsky, Al Kutchera, Farhad Moatamed, Craig Pow, Larry Decker, Daniel Farkas, Richard Levenson, Zvi Malik, Thomas Ried, Evelin Schrock, Cathy Bernier, Margaret Skokan, Greg Maguire, Tim Marshall, Derrick Elder, Randy Knudtson, Mike Olive, Anthony Arciniega, Dirk Soenksen, Nir Katzir and Yuval Garini.




Web page started 20050619S, updated 20050709A