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




George McNamara - Biography

August 2007 Version (C.V. in NIH Biosketch format, plus bio as work experience)


George McNamara, Ph.D.

Core Leader - Image Analysis

Analytical Imaging Core, DRI 6025

Miller School of Medicine, DRI & SCCC


Mailing address:

University of Miami

1450 NW 10th Ave (R-134)

Miami, FL 33136


305-243-8436 office







George McNamara, Ph.D.


Imaging Scientist, CHLA

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)





State University of New York at Albany

University of Illinois at Urbana‑Champaign






Genetics & Development

RESEARCH AND PROFESSIONAL EXPERIENCE:  Concluding with present position, list, in chronological order, previous employment, experience, and honors.  Include present membership on any Federal Government public advisory committee.  List, in chronological order, the titles, all authors, and complete references to all publications during the past three years and to representative earlier publications pertinent to this application.  If the list of publications in the last three years exceeds two pages, select the most pertinent publications. 

Positions and Employment

5/2007-            Core Leader, Analytical Imaging Facility, Diabetes Research Institute and Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL

1/2007-2/2007 Staff Research Associate V, Stem Cell Program, UC Davis Medical Center, Sacramento, CA.

2006-               Consultant, Division of Cancer Immunotherapeutic and Tumor Immunology (CITI) and Division of Molecular Medicine, City of Hope National Medical Center, Duarte, CA.

2006                Support Scientist, Division of Cancer Immunotherapeutic and Tumor Immunology (CITI) and Division of Molecular Medicine, City of Hope National Medical Center, Duarte, CA.

2005-2006       Support Scientist, Division of Cancer Immunotherapeutic and Tumor Immunology (CITI), City of Hope National Medical Center, Duarte, CA.

2005-               Consultant, Congressman Dixon Cellular Imaging Core, Saban Research Institute, Childrens Hospital Los Angeles, Los Angeles, CA.

2000-2005       Imaging Scientist, Congressman Dixon Cellular Imaging Core, Saban Research Institute, Childrens Hospital Los Angeles, Los Angeles, CA.

1997-2000       Applications Scientist, Applied Spectral Imaging, Inc., Carlsbad, CA.

1992-1997       Applications Scientist, Universal Imaging Corporation, West Chester, PA.

1989-1991       Research Associate, Department of Meat and Animal Science and Primate Research Center, University of Wisconsin‑Madison.

1987-1988       Associate Research Specialist, Department of Bacteriology, University of Wisconsin‑Madison.

1981-1986       Graduate Teaching Assistant, Department of Genetics & Development, University of Illinois at Urbana‑Champaign. Ph.D. in the laboratory of Professor Robert P. Futrelle.



2002                Henry L. Guenther Foundation award for “Small Animal In Vivo Fluorescence and Bioluminescence Tomography Instrument,

                        CHLA. Xenogen 3D imaging system purchase.

2001                Engineering development award for “In Vivo Fluorescence Emission Tomography”, CHLA.


Other Experience and Professional Memberships

2004                Journal of Histotechnology

2001                National Society for Histotechnology

2000                Histochemical Society                                                                       

1997                Royal Microscopical Society



Selected peer-reviewed publications

McNamara G, Yanai A, Khankaldyyan V, Laug WE: Low magnification confocal microscopy of tumor angiogenesis in S. Paddock (ed.), Confocal Microscopy: Methods and Protocols 2nd Edition. Humana Press. Totowa, submitted.

Chang L, Chang W-C, McNamara G, Aguilar B, Ostberg JR, Jensen MC: Enforced costimulation of CD4+ T cells leads to enhanced and sustained anti-tumor effector functioning. Submitted.

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.     Draft   Data 

Singh H, Serrano LM, Pfeiffer T, Olivares S, McNamara G, Smith DD, AI-Kadhimi Z, Forman SJ, Gillies SD, Jensen MC, Colcher D, Raubitschek A, Cooper LJN: Combining adoptive cellular and immunocytokine therapies to improve treatment of B-Lineage malignancy. Cancer Res 67: 2872-2880.

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.

McNamara G, Gupta A, Reynaert J, Coates TD, Boswell C: Spectral imaging microscopy web sites and data. Cytometry. 69A: 863-871. DOI: 10.1002/cyto.a.20304

Garini, Y, Young IT, McNamara G: Spectral Imaging: Principles and applications. Cytometry. 69A: 735-747. DOI: 10.1002/cyto.a.20311 

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. doi:10.1369/jhc.5B6902.2006

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.

 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. Supplemental figure 1 and video 1 at

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.

McNamara G: Color balancing histology images for presentations and publication. J Histotechnology 28: 81-88, 2005.

McNamara G: Introduction to Fluorescence Immunocytochemistry, in D.L. Spector, R. Goldman, (eds.), Basic Methods in Light Microscopy. Protocols and Concepts from Cells: A laboratory manual and Live Cell Imaging: A laboratory manual. Cold Spring Harbor Laboratory Press, 2005.

Sukumaran SK, McNamara G, Prasadarao NV: Escherichia coli K-1 interaction with human brain microvascular endothelial cells trigger phospholipase C-gamma 1 activation downstream of P13-kinase. J Biol Chem 278: 45753-45762. 2003. DOI: 10.1074/jbc.M307374200.

Wang X, Rosol M, Ge S, Peterson D, McNamara G, Pollack H, Kohn DB, Nelson MD, Crooks GM: Dynamic tracking of human hematopoietic stem cell engraftment using in vivo bioluminescence imaging. Blood 102: 3478-3482, 2003. . DOI 10.1182/blood-2003-05-1432.

Chantrain C, DeClerck Y, Groshen S, McNamara G: Computerized quantification of tissue vascularity using high resolution slide scanning of whole tumor sections. J. Histochem Cytochem 51: 151-157, 2003.

Wang X, Ge S, McNamara G, Hao QL, Crooks GM, Nolta JA: Albumin-expressing hepatocyte-like cells develop in the livers of immune-deficient mice that received transplants of highly purified human hematopoietic stem cells. Blood 101: 4201-4208, 2003.

Avramis IA, Christodoulopoulos G , Suzuki A, Laug WE, Gonzalez-Gomez I, McNamara G, Sausville EA, Avramis VI: In vitro and in vivo evaluation of the tyrosine kinase inhibitor NSC680410 against human leukemia and glioblastoma cell lines. Cancer Chemotherapy Pharmacology 50: 479-489, 2002.

Macville MV, Van Der Laak JA, Speel EJ, Katzir N, Garini Y, Soenksen D, McNamara G, de Wilde PC, Hanselaar AG, Hopman AH, Ried T: Spectral imaging of multi-color chromogenic dyes in pathological specimens. Anal Cell Pathol 22: 133-142, 2001.

Garini Y, McNamara G, Soenksen D, Cabib D, Buckwald RA: In-situ method of analyzing cells. US Patent 6,165,734, 2000.

Weier H-UG, Smida J, Zitzelsberger H, Lersch RA, Hung J, Hsieh HP, Salassidis K, McNamara G, Pedersen RA, Fung J,  Cytogenetic analysis of interphase cells using spectral imaging [SIm] technology. SPIE Proc 3920: 76-85, 2000.

McNamara G, Soenksen D, Cabib D, Buckwald RA:  In situ method of analyzing cells. US Patent 6,007,996, 1999.

Soenksen DC, McNamara G, Garini Y, Katzir N: Method of cancer cell detection. US Patent 5,995,645, 1999.

DiFilippantonio M, Ried T, McNamara G, Bieber FR: Microscopy and image analysis (Unit 4.4 in Supplement 22) in Current Protocols in Human Genetics. ISBN: 0-471-03420-7.  John Wiley & Sons. New York, 1999.

Zitzelsberger H, Fung J, Janish C, McNamara G, Bryant PE, Riches AC, Weier H-UG: Spectral karyotyping (SKY™) analysis of heritable effects of radiation-induced malignant transformation. SPIE Proc. 3605: 325-331, 1999.

McNamara G: Introduction to fluorescence immunocytochemistry, in D.L. Spector, R. Goldman, L. Leinwand (eds.), Cells: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1997. (reprinted in Spector and Goldman 2005).

McNamara G:  Fluorescence Microscopy. J. NIH Res. 6(10): 80, 1994.

McNamara G: Silver Grain Counting. J. NIH Res. 5(11): 70, 1993.

Rosenkrans CF Jr, Zeng GQ, MCNamara GT, Schoff PK, First NL: Development of bovine embryos in vitro as affected by energy substrates. Biol Reprod. 49: 459-462. 1993.

Science Websites

Boswell C, McNamara G (2006) Fluorescent Spectra: An interactive, exploratory website.

McNamara G, Boswell C (2006) PubSpectra

McNamara G (2006) Multi-Probe Microscopy

McNamara G (2006) Tiki Goddess (microscope slide scanning)

McNamara G (2006) George McNamara Homepage

Additional Publications

McNamara G, Boswell CA: Biomedical light microscopy imaging facility management. Lab Manager Magazine 2(3): 11-15, 2007.

Shading Correction and Background Subtraction. UIC T10009. 1997.

Using Optical Density (Scaled) for Densitometry. UIC T10012. 1997.

Christenson MA, McNamara G: Recent advances in multidimensional imaging. Biophotonics Intl. 1(2): 42-46, 1995.


MetaMorph imaging system (Molecular Devices): 11+ years (MetaMorph Premier: 1 year)

MetaFluor (ion ratio) imaging system (Molecular Devices): 10 years

Leica SP1 confocal microscope: 5 years

Leica DMRXA automated microscope: 5 years

Leica MZFLIII motorized fluorescence stereomicroscope: 5 years

Leica AS LMD laser microdissection system: 0.25+ year

Leica MP/SP5/FCS/FLIM confocal/multiphoton microscope: 0.2+ year

Leica SP5 confocal microscope: 0.2+ year

Zeiss LSM 510 META NLO confocal/multiphoton microscope: 1+ year

Zeiss LSM 510 confocal microscope 0.25+ year

Zeiss Apotome/Axiovert 200M microscope: 0.25+ year

SKY™ Spectral Imager (Applied Spectral Imaging Inc): 7+ years

Xenogen IVIS 3D small animal imager: 1+ year (co-authored grant; occasional user)

CompuCyte iCys laser scanning cytometer: 0.5 year

CompuCyte LSC/wincyte laser scanning cytometer: 0.25+ year

Additional imaging software includes: Adobe Photoshop CS2 /Fovea Pro 4.0, ImageJ, Compix SimplePCI, Diagnostic Instruments SPOT. Scanner software includes Hamrick VueScan, LaserSoft SilverFast Ai, and additional scanner software.

Application software includes: Microsoft Office (Word, Excel, Access, Outlook, PowerPoint, FrontPage), X1 desktop search, Adobe Acrobat, Adobe Premier Pro 2.0. The PubSpectra dataset (McNamara et al 2006 Cytometry) includes over 2000 fluorescent dye and filter set spectra in a standardized Excel format.

Work Experience

I have been a cell biologist for 20+ years. For my Ph.D. research in the department of Genetics & Development at the University of Illinois Urbana-Champaign, I studied cell motility, shape changes and chemotaxis by time-lapse cinematography and computerized motion analysis. I wrote many of the data analysis software for this work. Prof. Robert P. Futrelle, my Ph.D. advisor, and I invented a new cell motion visualization method called temporal area maps (TAM, see Temporal Area Maps at my homepage Since the original work I’ve figured out that TAM histograms can provide quantitative signatures of cell behavior (see the web page for information). During my first post-doc I used DNA transfection insertional mutagenesis and isolation of cell behavioral and developmental mutants of Dictyostelium. For one year I managed the University of Wisconsin Integrated Microscopy Resource’s Expert Vision motion analysis system, and was the major user. During my second post-doc, in the laboratory of Prof. Neal L. First, I used DNA transfection with oncogenes to isolate an immortalized bovine oviduct epithelial cell line for use in embryo co-culture experiments. I also isolated mouse embryonic stem cells, tested growth methods for bovine and rhesus reproductive cells in vitro to use as “feeder layers” for future culturing of bovine and primate embryonic cell lines, and worked toward the isolation of bovine embryonic stem cells for in vitro and cloning studies. I also gave lab pointers to a Ph.D. student, T. Kim, in the lab (I avoid the writing that I gave advice, since his co-advisors were Professors Neal First and Howard Temin).

During my five years at Universal Imaging Corp., I was an applications scientist at UIC, and the main technical support, person for MetaMorph Imaging System. While in Prof. First’s lab I was the most computer literate user and had adopted our Image-1/AT & Image-1/FL system. During my initial years at UIC I occasionally supported the Image-1 products as well as MetaMorph. Most of my work entailed phone, e-mail and in-person interactions with many of UIC’s thousand customers and their lab personnel, training salespeople and dealers, and serving as commercial faculty at several microscopy courses.

Many of the 100+ application notes that I initiated can still be found on UIC’s web site and CD-ROM’s. My time at UIC rekindled my interest in cell shape and motion analysis, which led to my taking F.J. Rohlf’s Elliptical Fourier Analysis (EFA) shape package (see, converting the Fortran code to Turbo Pascal, adding in averaging routines, and various reconstructed and mean shape options (originally displayed in Image-1/AT). My Pascal code was also the template for UIC EFA morphometry calculations in MetaMorph.

I contributed as a non-programmer to the development of MetaMorph, both in communicating customer needs and in specifying the way certain commands worked (ex. stack arithmetic: sum for temporal area map computation and the co-localization scatterplot). A co-worker, Neal Gliksman, and I pushed for the development of MetaGFP and co-wrote much of the application manual explaining FRET and co-localization data analysis. For 3 weeks in summer 1997 I had the pleasure of doing a mini-sabbatical in the laboratory of Prof. James Spudich, Stanford University, where I worked with Dr. James Sabry putting MetaGFP through its paces. Later that summer I was downsized. This worked out well because (1) UIC was later purchased I might not have thrived in its corporate culture, and (2) I ended up moving to the West Coast, taking a job with a much higher salary, and having great colleagues.

In September 1997 I was recruited to Applied Spectral Imaging (ASI) in Carlsbad, CA, by their Vice President, Dirk Soenksen. My job involved support of ASI’s novel spectral karyotyping (SKY™) 24-color fluorescence microscopy application, as well as searching for additional uses for the technology. The latter resulted in three patents for spectral (imaging) unmixing in spectral pathology. During this time I chaired a session on spectral imaging at the 1998 Fifth U.S.-Japan Joint Meeting of Histochemistry and Cytochemistry at UCSD in La Jolla. At ASI I was involved in sales, marketing, technical support, microscope maintenance, and applications development. I served as commercial faculty for two years at two different Cold Spring Harbor laboratory microscopy courses (“Advanced In Situ Hybridization and Immunocytochemistry” and “Molecular Cytogenetics”). I founded and still moderate the SkyUsers electronic group forum.

In March 2000 I was recruited to Childrens Hospital Los Angeles to manage the Saban Research Institute’s Congressman Julian Dixon Cellular Imaging Facility (Image Core), under the direction of Dr. Thomas D. Coates. Tom was an Image-1/AT and later MetaMorph customer who I met first at a hematology conference in Philadelphia and later visited his lab in Los Angeles to set up an XYZλ automated microscope, which I now oversee. My job is to provide expert light microscopy and image analysis assistance and training to researchers. A very important function of the Image Core has become its contribution to CHLA VIP tours for our Saban Research Institute and with the CHLA Foundation for general hospital fund raising and for new recruitments. As of July 2004 the CHLA Image Core has assisted over 230 users from the laboratories of over 100 principal investigators (most at CHLA, a few from our academic affiliate, USC). The Core consists of a Leica SP (3 laser, 4 detector) confocal inverted microscope, a Leica DM RXA fluorescence/DIC/phase contrast microscope with SkyVision-2 spectral imager (re: Macville et al 2001), a Leica MZ FL III fluorescence stereomicroscope with digital CCD camera and SimplePCI software (i.e. a collaboration involving tracking flow and diffusion of Molecular Probes fluorescent beads in cerebrospinal fluid or at high speed in cerebral blood flow), and Zeiss Axioplan fluorescence microscope. I also supervise Dr. Coates’ laboratory automated fluorescence digital imaging microscope system for Fura-2/BCECF, GFP and time-lapse microscopy (Sukumaran et al publications). We have several image analysis software packages, including Leica confocal TCS and LCS software, MetaMorph, SkyView/SpectraView/EasyFISH, SlideBook, SimplePCI, AnalyzePC, NIH Image/ImageJ, Adobe Photoshop/Fovea Pro, Xenogen IVIS 3D and more. I specified the purchase of the ‘best bang for the buck’ instrument in the Core: the Polaroid SprintScan 4000+/PathScan Enabler combination from Meyer Instruments for scanning in histology microscope slides (Chantrain et al 2003). In Spring 2004 I borrowed a tissue microarray (TMA) microscope slide from Prof. Michael Anderson, CHLA, and found that the Pathscan Enabler/Polaroid SprintScan 4000+ combination was able to scan the TMA well enough for quantitative immunohistochemistry with MetaMorph.

After brief Microsoft FrontPage training by Director Coates, I develop the Image Core web site, which in four years has well over one hundred eighty web pages of content (http://shelia/image - a CHLA Intranet site). I handle instrument scheduling and Core billing using a combination of Microsoft Outlook, Excel and Access (Using Microsoft Outlook For Time Reporting on my homepage Director Coates gave me brief training on Microsoft Access, and I did the rest. I have taught several “Scientific Imaging with Adobe Photoshop” classes to CHLA staff. I co-authored two funded proposals for small animal imaging at CHLA (Xenogen IVIS 3D system arrived June 2002) as well as a spectral imaging sub-contract section for an NIH grant awarded to Prof. Clive Taylor, USC. I have written some 20 instrument instruction documents for the Image Core, plus the many web pages, and continue adding to the now 1200+ page Multi-Probe Microscopy document I started in 1997 in support of my lecture at a Nikon AQLM course at MBL, Woods Hole, NA (go to for download instructions).

CHLA projects in 2002 include cerebral blood flow and cerebrospinal fluid flow measurements on the fluorescence stereomicroscope (Drs. Yamada and McComb), several immunofluorescence and immunohistochemistry projects on Leica and/or confocal microscopes, bacterial invasion experiments (Dr. J. Badger), and low magnification confocal microscopy of cerebral vascular casts to visualize human glioblastoma antiangiogenic therapies in a mouse orthoptic implantation model (Drs. Laug, Yamada and McComb). I assisted with the immunofluorescence microscopy of a hematopoietic stem cell model in which some of the cells differentiated into hepatocytes in mice (Wang et al 2003). I supervised upgrades the stereomicroscope with dual objective lenses (1x and 0.4x) and “on axis” motorized Z-series, a better digital camera and additional filter sets and of the Leica microscope from a DMRA/RF-4 to a RMRXA/RF-8 with eight fluorescence filter cube positions, for which we have 12 cubes available. The confocal microscope was upgraded with 37 C dish and objective lens warmers. I have occasionally assisted users with the Xenogen IVIS 3D small animal bioluminescence imaging system. CHLA projects in 2003 have resulted in publications in J Biol Chem for calcium imaging of cells in culture, and assisted in the Xenogen in vivo imaging and trained a user on the microscopy imaging for the first publication on tracking of human hematopoietic stem cells by in vivo bioluminescent imaging (Wang et al 2003).

The cover of the March 1, 2004 issue of Cancer Research is a pair of confocal fluorescent angiography images from a CHLA project that I was involved in training and operating our Leica SP1 confocal microscope (I am acknowledged in the paper, Chantrain et al 2004 Cancer Res 64: 1675-1686). In Spring of 2004 I was invited to join the editorial board of the Journal of Histotechnology. This came about because of an issue involving digital images for publication (my PhD and postdoc involved live cell work – my actual hands on experience at “histotechniques” is incredibly limited).

I am collaborating with Prof. Carl Boswell on a “fluorescence spectra database” web site (online mid-2004, homepage is and spectra server at The collaboration started in Spring 2003 and as of Summer 2004 the prototype web site is looking good. I assembled the spectral data (from many sources, nearly one thousand spectra of fluorophore and filter data); Carl and his team of University of Arizona web developers set up the database and developed the web server. The spectral data  collection sprang from Dr. Coates wanting me to prove that the filter set(s) we wanted to order, for new fluorophores, were better than the standard sets that we already owned. This led me to discovering Carl’s original spectra web site and our collaboration. This work was published in the August 2006 issue of Cytometry

I've collected hundreds of additional spectra and data, as well a wonderful Microsoft Excel spreadsheet from Prof. János Szöllösi for calculating FRET distances from spectra. Ironically, in spite of the nearly thousand spectra, I have not touched a spectrofluorometer since a graduate Immunocytochemistry course taught by Prof. Ed Voss, UIUC. All the spectra have been obtained by downloading data from the Internet, un-scanning data from graphs (using Silk Scientifics Un-Scan-It software), or the data equivalent of “clone by phone” – email requests for data. I used to feel a little guilty about unscanning data from publications. However, a fascinating fact that I really only fully understood in Spring 2004 is that in the USA, facts and data cannot be copyrighted (so says the US Constitution and the US Supreme Court has agreed). Ive been intrigued by the “Open Access” publication model since it was introduced, but my new understanding of copyrighting suggests that we are just seeing the tip of the iceberg in what data can and should be released. This led in June 2004 to me providing two fluorescence data sets to J. Paul Robinson, Purdue University, for inclusion on his Microscopy Society of America 2004 meeting CD-ROM (CD2 for Microscopy and Imaging, at One data set is small molecule fluorophore data (excitation, emission maxima, extinction coefficient, quantum yield, lifetime, references. 4000+ entries in Excel) and the other is similar data for fluorescent proteins (nearly 300 entries, plus amino acid substitution data for nearly all 150+ Aequorea victoria GFP mutants). I’m looking forward to someday publishing these data sets, but in the meantime – since as data they cannot be copyrighted anyway – I've given them to Prof. Robinson and others.

In March 2005 I joined City of Hope National Medical Center. In March 2006, my supervisor decided he did not need me. Prof. Hua Yu and Prof. Richard Jove helped me out by hiring me part time while I started job hunting. I moved to UC Davis Medical Center in January 2007, and left in February 2007.

In May 2007 I joined University of Miami to become the Core Leader for the UM School of Medicine's Analytical Imaging Facility ("Image Core"). The Image Core is jointly managed by the Diabetes Research Institute and the Sylvester Comprehensive Cancer Center.


Here's what I looked like in April 2002 (maybe a little shinier than usual). 


12/2002: Here's me sitting at the CHLA Image Core's Leica SP confocal microscope.


Copyright ©2000-2007 George McNamara

This page was last updated on 08/18/07 .