Dr. James H. Werner Profile

Dr. James H. Werner

Technical Staff Member at Los Alamos National Lab

SPIE Involvement:

Author

Publications (25)

Proceedings Article | 13 March 2024 Presentation

Super-resolution and lifetime imaging of nano-emitters

Duncan Ryan, James Werner, Rebecca Sandoval, Bibek Dhakal, Alan Van Orden, Martin Gelfand

Proceedings Volume PC12849, PC128490Q (2024) https://doi.org/10.1117/12.3000581

KEYWORDS: Super resolution, Fluorescence lifetime imaging, Quantum emitters, Microscopy, Fluorophores, Cameras, Super resolution microscopy, Single photon detectors, Semiconductor quantum dots, Quenching

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Proceedings Article | 13 March 2024 Presentation

SPAD arrays and crossed-delay line detectors for quantum ghost imaging

Duncan Ryan, James Werner, Kristina Meier, Rebecca Sandoval, David Thompson, David Palmer, Raymond Newell, Edoardo Charbon, Claudio Bruschini

Proceedings Volume PC12863, PC128630D (2024) https://doi.org/10.1117/12.3000584

KEYWORDS: Quantum ghost imaging, Single photon avalanche diodes, Imaging arrays, Detector arrays, Quantum devices, Quantum correlations, Cameras, Quantum temporal imaging, Quantum technology applications, Quantum limits

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Proceedings Article | 12 March 2024 Presentation + Paper

Quantum ghost imaging of undisturbed live plants

Duncan Ryan, Kristina Meier, Rebecca Sandoval, David Thompson, David Palmer, Raymond Newell, Kati Seitz, Demosthenes Morales, David Hanson, James Werner

Proceedings Volume 12854, 128540C (2024) https://doi.org/10.1117/12.3000583

KEYWORDS: Quantum ghost imaging, Quantum detection, Quantum correlations, Windows, Near infrared, Sensors, Biological imaging, Single photon detectors, Image transmission, Photodetectors

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Proceedings Article | 15 March 2023 Presentation + Paper

Time-resolved super-resolution microscopy to image photoluminescence lifetimes and spatially resolve dual emitter semiconductor nanostructures

Megan Dunlap, Liam Koch, Duncan Ryan, Peter Goodwin, James Werner, Paul Bourdin, Jennifer Hollingsworth, Chris Sheehan, Martin Gelfand, Alan Van Orden

Proceedings Volume 12386, 123860C (2023) https://doi.org/10.1117/12.2650337

KEYWORDS: Photons, Quantum emitters, Pulsed laser operation, Point spread functions, Super resolution, Semiconductors, Photoluminescence, Super resolution microscopy, Nanostructures, Time correlated single photon counting

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Proceedings Article | 15 March 2023 Presentation

Super-resolution localization microscopy with orientation and spectral discrimination (Conference Presentation)

Duncan Ryan, Peter Goodwin, James Werner, Somak Majumder, Jennifer Hollingsworth, Megan Dunlap, Alan Van Orden, Martin Gelfand

Proceedings Volume PC12386, PC123860C (2023) https://doi.org/10.1117/12.2647902

KEYWORDS: Microscopy, Atmospheric particles, Super resolution, Quantum dots, Semiconductors, Particles, Optical microscopy, Nanolithography, Nanocrystals, Microscopes

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Proceedings Article | 9 March 2023 Presentation

Biological quantum imaging with non-degenerate photon pairs

Duncan Ryan, James Werner, Kristina Meier, David Thompson, Peter Goodwin, Rebecca Holmes, Raymond Newell, Demosthenes Morales, David Hanson, Scott Twary, Kati Seitz

Proceedings Volume PC12447, PC1244738 (2023) https://doi.org/10.1117/12.2647903

KEYWORDS: Near infrared, Imaging devices, Photosynthesis, Photodetectors, Microscopes, Imaging technologies

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Proceedings Article | 8 March 2023 Presentation + Paper

Quantum ghost imaging for non-destructive plant imaging using highly non-degenerate spontaneous parametric downconversion

Kristina Meier, Duncan Ryan, David Thompson, Raymond Newell, Rebecca Holmes Sandoval, James Werner

Proceedings Volume 12447, 124471F (2023) https://doi.org/10.1117/12.2663941

KEYWORDS: Quantum ghost imaging, Crystals, Biological imaging, Cameras, Quantum entanglement, Photonic crystals, Nonlinear crystals, Quantum processes, Nondestructive evaluation, Single photon avalanche diodes

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Proceedings Article | 13 February 2020 Presentation + Paper

Dual-color super-resolution imaging of quantum dot clusters

Duncan Ryan, Megan Dunlap, Somak Majumder, Chris Sheehan, James Werner, Jennifer Hollingsworth, Martin Gelfand, Alan Van Orden, Peter Goodwin

Proceedings Volume 11246, 112460B (2020) https://doi.org/10.1117/12.2542352

KEYWORDS: Super resolution, Atmospheric particles, Quantum dots, Energy transfer, Luminescence, Beam splitters, Sensors, Fluorescence resonance energy transfer, Particles, Scanning electron microscopy

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Proceedings Article | 13 February 2020 Presentation + Paper

Single molecule localization with four avalanche photodiode detectors

Megan Dunlap, Duncan Ryan, Peter Goodwin, James Werner, Somak Majumder, Jennifer Hollingsworth, Martin Gelfand, Alan Van Orden

Proceedings Volume 11246, 112460O (2020) https://doi.org/10.1117/12.2546573

KEYWORDS: Sensors, Point spread functions, Monte Carlo methods, Optical fibers, Avalanche photodetectors, Avalanche photodiodes, Luminescence, Molecules, Time correlated photon counting, Super resolution microscopy, Fluorescence lifetime imaging, Single photon detectors, Single molecule spectroscopy, Quantum dots

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SPIE Journal Paper | 25 October 2016 Open Access

Light-sheet microscopy by confocal line scanning of dual-Bessel beams

Pengfei Zhang, Mary Phipps, Peter Goodwin, James Werner

JBO, Vol. 21, Issue 10, 100502, (October 2016) https://doi.org/10.1117/12.10.1117/1.JBO.21.10.100502

KEYWORDS: Bessel beams, Digital micromirror devices, Confocal microscopy, Luminescence, Microscopy, Imaging systems, Microscopes, Spatial filters, Mirrors, Photons

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Proceedings Article | 12 March 2015 Paper

Three dimensional time-gated tracking of non-blinking quantum dots in live cells

Matthew DeVore, Dominik Stich, Aaron Keller, Yagna Ghosh, Peter Goodwin, Mary Phipps, Michael Stewart, Cédric Cleyrat, Bridget Wilson, Diane Lidke, Jennifer Hollingsworth, James Werner

Proceedings Volume 9338, 933812 (2015) https://doi.org/10.1117/12.2082943

KEYWORDS: Luminescence, Microscopes, Quantum dots, Particles, Signal to noise ratio, Sensors, Proteins, Molecules, Receptors, Fluorescent proteins

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Proceedings Article | 9 September 2014 Paper

The optical properties of conjugated materials and their aggregates: towards imaging of films and devices

Linda Peteanu, Jiyun Hong, SuKyung Jeon, Janice Kim, Diane Devi, Jurjen Wildeman, Matthew Sfeir, James Werner, Andrew Shreve

Proceedings Volume 9165, 91650L (2014) https://doi.org/10.1117/12.2063460

KEYWORDS: Fluorescence lifetime imaging, Polymers, Microscopy, Luminescence, Picosecond phenomena, Gold, Optical properties, Chromophores, Solar energy, Nanomaterials

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Proceedings Article | 4 March 2014 Paper

Fast, 3D imaging via confocal line scanning of a Bessel beam using a single galvo mirror

Pengfei Zhang, Peter Goodwin, James Werner

Proceedings Volume 8947, 89471K (2014) https://doi.org/10.1117/12.2036848

KEYWORDS: Luminescence, Bessel beams, Image filtering, Stereoscopy, Confocal microscopy, Cameras, 3D image processing, Mirrors, Microscopes, Optical filters

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Proceedings Article | 4 March 2014 Paper

Enhanced 3D localization of individual RNA transcripts via astigmatic imaging

Evan Perillo, Leyma De Haro, Mary Phipps, Jennifer Martinez, Hsin-Chih Yeh, Andrew Dunn, Douglas Shepherd, James Werner

Proceedings Volume 8950, 895003 (2014) https://doi.org/10.1117/12.2038197

KEYWORDS: 3D image processing, Image resolution, Microscopes, Point spread functions, Imaging systems, Calibration, Molecules, 3D image enhancement, Tissues, Image processing

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SPIE Journal Paper | 10 January 2014 Open Access

Actin restructuring during Salmonella typhimurium infection investigated by confocal and super-resolution microscopy

Jason Han, Yuliya Kunde, Elizabeth Hong-Geller, James Werner

JBO, Vol. 19, Issue 01, 016011, (January 2014) https://doi.org/10.1117/12.10.1117/1.JBO.19.1.016011

KEYWORDS: Bacteria, Microscopy, Confocal microscopy, Cytoskeletons, Luminescence, Microscopes, Optical microscopy, Molecules, Visualization, Proteins

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Proceedings Article | 13 February 2012 Paper

New tools for discovering the role sRNA plays in cellular regulation

Douglas Shepherd, Nan Li, Elizabeth Hong-Geller, Brian Munsky, James Werner

Proceedings Volume 8228, 822808 (2012) https://doi.org/10.1117/12.910540

KEYWORDS: Luminescence, Genetics, Molecules, Multiplexing, 3D image processing, Stochastic processes, Imaging systems, Optical filters, Microscopes, Image filtering

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Proceedings Article | 13 February 2012 Paper

"Sizing" the oligomers of Azami Green fluorescent protein with FCS and antibunching

Jamshid Temirov, James Werner, Peter Goodwin, Andrew Bradbury

Proceedings Volume 8228, 82280J (2012) https://doi.org/10.1117/12.906843

KEYWORDS: Fluorescence correlation spectroscopy, Molecules, Proteins, Fluorescent proteins, Green fluorescent protein, Luminescence, Diffusion, Fluorescence spectroscopy, Sensors, Molecular spectroscopy

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Proceedings Article | 17 February 2010 Paper

Photophysical characterization of fluorescent metal nanoclusters synthesized using oligonucleotides, proteins and small molecule ligands

Hsin-Chih Yeh, Jaswinder Sharma, Hyojong Yoo, Jennifer Martinez, James Werner

Proceedings Volume 7576, 75760N (2010) https://doi.org/10.1117/12.842192

KEYWORDS: Luminescence, Metals, Silver, Gold, Fluorescence correlation spectroscopy, Quantum efficiency, Molecules, Proteins, Chemical species, Transition metals

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Proceedings Article | 25 February 2009 Paper

Going beyond 2D: following membrane diffusion and topography in the IgE-Fc[epsilon]RI system using 3-dimensional tracking microscopy

Nathan Wells, Guillaume Lessard, Mary Phipps, Peter Goodwin, Diane Lidke, Bridget Wilson, James Werner

Proceedings Volume 7185, 71850Z (2009) https://doi.org/10.1117/12.809412

KEYWORDS: Diffusion, Receptors, Microscopes, Plasma, Microscopy, Quantum dots, Particles, Confocal microscopy, Molecules, Signal processing

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SPIE Journal Paper | 1 May 2008 Open Access

Probing dimerization and intraprotein fluorescence resonance energy transfer in a far-red fluorescent protein from the sea anemone Heteractis crispa

Guillaume Lessard, Satoshi Habuchi, James Werner, Peter Goodwin, Frans De Schryver, Johan Hofkens, Mircea Cotlet

JBO, Vol. 13, Issue 03, 031212, (May 2008) https://doi.org/10.1117/12.10.1117/1.2937477

KEYWORDS: Chromophores, Luminescence, Green fluorescent protein, Fluorescence resonance energy transfer, Proteins, Fluorescence correlation spectroscopy, Fluorescent proteins, Fluorescence spectroscopy, Molecules, Diffusion

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Proceedings Article | 27 February 2006 Paper

Three-dimensional tracking of fluorescent particles

Guillaume Lessard, Peter Goodwin, James Werner

Proceedings Volume 6092, 609205 (2006) https://doi.org/10.1117/12.650191

KEYWORDS: Particles, Sensors, Monte Carlo methods, Molecules, Luminescence, Diffusion, Fluorescence correlation spectroscopy, Photons, 3D acquisition, Target detection

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Proceedings Article | 27 February 2006 Paper

Surface-immobilized antibody-antigen binding studies by single molecule fluorescence imaging

Jamshid Temirov, Andrew Bradbury, James Werner

Proceedings Volume 6092, 60920O (2006) https://doi.org/10.1117/12.645334

KEYWORDS: Molecules, Quantum dots, Luminescence, Glasses, Silver, Microscopy, Proteins, Solids, Ultraviolet radiation, Cameras

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Proceedings Article | 27 February 2006 Paper

Time-resolved detection of the one- and two-photon excited fluorescence of single molecules of a folding enhanced green fluorescent protein

Mircea Cotlet, Peter Goodwin, Geoffrey Waldo, James Werner

Proceedings Volume 6092, 609204 (2006) https://doi.org/10.1117/12.646697

KEYWORDS: Luminescence, Molecules, Green fluorescent protein, Signal detection, Chromophores, Fluorescence spectroscopy, Proteins, Molecular lasers, Absorption, Rhodamine

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Proceedings Article | 22 February 2006 Paper

Single molecule spectroscopic characterization of a far-red fluorescent protein (HcRed) from the Anthozoa coral Heteractis crispa

Mircea Cotlet, Satoshi Habuchi, Jennifer Whitier, James Werner, Frans De Schryver, Johan Hofkens, Peter Goodwin

Proceedings Volume 6098, 609804 (2006) https://doi.org/10.1117/12.646811

KEYWORDS: Luminescence, Chromophores, Proteins, Molecules, Molecular spectroscopy, Fluorescence spectroscopy, Green fluorescent protein, Absorption, Spectroscopy, Fluorescent proteins

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We report on the photophysical properties of a far-red intrinsic fluorescent protein by means of single molecule and ensemble spectroscopic methods. The green fluorescent protein (GFP) from Aequorea victoria is a popular fluorescent marker with genetically encoded fluorescence and which can be fused to any biological structure without affecting its function. GFP and its variants provide emission colors from blue to yellowish green. Red intrinsic fluorescent proteins from Anthozoa species represent a recent addition to the emission color palette provided by GFPs. Red intrinsic fluorescent markers are on high demand in protein-protein interaction studies based on fluorescence-resonance energy transfer or in multicolor tracking studies or in cellular investigations where autofluorescence possesses a problem. Here we address the photophysical properties of a far-red fluorescent protein (HcRed), a mutant engineered from a chromoprotein cloned from the sea anemone Heteractis crispa, by using a combination of ensemble and single molecule spectroscopic methods. We show evidence for the presence of HcRed protein as an oligomer and for incomplete maturation of its chromophore. Incomplete maturation results in the presence of an immature (yellow) species absorbing/fluorescing at 490/530-nm. This yellow chromophore is involved in a fast resonance-energy transfer with the mature (purple) chromophore. The mature chromophore of HcRed is found to adopt two conformations, a Transoriented form absorbing and 565-nm and non-fluorescent in solution and a Cis-oriented form absorbing at 590-nm and emitting at 645-nm. These two forms co-exist in solution in thermal equilibrium. Excitation-power dependence fluorescence correlation spectroscopy of HcRed shows evidence for singlet-triplet transitions in the microseconds time scale and for cis-trans isomerization occurring in a time scale of tens of microseconds. Single molecule fluorescence data recorded from immobilized HcRed proteins, all point to the presence of two classes of molecules: proteins with Cis and Trans-oriented chromophores. Immobilization of HcRed in water-filled pores of polyvinyl alcohol leads to a polymer matrix - protein barrel interaction which results in a 'freezing' of the chromophore in a stable conformation for which non-radiative deactivation pathways are either suppressed or reduced. As a result, proteins with both Cis- and Trans-oriented chromophores can be detected at the single molecule level. Polymer chain motion is suggested as a mediator for an eventual cis-trans isomerization of the chromophore in the case of single immobilized proteins.

Proceedings Article | 3 May 1999 Paper

Current status of DNA sequencing by single molecule detection

James Werner, Hong Cai, Peter Goodwin, Richard Keller

Proceedings Volume 3602, (1999) https://doi.org/10.1117/12.347535

KEYWORDS: Molecules, Luminescence, Laser beam diagnostics, Molecular lasers, Laser development, Rhodamine, Laser induced fluorescence, Fluorescence spectroscopy, Error analysis, Optical tweezers

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