Dr. Timothy Holmes Profile

Dr. Timothy Holmes

Chief Executive Officer at Lickenbrock Technologies LLC

SPIE Involvement:

Author

Publications (20)

Proceedings Article | 14 November 2018 Paper

Practical aspects of multiframe blind deconvolution for ground based telescopes

Melena Abijaoude, Timothy Schulz, David Gray, Mark Ostroot, Miguel Pineros, Timothy Holmes

Proceedings Volume 10772, 1077212 (2018) https://doi.org/10.1117/12.2321285

KEYWORDS: Deconvolution, Telescopes, Point spread functions, Atmospheric turbulence, Fourier transforms, Computer simulations, Signal to noise ratio, Convolution, Spectral resolution, Computer architecture

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Proceedings Article | 14 November 2018 Paper

Advances in multiframe blind deconvolution for ground based telescopes

Timothy Schulz, Melena Abijaoude, David Gray, Mark Ostroot, Miguel Pineros, Timothy Holmes

Proceedings Volume 10772, 107720F (2018) https://doi.org/10.1117/12.2320332

KEYWORDS: Telescopes, Expectation maximization algorithms, Point spread functions, Fourier transforms, Adaptive optics, Deconvolution, Contrast transfer function, Algorithm development, Mirrors, Reconstruction algorithms

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Proceedings Article | 20 March 2015 Paper

En-face imaging of the ellipsoid zone in the retina from optical coherence tomography B-scans

T. Holmes, S. Larkin, M. Downing, K. Csaky

Proceedings Volume 9307, 93071O (2015) https://doi.org/10.1117/12.2074193

KEYWORDS: Reflectivity, Optical coherence tomography, Retina, Optical flow, Algorithm development, Eye, Scanning laser ophthalmoscopy, Software development, Image segmentation, Optical alignment

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Proceedings Article | 9 March 2015 Paper

3D widefield light microscope image reconstruction without dyes

Sean Larkin, J. Larson, C. Holmes, M. Vaicik, M. Turturro, Alexander Jurkevich, S. Sinha, T. Ezashi, G. Papavasiliou, E. Brey, T. Holmes

Proceedings Volume 9330, 93300S (2015) https://doi.org/10.1117/12.2074209

KEYWORDS: Point spread functions, Principal component analysis, 3D image reconstruction, 3D image processing, Reconstruction algorithms, Absorption, Microscopes, Deconvolution, 3D modeling, Objectives

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SPIE Journal Paper | 29 November 2012 Open Access

Dynamic indocyanine green angiography measurements

Tim Holmes, Alessandro Invernizzi, Sean Larkin, Giovanni Staurenghi

JBO, Vol. 17, Issue 11, 116028, (November 2012) https://doi.org/10.1117/12.10.1117/1.JBO.17.11.116028

KEYWORDS: Optical coherence tomography, Indocyanine green, Angiography, Arteries, Eye, Blood, Tissues, Veins, Mathematical modeling, Capillaries

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Proceedings Article | 3 March 2010 Paper

Perfusion measures from dynamic ICG scanning laser ophthalmoscopy

Sean Larkin, Alessandro Invernizzi, David Beecher, Giovanni Staurenghi, Tim Holmes

Proceedings Volume 7550, 75500H (2010) https://doi.org/10.1117/12.839534

KEYWORDS: Capillaries, Blood, Vignetting, Eye, Scanning laser ophthalmoscopy, Image processing, Blood circulation, Visualization, Blood vessels, Indocyanine green

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Proceedings Article | 3 March 2010 Paper

Spectral characterization of an ophthalmic fundus camera

Clayton Miller, Carl Bassi, Dale Brodsky, Timothy Holmes

Proceedings Volume 7550, 75501U (2010) https://doi.org/10.1117/12.844855

KEYWORDS: Cameras, Sensors, Eye, Imaging systems, Retina, Photons, Reflectivity, CCD cameras, Xenon, Charge-coupled devices

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Proceedings Article | 25 February 2009 Paper

Image analysis software for following progression of peripheral neuropathy

Thomas Epplin-Zapf, Clayton Miller, Sean Larkin, Eduardo Hermesmeyer, Jenny Macy, Marco Pellegrini, Saverio Luccarelli, Giovanni Staurenghi, Timothy Holmes

Proceedings Volume 7169, 71691C (2009) https://doi.org/10.1117/12.814672

KEYWORDS: Electromyography, Nerve, Cornea, Image analysis, Neurons, Software, Optical fibers, Image segmentation, Biopsy, Statistical analysis

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Proceedings Article | 30 March 2007 Paper

The effect of blood vessels on the computation of the scanning laser ophthalmoscope retinal thickness map

A. Mantri, Y. Li, N. Hutchings, J. Flanagan, T. Holmes

Proceedings Volume 6514, 65142X (2007) https://doi.org/10.1117/12.710124

KEYWORDS: Blood vessels, Optical coherence tomography, Scanning laser ophthalmoscopy, Scanning laser ophthalmoscopes, Image segmentation, Retina, Reflectivity, Point spread functions, Data acquisition, Detection and tracking algorithms

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Proceedings Article | 29 March 2007 Paper

Anatomically constrained maximum likelihood estimation for estimating retinal thickness from scanning laser ophthalmoscope data

Tim Holmes, Brian Northan, Gerhard Zinser, Natalie Hutchings, Ying Li, Dirk-Uwe Bartsch, John Flanagan

Proceedings Volume 6514, 651419 (2007) https://doi.org/10.1117/12.709453

KEYWORDS: Optical coherence tomography, Scanning laser ophthalmoscopy, Eye, Retina, Point spread functions, Scanning laser ophthalmoscopes, Reflectivity, Pathology, Algorithm development, Databases

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Proceedings Article | 26 October 2004 Paper

Subpixel deconvolution of 3D optical microscope imagery

David Biggs, Chou-Lung Wang, Timothy Holmes, Alexey Khodjakov

Proceedings Volume 5559, (2004) https://doi.org/10.1117/12.559526

KEYWORDS: Deconvolution, Super resolution, Point spread functions, Microscopes, 3D image processing, Microscopy, Signal to noise ratio, Cameras, Diffraction, Image processing

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Proceedings Article | 13 July 2004 Paper

Object segmentation, quantification, counting, and tracking

Asad Abu-Tarif, Vitaliy Khiznichenko, Brian Northan, Tim Holmes, Phillip Yoon, Jonathan Girroir, Paul Brathwaite

Proceedings Volume 5324, (2004) https://doi.org/10.1117/12.529117

KEYWORDS: Image segmentation, Detection and tracking algorithms, Image processing algorithms and systems, Reconstruction algorithms, Algorithm development, 3D image processing, Automatic tracking, Digital image correlation, Object recognition, Deconvolution

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Proceedings Article | 21 June 2004 Paper

Fluorescence resonance energy transfer imaging by maximum likelihood estimation

Yupeng Zhang, Yumin Yuan, Timothy Holmes

Proceedings Volume 5323, (2004) https://doi.org/10.1117/12.524847

KEYWORDS: Fluorescence resonance energy transfer, Optical filters, Image filtering, Calibration, Control systems, Quantum efficiency, Image analysis, Proteins, Luminescence, Electronic filtering

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Proceedings Article | 9 June 1998 Paper

Motion-compensated blind deconvolution of scanning laser opthalmoscope imagery

Nathan O'Connor, Dirk-Uwe Bartsch, William Freeman, Timothy Holmes

Proceedings Volume 3261, (1998) https://doi.org/10.1117/12.310540

KEYWORDS: Deconvolution, Point spread functions, Scanning laser ophthalmoscopy, Tomography, Eye, Confocal microscopy, Expectation maximization algorithms, Image registration, Data acquisition, Raster graphics

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Proceedings Article | 9 June 1998 Paper

Data correction methods for 3D light microscopy

Chuo-Lung Wang, Nathan O'Connor, Michel Wang, James Turner, Timothy Holmes

Proceedings Volume 3261, (1998) https://doi.org/10.1117/12.310544

KEYWORDS: Digital filtering, Data corrections, CCD cameras, Microscopy, Charge-coupled devices, Calibration, Image filtering, Electronic filtering, Cameras, 3D image processing

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Proceedings Article | 10 April 1996 Paper

ML-blind deconvolution algorithm: recent developments

Santosh Bhattacharyya, Donald Szarowski, James Turner, Nathan O'Connor, Timothy Holmes

Proceedings Volume 2655, (1996) https://doi.org/10.1117/12.237475

KEYWORDS: Point spread functions, Reconstruction algorithms, Deconvolution, Algorithm development, 3D image processing, Microscopes, Expectation maximization algorithms, Neodymium, Data processing, Objectives

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Proceedings Article | 30 September 1994 Paper

Simultaneous image and point spread function reconstruction for 3D light microscopy

Timothy Holmes, Santosh Bhattacharyya, Joshua Cooper, David Hanzel, Vijaykumar Krishnamurthi, Wen-Chieh Lin, Badrinath Roysam, Donald Szarowski, James Turner

Proceedings Volume 2302, (1994) https://doi.org/10.1117/12.188054

KEYWORDS: Point spread functions, Reconstruction algorithms, Deconvolution, Luminescence, Expectation maximization algorithms, Confocal microscopy, 3D image reconstruction, Photomicroscopy, Microscopy, Model-based design

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Proceedings Article | 26 June 1992 Paper

Blind deconvolution of 2D and 3D fluorescent micrographs

Vijaykumar Krishnamurthi, Yi-Hwa Liu, Timothy Holmes, Badrinath Roysam, James Turner

Proceedings Volume 1660, (1992) https://doi.org/10.1117/12.59544

KEYWORDS: Point spread functions, Deconvolution, Expectation maximization algorithms, Reconstruction algorithms, 3D image processing, Computer simulations, Optical transfer functions, 3D modeling, Photomicroscopy, Calibration

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This paper presents recent results of our reconstructions of 3-D data from Drosophila chromosomes as well as our simulations with a refined version of the algorithm used in the former. It is well known that the calibration of the point spread function (PSF) of a fluorescence microscope is a tedious process and involves esoteric techniques in most cases. This problem is further compounded in the case of confocal microscopy where the measured intensities are usually low. A number of techniques have been developed to solve this problem, all of which are methods in blind deconvolution. These are so called because the measured PSF is not required in the deconvolution of degraded images from any optical system. Our own efforts in this area involved the maximum likelihood (ML) method, the numerical solution to which is obtained by the expectation maximization (EM) algorithm. Based on the reasonable early results obtained during our simulations with 2-D phantoms, we carried out experiments with real 3-D data. We found that the blind deconvolution method using the ML approach gave reasonable reconstructions. Next we tried to perform the reconstructions using some 2-D data, but we found that the results were not encouraging. We surmised that the poor reconstructions were primarily due to the large values of dark current in the input data. This, coupled with the fact that we are likely to have similar data with considerable dark current from a confocal microscope prompted us to look into ways of constraining the solution of the PSF. We observed that in the 2-D case, the reconstructed PSF has a tendency to retain values larger than those of the theoretical PSF in regions away from the center (outside of those we considered to be its region of support). This observation motivated us to apply an upper bound constraint on the PSF in these regions. Furthermore, we constrain the solution of the PSF to be a bandlimited function, as in the case in the true situation. We have derived two separate approaches for implementing the constraint. One approach involves the mathematical rigors of Lagrange multipliers. This approach is discussed in another paper. The second approach involves an adaptation of the Gershberg Saxton algorithm, which ensures bandlimitedness and non-negativity of the PSF. Although the latter approach is mathematically less rigorous than the former, we currently favor it because it has a simpler implementation on a computer and has smaller memory requirements. The next section describes briefly the theory and derivation of these constraint equations using Lagrange multipliers.

Proceedings Article | 26 June 1992 Paper

Algorithms for 3D brightfield microscopy

Byron Willis, Badrinath Roysam, James Turner, Timothy Holmes

Proceedings Volume 1660, (1992) https://doi.org/10.1117/12.59545

KEYWORDS: Algorithm development, Reconstruction algorithms, 3D image processing, Absorbance, Microscopy, Optical transfer functions, Algorithms, Photomicroscopy, Interference (communication), Biomedical optics

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Proceedings Article | 1 May 1991 Paper

Preliminary tests of maximum likelihood image reconstruction method on 3-D real data and some practical considerations for the data corrections

Yi-Hwa Liu, Timothy Holmes, Matthew Koshy

Proceedings Volume 1428, (1991) https://doi.org/10.1117/12.44141

KEYWORDS: 3D image processing, 3D modeling, 3D image reconstruction, Image restoration, Point spread functions, Data corrections, Luminescence, Expectation maximization algorithms, Laser systems engineering, Microscopy

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Showing 5 of 20 publications

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