George McNamara, Ph.D.

Du et al 1998 PhotoChemCAD
Jonathan S. Lindsey, NCSU
www.photochemCAD.com
If you like PhotoChemCAD, see also:
FRETview - Stevens et al 2007 Java program
FRETcalc - Stepensky 2007 ImageJ plugin

Invitrogen / Molecular Probes Inc.

www.probes.com

MPI Spectra (original web list)

http://probes.invitrogen.com/resources/spectraviewer/

Chroma Technology (250+ filters and $500 to UA)
Omega Optical (200+ filters)
Semrock (several filters)

Sorry that only a few filters are available on the UA site - Carl Boswell did a great job getting free development from the U Arizona web development center.

See Acknowledgments for the full list.

The spectra page loads slowly because it has about 1000 dye, filter, light source and detector spectra to load. So far, the site has been put together on a volunteer basis by Carl Boswell (University of Arizona, Department of Molecular and Cellular Biology and The Arizona Cancer Center), James Reyneart and Amit Gupta (University of Arizona, Learning Technologies Center). Some funding has been contributed by donor corporations. If/when additional money is available, Carl will have the UA-LTC staff optimize performance.

If you have web ad blockers, such as Google Toolbar or PopUpCop, you may need to inactivate them for the spectra page (i.e. ctrl-click to open the graphing page). You will also need to enable Java scripts (i.e. in PopUpCop and/or IE6).

The spectra are from many sources. See Data Sources for the list (as of July 2004). I have inputted many spectra from the scientific literature and from the Internet, using Un-Scan-It 6.0 from Silk Scientific to convert graphs to data for entry into Microsoft Excel.

The United States Constitution's section on copyrights and patents states that facts cannot be copyrighted. Current US copyright law, and the U.S. Supreme Court have not explicitly ruled on the copyright status of scientific data in peer reviewed publications. The closest I've found is the 1991 decision in Feist Publications, Inc. vs Rural Telephone Service Co., (see http://www.techlawjournal.com/cong106/database/19910327feist.htm for full online text or search web for Supreme Court Feist Rural Telephone), which makes clear that unoriginal compilations of facts -- i.e. the white pages of a telephone directory -- cannot be copyrighted. It is not obvious to me how copyright requirements for "originality" fit with respect to scientific data facts: could someone copyright the value for the speed of light in a vacuum? If not, how can an author or publisher copyright a table of data, of say excitation and emission maxima? How can anyone copyright a typical graph of absorption, excitation and emission spectra?

Recent publications:

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: Draft Data

Singh H, Serrano LM, Pfeiffer T, Olivares S, McNamara G, Smith DD, Al-Kadhimi Z, Forman SJ, Gillies SD, Jensen MC, Colcher D, Raubitschek A, Cooper LJ (2007) Combining adoptive cellular and immunocytokine therapies to improve treatment of B-lineage malignancy. Cancer Res 67: 2872-2880. PubMed abstract PMID: 17363611. Cancer Research abstract and supplemental data videos.

Balic M, Lin H, Datar RH, Young L, Hawes D, Armando G, McNamara G, Cote RJ: The majority of early disseminated cancer stem cells detected in bone marrow of breast cancer patients have a stem cell phenotype. Clin Cancer Res 12: 5615-5621 (2006). PubMed Abstract.

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.

Biomedical Light Microscopy Spectra sites of interest:

Fluorescent Spectra Web Site (this work) Graphing page / Calculation page Fluorescent Dyes (ex, em data download) Multi-Probe Microscopy (doc download [zip])	http://www.mcb.arizona.edu/ipc/fret/default.htm http://www.mcb.arizona.edu/ipc/fret/indexA.html http://home.earthlink.net/~pubspectra http://home.earthlink.net/~mpmicro Click to Spectra_Links (this site) for more links
Carl Boswell, University of Arizona	http://www.mcb.arizona.edu/IPC/spectra_page.htm
Molecular Probes, Inc.	http://www.probes.com/servlets/spectra (web list) http://probes.invitrogen.com/resources/spectraviewer/ (2005 Java applet)
Aryeh Weiss (Martin Wessendorf data)	http://optics.jct.ac.il/~aryeh/Spectra
PhotoChemCAD 2.0 (Jonathan S. Lindsey)	http://www.photochemcad.com
Jack Goldsmith (USCA)	http://www.usca.edu/chemistry/spectra
BD Biosciences	http://www.bdbiosciences.com/spectra
Zeiss (formerly Bio-Rad)	http://microscopy.bio-rad.com/fluorescence/fluorophoreDatab.htm
Zeiss (formerly Bio-Rad) multiphoton	http://microscopy.bio-rad.com/products/multiphoton/Radiance2100MP/mpspectra.htm
Scott Prahl OMLCs web based optical calculators	http://omlc.ogi.edu/spectra/index.html http://omlc.ogi.edu/calc/index.html
Chroma Technology	http://www.chroma.com
Omega Optical	http://www.omega-filters.com
Semrock	http://www.semrock.com

And now back to Carl & my web...

Fluorescence Spectra Graph Page Examples

http://www.mcb.arizona.edu/ipc/fret/indexA.html

Spectra Comparison Page

DAPI (dsDNA), Fluorescein (pH 9), Cy3B, To-Pro-3, Alexa Fluor 750

EBFP, ECFP, EYFP, DsRed, HcRed1, DY-700, DY-780

Spectra Performance Calculations Page:

Cy3B (Amersham Biosciences - GE Healthcare)

Selected Publications (ok, most of my publications - see also my NIH Biosketch):

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.

Garini Y, Young, IT, McNamara G: Spectral imaging: principles and applications. Cytometry. 69A: 735-747. PubMed Abstract. Link.

Serrano LM, Pfeiffer T, Olivares S, Numbenjapon T, Bennitt J, Kim D, Smith D, McNamara G, Al-Khadimi Z, Rosenthal J, Forman SJ, Jensen MC, Cooper LC: Differentiation of naive cord blood T cells into CD19-specific cytolytic effectors for post-transplant adoptive immunotherapy. Blood 107: 2643-2652, 2006. PubMed Abstract.

Wang X, Ge S, Gonzalez I, McNamara G, Rountree CB, Xi KK, Huang G, Bhushan A, Crooks GM: Formation of pancreatic duct epithelium from bone marrow during neonatal development. Stem Cells 24: 307-317, 2006. PubMed Abstract.

Ge S, Crooks GM, McNamara G, Wang X: Fluorescent immunohistochemistry and In situ hybridization analysis of mouse pancreas using low power antigen retrieval technique. J Histochem Cytochem 54: 843-847, 2006. http://www.jhc.org/cgi/content/abstract/jhc.5B6902.2006v1. doi:10.1369/jhc.5B6902.2006. PubMed Abstract.

McNamara G, DiFilippantonio M, Ried T: Microscopy and image analysis (Unit 4.4) in Current Protocols in Human Genetics. 4.4.1-4.4.34. ISBN: 0-471-03420-7. John Wiley & Sons. New York, 2005.

G. McNamara (2005) Color Balancing Histology Images for Presentations and Publication. The Journal of Histotechnology 28(2): 81-88. (June 2005). Full text PDF: McNamara2005JoH28n2pp81-88.pdf

S.K. Sukumaran, G. McNamara, N.V. Prasadarao (2003) Escherichia coli K-1 interaction with human brain microvascular endothelial cells trigger phospholipase C-gamma 1 activation downstream of P13-kinase. J Biol Chem (epub Sep 2, 2003). DOI: 10.1074/jbc.M307374200. Sunil Sukumaran and Prof. Nemani Prasadarao have published several papers, in JBC and elsewhere, using this bacterial invasion of endothelial cells system. In this paper I assisted them with Fura-2/AM calcium imaging experiments on the "CoatesScope" imaging system in my boss' lab (Prof. Thomas D. Coates, CHLA). In summer 2003 Sunil moved to Singapore.

X. Wang, M. Rosol, S. Ge, D. Peterson, G. McNamara, H. Pollack, D.B. Kohn, M.D. Nelson, G.M. Crooks (2003) Dynamic tracking of human hematopoietic stem cell engraftment using in vivo bioluminescence imaging. Blood 102: 3478-3482. (free access) PDF at Blood. DOI 10.1182/blood-2003-05-1432. PubMed abstract PMID 12946998. Gay Crooks lab has been studying hematopoietic stem cells (HSCs) for a long time. Xiuli Wang and Shundi Ge introduced a humanized version of the firefly luciferase gene into human HSCs with the help of Denise Peterson and Prof. Don Kohn. The luciferase expression was verified in multiwell plate assays in Marv Nelson's Xenogen 3D IVIS instrument (HSCs are a lot dimmer than mesenchymal stem cells that expressed the same construct). Xiuli and Shundi then injected the HSCs into mice. Mike Rosol and Harvey Pollack (and a couple of times, me), imaged the "glow in the dark" mice in the Xenogen system. Each imaging session took a few minutes with the mouse being under a gas anesthesia (Harvey made several improvements to Xenogen's gas rig). After imaging the mice were returned to their cages. The key to the paper is that in traditional HSC tracking experiments, mice are sacrificed at each time point. With the Xenogen instrument, we were able to image each mouse, return it to its cage, and then image a few days later. As a longitudinal study, each mouse served as its own control.

X. Wang, S. Ge, G. McNamara G, Q.L. Hao, G.M. Crooks, J.A. Nolta (2003) Albumin expressing hepatocyte-like cells develop in the livers of immune-deficient mice transmitted with highly purified human hematopoietic stem cells. Blood 101: 4201-4208. Jan Nolta's lab, in collaboration with Gay Crooks' lab, established an excellent model to test the hypothesis that human hematopoietic stem cells (or more likely their progeny) can differentiate into liver hepatocytes. This field of research, known as "regenerative medicine", has great potential for reducing the need for organ donor transplants, but is marred by controversies involving irreproducible results (which I suspect are often due to inadequate description of methodology multiplied by incapacity/unwilling to use exactly the same methods in other labs) as well as by certain domineering personalities who hold the field back with their personal agendas (of course that's just my opinion). Being cutting edge research the field also runs into interesting biology, including pluripotency (ability of a blood stem cell to produce progeny that differentiate into hepatocytes), trans-differentiation (a cell in one lineage, i.e. a differentiated blood cell, to change phenotype or have one or more of its progeny, to become a hepatocyte), as well as cell fusion (i.e. a blood cell fusing with a liver cell, and the cell or its progeny having both genomes and differentiation markers of one or both parental cells). The bottom line is that there is plenty of room for good work in the field and Jan's model is a good one to work on.

C.F. Chantrain, Y.A. DeClerck, S. Groshen, G. McNamara (2003) Computerized quantification of tissue vascularization using high-resolution slide scanning of whole tumor sections. J. Histochem. Cytochem. 51: 151.158. Polaroid SprintScan 4000Plus 35 mm film scanner and Meyer Instruments Pathscan microscope slide adapter to scan histology slides. See our Tiki God and Tiki Goddess for examples of Pathscan images, or the Meyer Instruments Pathscan enabler III web page (Polaroid went bankrupt. so Meyer now uses a modified Microtek ArtixScan 4000tf scanner. Except for the logo, the ArtixScan is probably identical to the SprintScan). In early 2003 Christophe Chantrain returned to Belgium to save lives (he is a pediatrician) and do research.

I.A. Avramis, G. Christodoulopoulos, A. Suzuki, W.E. Laug, I. Gonzalez-Gomez, G. McNamara, E.A. Sausville, V.I. Avramis (2002) In vitro and in vivo evaluations of the tyrosine kinase inhibitor NSC 680410 against human leukemia and glioblastoma cell lines. Cancer Chemother Pharmacol. 50: 479-489.

M.V. Macville, J.A. Van der Laak, E.J. Speel, N. Katzir, Y. Garini, D. Soenksen, G. McNamara, P.C. de Wilde, A.G. Hanselaar, A.H. Hopman, T. Ried (2001) Spectral imaging of multi-color chromogenic dyes in pathological specimens. Anal Cell Pathol. 22: 133-142. (Analytical Cell Pathology). Please contact Merryn Macville for a reprint <merryn.macville [at] gen.unimaas.nl>.

The three patents are from when I was at Applied Spectral Imaging, Inc. ("ASI", www.spectral-imaging.com) in Carlsbad, CA. For more information on spectral imaging, spectral imaging microscopy, spectral karyotyping (SKY^TM), and spectral pathology, check the ASI web site or my Seminars page. Dirk Soenksen is now at Aperio (www.aperio.com) making high resolution slide scanners (you can think of this as either a microscope without eyepieces or a microscope resolution version of the SprintScan/PathScan combination). Yuval Garini is again with Ted Young's group at Delft University of Technology in the Netherlands (Yuval's homepage). Nir Katzir is still at ASI. Dario Cabib and Bob Buckwald co-founded ASI. They are still involved with ASI but spend most of their time at C.I. Systems (they spun ASI out of C.I. ~1993).

	Temporal Area Map of a Dictyostelium discoideum ameba (TAM). The time-lapse series of 49 phase contrast images of a Dicty cell quivering (extending pseudopods over time but not going anywhere) was acquired ca. 1990 on a Nikon Diaphot microscope, (Dage-MTI?) video camera and Image-1/AT imaging system, while I was a post-doc in the laboratory of Professor Neal L. First, University of Wisconsin-Madison. The 49 images were binarized (cell = 1, background = 0), and then added together. The white area in the middle = 49, meaning the cell covered those pixels for the entire time series. The blue extensions are where the cell extended and then retracted a pseudopod. I obtained some advice from UIC's Dave Szent-Gyorgyi on doing image arithmetic in the video buffers of the Image-1/AT's MVP-AT frame grabber card (thanks again, Dave). This is now trivial to do in current image analysis software (ex. Stack Arithmetic: Sum, in MDC/UIC's MetaMorph). In fact, how easy it is to compute this image is a good test of how user friendly an image processing software product is. See the Temporal Area Map web page for additional information on TAM and the use of TAM histograms for chemotaxis and populations studies.

	Carl Boswell & George McNamara Fluorescence Spectra Web Server - developed and hosted at the University of Arizona. The logo is a merger of fluorescein (pH 9) fluorescence excitation and emission spectra, with a 2003 Pink Floyd Dark Side of the Moon (DSOTM) logo. Carl introduced me something called synchronicity. If you enjoy listening to Pink Floyd, and enjoy rainbows (spectra), check out the Dark Side of the Rainbow (DSOTR) web site (or do a Google search on the phrase). Did Roger Waters or David Gilmour or Sid Barrett have a crush on Judy Garland growing up?

	Tiki God and Tiki Goddess. Trichrome tissue section of a young mouse body, and mouse head & body cross sections, respectively, acquired with a Polaroid SprintScan 4000+ and Pathscan Enabler microscope slide adapter. Tiki Goddess, was stitched together with Photoshop. Tiki God is about 30 mm long, Tiki Goddess is ~40 mm long. For more on the Tiki's, please see http://home.earthlink.net/~tiki_goddess/ (note: lowercase tiki_goddess and backspace are required) The direct web link to the full size Tiki Goddess is http://home.earthlink.net/~tiki_goddess/TikiGoddess11.jpg (you may want to download and worship her at full size on your own computer if your web browser shrinks her for display purposes. Some web browsers also have a hard to find zoom option if you move the cursor near the shrunken image).

A. My boss at CHLA, Tom Coates, named Tiki God. At the time (2000), I had not stitched together Tiki Goddess.

A. You are welcome to send personal checks to the Tiki's, care of me (make them out to me). Sorry, but Church of the Tiki's is not a tax exempt organization. An alternative way to honor the Tiki's is to make a contribution to the CHLA Foundation ... or now that I'm at City of Hope (CoH), you can donate there as well.

Q. Is Tiki a God or a Goddess? That is, is the tissue section from a male or female mouse.

A. Goddess. After many years of asking anatomists and developmental biologists what sex mouse the tissue section is derived from, Bob Munn and Sandy Borowsky at the UC Davis Center for Comparative Medicine, pointed out some sexually dimorphic features that indicate female. They had access to the slide - you are welcome to email me (geomcnamara@earthlink.net) what sex you think Tiki is and why.

12/2002 Photo at the CHLA Saban Research Institute Congressman Julian Dixon Cellular Imaging Core ("Image Core") Leica SP1/DMIRBE Confocal Microscope.