Prof. Joel Kubby Profile

Prof. Joel Kubby

DECEASED at Univ of California Santa Cruz

SPIE Involvement:

Editor | Author

Publications (37)

Proceedings Article | 23 February 2018 Presentation + Paper

Conjugate adaptive optics with remote focusing in multiphoton microscopy

Xiaodong Tao, Tuwin Lam, Bingzhao Zhu, Marc Reinig, Joel Kubby, Qinggele Li

Proceedings Volume 10502, 105020E (2018) https://doi.org/10.1117/12.2292492

KEYWORDS: Scattering, Spatial light modulators, Adaptive optics, Skull, Laser scattering, 3D scanning, Light scattering, Objectives, Wavefronts, Two photon imaging

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Proceedings Article | 8 February 2017 Presentation + Paper

A three-photon microscope with adaptive optics for deep-tissue in vivo structural and functional brain imaging

Xiaodong Tao, Ju Lu, Tuwin Lam, Ramiro Rodriguez, Yi Zuo, Joel Kubby

Proceedings Volume 10051, 100510R (2017) https://doi.org/10.1117/12.2253922

KEYWORDS: Adaptive optics, Microscopy, Brain imaging, Brain, Scattering, Neurons, Calcium, In vivo imaging, Luminescence, Tissues, Microscopes, Imaging systems, Wavefronts, Neuroimaging

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SPIE Journal Paper | 2 December 2016 Open Access

Special Section Guest Editorial:Adaptive Optics and Wavefront Control for Biological Systems

Thomas Bifano, Joel Kubby, Sylvain Gigan

JBO, Vol. 21, Issue 12, 121501, (December 2016) https://doi.org/10.1117/12.10.1117/1.JBO.21.12.121501

KEYWORDS: Control systems, Wavefronts, Adaptive optics, Geometrical optics, Tissue optics, Biomedical optics, Microelectromechanical systems, Photonics, Microscopy, Medical research

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SPIE Journal Paper | 13 October 2016 Open Access

Enhancing image quality in cleared tissue with adaptive optics

Marc Reinig, Samuel Novak, Xiaodong Tao, Laurent Bentolila, Dustin Roberts, Allan MacKenzie-Graham, Sirie Godshalk, Mary Raven, David Knowles, Joel Kubby

JBO, Vol. 21, Issue 12, 121508, (October 2016) https://doi.org/10.1117/12.10.1117/1.JBO.21.12.121508

KEYWORDS: Adaptive optics, Monochromatic aberrations, Wavefronts, Tissues, Brain, Tissue optics, Image quality, Image enhancement, Neuroimaging, Scattering

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Proceedings Article | 15 March 2016 Presentation + Paper

High-speed channel demixing by scanning interferometric focusing with binary transmission matrix

Xiaodong Tao, Dare Bodington, Marc Reinig, Joel Kubby

Proceedings Volume 9717, 97170X (2016) https://doi.org/10.1117/12.2214349

KEYWORDS: Binary data, Dynamic light scattering, Light scattering, Adaptive optics, Wavefronts, Scattering, Interferometry, Multiple scattering, Modulation, Digital micromirror devices, Imaging systems, Tissues, Modulators, Mirrors

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Proceedings Article | 15 March 2016 Presentation + Paper

Non-iterative adaptive optical microscopy using wavefront sensing

J. Kubby, X. Tao, O. Azucena

Proceedings Volume 9718, 971805 (2016) https://doi.org/10.1117/12.2214275

KEYWORDS: Wavefront sensors, Adaptive optics, Tissues, Wavefronts, Stars, Point spread functions, Sensors, Confocal microscopy, Diffraction, Mirrors

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Proceedings Article | 9 March 2016 Presentation + Paper

Adaptive optics microscopy enhances image quality in deep layers of CLARITY processed brains of YFP-H mice

Florian Ermini, Xiaodong Tao, Joel Kubby, Laurent Bentolila, Dustin Roberts, Allan MacKenzie-Graham, Marc Reinig, Samuel Novack, S. Godshalk, M. Raven

Proceedings Volume 9690, 969008 (2016) https://doi.org/10.1117/12.2213283

KEYWORDS: Adaptive optics, Brain, Wavefronts, Microscopy, Tissues, Refractive index, Image enhancement, Image quality, Image processing, Tissue optics, Monochromatic aberrations, Neuroimaging, Point spread functions

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Proceedings Article | 27 February 2015 Paper

Large size MOEMS Fabry-Perot interferometer filter for focal plane array hyperspectral imaging

J. Chee, J. Hwu, T. Kim, J. Kubby, S. Velicu, N. Gupta

Proceedings Volume 9375, 93750K (2015) https://doi.org/10.1117/12.2076615

KEYWORDS: Electronic filtering, Staring arrays, Microopto electromechanical systems, Silicon, Electrodes, Computer aided design, Fabry–Perot interferometry, Hyperspectral imaging, Optical filters, Long wavelength infrared

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Proceedings Article | 21 May 2014 Paper

Miniaturized imaging spectrometer based on Fabry-Perot MOEMS filters and HgCdTe infrared focal plane arrays

S. Velicu, J. Bergeson, C. Buurma, Tae Sung Kim, J. Kubby, N. Gupta

Proceedings Volume 9100, 91000F (2014) https://doi.org/10.1117/12.2053902

KEYWORDS: Electronic filtering, Reflectivity, Spectroscopy, Semiconducting wafers, Infrared imaging, Infrared radiation, Interfaces, Staring arrays, Long wavelength infrared, Spectral resolution

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Imaging spectrometry can be utilized in the midwave infrared (MWIR) and long wave infrared (LWIR) bands to detect, identify and map complex chemical agents based on their rotational and vibrational emission spectra. Hyperspectral datasets are typically obtained using grating or Fourier transform spectrometers to separate the incoming light into spectral bands. At present, these spectrometers are large, cumbersome, slow and expensive, and their resolution is limited by bulky mechanical components such as mirrors and gratings. As such, low-cost, miniaturized imaging spectrometers are of great interest. Microfabrication of micro-electro-mechanicalsystems (MEMS)-based components opens the door for producing low-cost, reliable optical systems. We present here our work on developing a miniaturized IR imaging spectrometer by coupling a mercury cadmium telluride (HgCdTe)-based infrared focal plane array (FPA) with a MEMS-based Fabry-Perot filter (FPF). The two membranes are fabricated from silicon-oninsulator (SOI) wafers using bulk micromachining technology. The fixed membrane is a standard silicon membrane, fabricated using back etching processes. The movable membrane is implemented as an X-beam structure to improve mechanical stability. The geometries of the distributed Bragg reflector (DBR)-based tunable FPFs are modeled to achieve the desired spectral resolution and wavelength range. Additionally, acceptable fabrication tolerances are determined by modeling the spectral performance of the FPFs as a function of DBR surface roughness and membrane curvature. These fabrication non-idealities are then mitigated by developing an optimized DBR process flow yielding high-performance FPF cavities. Zinc Sulfide (ZnS) and Germanium (Ge) are chosen as the low and the high index materials, respectively, and are deposited using an electron beam process. Simulations are presented showing the impact of these changes and non-idealities in both a device and systems level.

SPIE Journal Paper | 21 March 2014 Open Access

Special Section Guest Editorial: Emerging MOEMS Technology and Applications

M. Edward Motamedi, Joel Kubby, Patrick Oden, Wibool Piyawattanametha

JM3, Vol. 13, Issue 01, 011101, (March 2014) https://doi.org/10.1117/12.10.1117/1.JMM.13.1.011101

KEYWORDS: Microopto electromechanical systems, Microelectromechanical systems, Micro optics, Mirrors, Photonics, Technologies and applications, Digital micromirror devices, Microsystems, Actuators

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SPIE Journal Paper | 13 March 2014

Design and fabrication of Fabry–Perot filters for infrared hyperspectral imagers

Michael Morley, Silviu Velicu, Yong Chang, Christoph Grein, Dmitry Kozak, Bautista Fernandez, Joel Kubby, Neelam Gupta

JM3, Vol. 13, Issue 01, 011116, (March 2014) https://doi.org/10.1117/12.10.1117/1.JMM.13.1.011116

KEYWORDS: Electronic filtering, Reflectivity, Infrared imaging, Hyperspectral imaging, Imaging systems, Optical filters, Infrared radiation, Semiconducting wafers, Image filtering, Surface roughness

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Proceedings Article | 7 March 2014 Paper

Adaptive optics two photon microscopy with direct wavefront sensing using autofluorescent guide-stars

Xiaodong Tao, Andrew Norton, Matthew Kissel, Oscar Azucena, Joel Kubby

Proceedings Volume 8978, 89780D (2014) https://doi.org/10.1117/12.2044090

KEYWORDS: Wavefronts, Wavefront sensors, Adaptive optics, Two photon excitation microscopy, Microscopes, Two photon imaging, Fluorescent proteins, Green fluorescent protein, Objectives, Control systems

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Proceedings Article | 7 March 2014 Paper

Development and testing of an AO-structured illumination microscope

Matthew Kissel, Oscar Azucena, Juan Díaz León, Marc Reinig, Joel Kubby

Proceedings Volume 8978, 89780G (2014) https://doi.org/10.1117/12.2044092

KEYWORDS: Adaptive optics, Tissues, Imaging systems, Tissue optics, Microscopes, Spatial frequencies, Super resolution, Wavefronts, Reconstruction algorithms, Image resolution

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SPIE Journal Paper | 12 August 2013 Open Access

High-stroke, high-order MEMS deformable mirrors

Bautista Fernandez, Mohamed Bouchti, Joel Kubby

JM3, Vol. 12, Issue 03, 033012, (August 2013) https://doi.org/10.1117/12.10.1117/1.JMM.12.3.033012

KEYWORDS: Actuators, Microelectromechanical systems, Deformable mirrors, Mirrors, Gold, Semiconducting wafers, Copper, Chemical mechanical planarization, Power supplies, Ceramics

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Proceedings Article | 5 March 2013 Paper

Interferometric focusing of guide-stars for direct wavefront sensing

Xiaodong Tao, Ziah Dean, Oscar Azucena, Joel Kubby, Christopher Chien

Proceedings Volume 8617, 86170E (2013) https://doi.org/10.1117/12.2006118

KEYWORDS: Light scattering, Tissues, Wavefronts, Scattering, Wavefront sensors, Spatial light modulators, Interferometry, Signal to noise ratio, Laser scattering, Adaptive optics

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Proceedings Article | 16 February 2012 Paper

Adaptive optics confocal microscopy using fluorescent protein guide-stars for brain tissue imaging

Oscar Azucena, Diana Chen, Yi Zuo, Joel Kubby, Min Fu, Xiaodong Tao

Proceedings Volume 8253, 82530M (2012) https://doi.org/10.1117/12.911956

KEYWORDS: Wavefronts, Adaptive optics, Wavefront sensors, Fluorescent proteins, Confocal microscopy, Brain, Dendrites, Tissue optics, Tissues, Microscopes

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Proceedings Article | 26 March 2011 Paper

Adaptive optics confocal fluorescence microscopy with direct wavefront sensing for brain tissue imaging

Min Fu, Xiaodong Tao, Bautista Fernandez, Oscar Azucena, Joel Kubby, Diana Chen, Yi Zuo

Proceedings Volume 7931, 79310L (2011) https://doi.org/10.1117/12.876524

KEYWORDS: Confocal microscopy, Tissues, Wavefronts, Brain, Wavefront sensors, Adaptive optics, Neuroimaging, Optical filters, Microscopes, Luminescence

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Proceedings Article | 14 February 2011 Paper

Fabrication and testing of MEMS-based optical filter combined with a HgCdTe detector

Dmitry Kozak, Silviu Velicu, Bautista Fernandez, Joel Kubby, Michael Morley

Proceedings Volume 7930, 79300L (2011) https://doi.org/10.1117/12.874345

KEYWORDS: Silicon, Semiconducting wafers, Etching, Optical filters, Sensors, Mid-IR, Oxides, Reflectivity, Germanium, Mercury cadmium telluride

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Proceedings Article | 14 February 2011 Paper

Adaptive optics wide-field microscope corrections using a MEMS DM and Shack-Hartmann wavefront sensor

Joel Kubby, Donald Gavel, William Sullivan, Marc Reinig, Justin Crest, Xiaodong Tao, Scot Olivier, Shaila Kotadia, Oscar Azucena

Proceedings Volume 7931, 79310J (2011) https://doi.org/10.1117/12.876439

KEYWORDS: Adaptive optics, Wavefront sensors, Microscopes, Wavefronts, Imaging systems, Objectives, Actuators, Cameras, Deformable mirrors, Microelectromechanical systems

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Proceedings Article | 14 February 2011 Paper

Characterization and annealing of high-stroke monolithic gold MEMS deformable mirror for adaptive optics

Joel Kubby, Bautista Fernández

Proceedings Volume 7931, 79310A (2011) https://doi.org/10.1117/12.876530

KEYWORDS: Annealing, Actuators, Gold, Microelectromechanical systems, Semiconducting wafers, Mirrors, Copper, Deformable mirrors, Adaptive optics, Chemical mechanical planarization

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Proceedings Article | 11 February 2011 Paper

Applications of MEMS in segmented mirror space telescopes

Brij Agrawal, Joel Kubby

Proceedings Volume 7931, 793102 (2011) https://doi.org/10.1117/12.876503

KEYWORDS: Mirrors, Deformable mirrors, Space telescopes, Actuators, Microelectromechanical systems, Adaptive optics, Wavefronts, Adaptive control, Sensors, Control systems

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SPIE Journal Paper | 1 November 2010

High-aspect-ratio microelectromechanical systems deformable mirrors for adaptive optics

Bautista Fernandez, Joel Kubby

JM3, Vol. 9, Issue 04, 041106, (November 2010) https://doi.org/10.1117/12.10.1117/1.3497576

KEYWORDS: Actuators, Microelectromechanical systems, Adaptive optics, Mirrors, Deformable mirrors, Interferometers, Semiconducting wafers, Finite element methods, Gold, Astronomy

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Proceedings Article | 18 February 2010 Paper

Implementation of adaptive optics in fluorescent microscopy using wavefront sensing and correction

Joel Kubby, Peter Kner, Justin Crest, Scot Olivier, Donald Gavel, Daren Dillon, William Sullivan, Jian Cao, Oscar Azucena

Proceedings Volume 7595, 75950I (2010) https://doi.org/10.1117/12.846380

KEYWORDS: Adaptive optics, Wavefront sensors, Wavefronts, Microscopes, Microscopy, Confocal microscopy, Deformable mirrors, Objectives, Cameras, Diffraction

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Proceedings Article | 18 February 2010 Paper

Prototyping of MWIR MEMS-based optical filter combined with HgCdTe detector

Bautista Fernandez, Dmitry Kozak, Joel Kubby, Silviu Velicu

Proceedings Volume 7594, 75940W (2010) https://doi.org/10.1117/12.842700

KEYWORDS: Sensors, Mercury cadmium telluride, Silicon, Optical filters, Prototyping, Mid-IR, Fabry–Perot interferometry, Mirrors, Microelectromechanical systems, Oxides

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Proceedings Article | 24 February 2009 Paper

Initial performance results for high-aspect ratio gold MEMS deformable mirrors

Bautista Fernández, Joel Kubby

Proceedings Volume 7209, 72090O (2009) https://doi.org/10.1117/12.809617

KEYWORDS: Actuators, Microelectromechanical systems, Deformable mirrors, Semiconducting wafers, Finite element methods, Interferometers, Gold, Adaptive optics, Mirrors, Large telescopes

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Proceedings Article | 24 February 2009 Paper

Implementation of a Shack-Hartmann wavefront sensor for the measurement of embryo-induced aberrations using fluorescent microscopy

Jian Cao, Scot Olivier, Joel Kubby, Daren Dillon, Oscar Azucena, Justin Crest, William Sullivan, Donald Gavel, Peter Kner

Proceedings Volume 7209, 720906 (2009) https://doi.org/10.1117/12.809633

KEYWORDS: Wavefronts, Adaptive optics, Wavefront sensors, Objectives, Point spread functions, Microscopy, Microscopes, Image sensors, Sensors, Cameras

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Proceedings Article | 23 July 2008 Paper

Small solutions to the large telescope problem: a massively replicated MEMS spectrograph

Andrew Sheinis, Nicholas Konidaris, Joel Kubby

Proceedings Volume 7018, 70182I (2008) https://doi.org/10.1117/12.787012

KEYWORDS: Spectrographs, Diffraction gratings, Actuators, Microelectromechanical systems, Telescopes, Astronomy, Optical design, Near infrared, Gold, Large telescopes

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Proceedings Article | 27 February 2008 Paper

Nonlinear plate equation analysis for the design of large stroke deformable mirror

Oscar Azucena, Bautista Fernandez, Joel Kubby

Proceedings Volume 6888, 68880Q (2008) https://doi.org/10.1117/12.766873

KEYWORDS: Actuators, Mirrors, Microelectromechanical systems, Adaptive optics, Deformable mirrors, Astronomical imaging, Gold, Wavefronts, Imaging systems, Time metrology

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Proceedings Article | 8 February 2008 Paper

Simulation and interferometer results of MEMS deformable mirrors

Joel Kubby, Bautista Fernández

Proceedings Volume 6888, 68880R (2008) https://doi.org/10.1117/12.766886

KEYWORDS: Actuators, Mirrors, Interferometers, Semiconducting wafers, Microelectromechanical systems, Adaptive optics, Electrodes, Deformable mirrors, Glasses, Finite element methods

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Proceedings Article | 9 February 2007 Paper

Design of a MEMS laser guide star pulse tracker

Luke Johnson, Joel Kubby, Oscar Azucena

Proceedings Volume 6467, 64670I (2007) https://doi.org/10.1117/12.713465

KEYWORDS: Mirrors, Actuators, Electrodes, Capacitors, Microelectromechanical systems, Sodium, Adaptive optics, Laser guide stars, Pulsed laser operation, Finite element methods

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Proceedings Article | 6 February 2007 Paper

Design, processing, and materials for large-stroke actuators

Joel Kubby, Bautista Fernández

Proceedings Volume 6467, 64670T (2007) https://doi.org/10.1117/12.699665

KEYWORDS: Actuators, Deformable mirrors, Adaptive optics, Microelectromechanical systems, Mirrors, Manufacturing, Surface micromachining, Astronomy, Gold, Finite element methods

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Proceedings Article | 23 January 2006 Paper

Large stroke actuators for adaptive optics

B. Fernández, J. Kubby

Proceedings Volume 6113, 61130U (2006) https://doi.org/10.1117/12.644796

KEYWORDS: Actuators, Adaptive optics, Computer aided design, Deformable mirrors, Nickel, Solids, Control systems, SolidWorks, Surface finishing, Microelectromechanical systems

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Proceedings Article | 1 July 2004 Paper

Optical MEMS platform for low-cost on-chip integration of planar light circuits and optical switching

Peter Nystrom, Yao Rong Wang, Kristine German, James Diehl, Kathleen Feinberg, Nancy Jia, Peter Gulvin, Larry Herko, Xueyuan Liu, Jingkuang Chen, John Meyers, Pinyen Lin, Joel Kubby, Jun Ma

Proceedings Volume 5357, (2004) https://doi.org/10.1117/12.528996

KEYWORDS: Waveguides, Switches, Microelectromechanical systems, Optical switching, Photonic integrated circuits, Silicon, Actuators, Integrated optics, Microopto electromechanical systems, Optics manufacturing

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Proceedings Article | 27 March 2002 Paper

Advances in MEMS integration with planar waveguide devices

Joel Kubby

Proceedings Volume 4654, (2002) https://doi.org/10.1117/12.463840

KEYWORDS: Switches, Waveguides, Switching, Photonic integrated circuits, Optical switching, Signal attenuation, Mirrors, Microelectromechanical systems, Silica, Silicon

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Proceedings Article | 18 May 2001 Paper

Hybrid integration of light-emitters and detectors with SOI-based micro-opto-electro-mechanical systems (MOEMS)

Steve Delvecchio, Yi Su, Nena Golubovic-Laikopoulos, David Burns, Joel Kubby, Troy Daiber, Jen-Tsorng Chang, Thomas Plowman, Janusz Bryzek, Jingkuang Chen, Michel Rosa, Raji Mali, Jim Calamita, Andrew Zosel, Tom Pumo, Alex Tran, Anis Husain, Arthur Morris, Shifang Zhou, Bruce Scharf, John Gilbert, Robert Lofthus, Tom Korsmeyer, Bill Nowak, Decai Sun, Vladimir Rabinovich, C.-C. Lin, Charles Hsu, Peter Gulvin, Jim Hartman, Li Fan

Proceedings Volume 4293, (2001) https://doi.org/10.1117/12.426941

KEYWORDS: Mirrors, Microopto electromechanical systems, Microelectromechanical systems, Semiconductor lasers, Optics manufacturing, Silicon, Semiconducting wafers, Sensors, Transistors, Integrated optics

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Proceedings Article | 5 September 1997 Paper

Vibration signature analysis sensors for predictive diagnostics

Olivera Vitomirov, Jingkuang Chen, Eric Peeters, Joel Kubby

Proceedings Volume 3224, (1997) https://doi.org/10.1117/12.301968

KEYWORDS: Sensors, Diagnostics, Wheatstone bridges, Printing, Mechanical sensors, Silicon, Resonators, Bridges, Multiplexing, Transistors

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Proceedings Article | 2 September 1997 Paper

Design, modeling and verification of MEMS silicon torsion mirror

Subrata Mukherjee, Joel Kubby, D. Taylor, Olivera Vitomirov, Eric Peeters, F. Pan, Jingkuang Chen

Proceedings Volume 3226, (1997) https://doi.org/10.1117/12.284559

KEYWORDS: Mirrors, Microelectromechanical systems, Silicon, Computer aided design, Semiconductor lasers, Nonimpact printing, Instrument modeling, Performance modeling, Raster graphics, Scanners

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Showing 5 of 37 publications

Proceedings Volume Editor (22)

SPIE Conference Volume | 26 March 2018

Adaptive Optics and Wavefront Control for Biological Systems IV

SPIE Conference Volume | 15 March 2017

Adaptive Optics and Wavefront Control for Biological Systems III

SPIE Conference Volume | 7 July 2016

Adaptive Optics and Wavefront Control for Biological Systems II

SPIE Conference Volume | 14 April 2015

Adaptive Optics and Wavefront Control for Biological Systems

SPIE Conference Volume | 8 April 2014

Silicon Photonics IX

Showing 5 of 22 publications

Conference Committee Involvement (28)

Adaptive Optics and Wavefront Control for Biological Systems IV

27 January 2018 | San Francisco, California, United States

Silicon Photonics XII

30 January 2017 | San Francisco, California, United States

Adaptive Optics and Wavefront Control for Biological Systems III

28 January 2017 | San Francisco, California, United States

Silicon Photonics XI

15 February 2016 | San Francisco, California, United States

Adaptive Optics and Wavefront Control for Biological Systems II

13 February 2016 | San Francisco, California, United States

Silicon Photonics X

9 February 2015 | San Francisco, California, United States

Adaptive Optics and Wavefront Control for Biological Systems

7 February 2015 | San Francisco, California, United States

Silicon Photonics IX

3 February 2014 | San Francisco, California, United States

MEMS Adaptive Optics VIII

2 February 2014 | San Francisco, California, United States

MEMS Adaptive Optics VII

5 February 2013 | San Francisco, California, United States

Silicon Photonics VIII

4 February 2013 | San Francisco, California, United States

MEMS Adaptive Optics VI

25 January 2012 | San Francisco, California, United States

Silicon Photonics VII

22 January 2012 | San Francisco, California, United States

MEMS Adaptive Optics V

27 January 2011 | San Francisco, California, United States

Silicon Photonics VI

23 January 2011 | San Francisco, California, United States

MEMS Adaptive Optics IV

27 January 2010 | San Francisco, California, United States

Silicon Photonics V

24 January 2010 | San Francisco, California, United States

MEMS Adaptive Optics III

27 January 2009 | San Jose, California, United States

Silicon Photonics IV

26 January 2009 | San Jose, California, United States

MEMS Adaptive Optics II

22 January 2008 | San Jose, California, United States

Silicon Photonics III

21 January 2008 | San Jose, California, United States

MEMS Adaptive Optics

24 January 2007 | San Jose, California, United States

Silicon Photonics II

22 January 2007 | San Jose, California, United States

Silicon Photonics

25 January 2006 | San Jose, California, United States

MEMS/MOEMS Components and Their Applications III

23 January 2006 | San Jose, California, United States

Optoelectronic Integration on Silicon III

25 January 2005 | San Jose, California, United States

Optoelectronic Integration on Silicon II

27 January 2004 | San Jose, CA, United States

Optoelectronic Integration on Silicon

29 January 2003 | San Jose, CA, United States

Showing 5 of 28 Conference Committees

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