Dr. David W. Allen Profile

Dr. David W. Allen

Research Chemist at National Institute of Standards and Technology

SPIE Involvement:

Conference Program Committee | Author | Editor

Area of Expertise:

remote sensing , hyperspectral imaging , spectral signatures , optical standards , calibration , radiometry

Publications (54)

SPIE Journal Paper | 7 May 2024 Open Access

Open Access

Hyperspectral dark-field microscopy of human breast lumpectomy samples for tumor margin detection in breast-conserving surgery

Jeeseong Hwang, Philip Cheney, Stephen Kanick, Hanh N. Le, David McClatchy, Helen Zhang, Nian Liu, Zhan-Qian John Lu, Tae Joon Cho, Kimberly Briggman, David Allen, Wendy Wells, Brian Pogue

JBO, Vol. 29, Issue 09, 093503, (May 2024) https://doi.org/10.1117/12.10.1117/1.JBO.29.9.093503

KEYWORDS: Tissues, Biological samples, Image segmentation, Tumors, Breast, Microscopy, Printed circuit board testing, Blood, Library classification systems, Surgery

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SignificanceHyperspectral dark-field microscopy (HSDFM) and data cube analysis algorithms demonstrate successful detection and classification of various tissue types, including carcinoma regions in human post-lumpectomy breast tissues excised during breast-conserving surgeries.AimWe expand the application of HSDFM to the classification of tissue types and tumor subtypes in pre-histopathology human breast lumpectomy samples.ApproachBreast tissues excised during breast-conserving surgeries were imaged by the HSDFM and analyzed. The performance of the HSDFM is evaluated by comparing the backscattering intensity spectra of polystyrene microbead solutions with the Monte Carlo simulation of the experimental data. For classification algorithms, two analysis approaches, a supervised technique based on the spectral angle mapper (SAM) algorithm and an unsupervised technique based on the K-means algorithm are applied to classify various tissue types including carcinoma subtypes. In the supervised technique, the SAM algorithm with manually extracted endmembers guided by H&E annotations is used as reference spectra, allowing for segmentation maps with classified tissue types including carcinoma subtypes.ResultsThe manually extracted endmembers of known tissue types and their corresponding threshold spectral correlation angles for classification make a good reference library that validates endmembers computed by the unsupervised K-means algorithm. The unsupervised K-means algorithm, with no a priori information, produces abundance maps with dominant endmembers of various tissue types, including carcinoma subtypes of invasive ductal carcinoma and invasive mucinous carcinoma. The two carcinomas’ unique endmembers produced by the two methods agree with each other within <2% residual error margin.ConclusionsOur report demonstrates a robust procedure for the validation of an unsupervised algorithm with the essential set of parameters based on the ground truth, histopathological information. We have demonstrated that a trained library of the histopathology-guided endmembers and associated threshold spectral correlation angles computed against well-defined reference data cubes serve such parameters. Two classification algorithms, supervised and unsupervised algorithms, are employed to identify regions with carcinoma subtypes of invasive ductal carcinoma and invasive mucinous carcinoma present in the tissues. The two carcinomas’ unique endmembers used by the two methods agree to <2% residual error margin. This library of high quality and collected under an environment with no ambient background may be instrumental to develop or validate more advanced unsupervised data cube analysis algorithms, such as effective neural networks for efficient subtype classification.

Proceedings Article | 13 March 2024 Poster

Poster

Hyperspectral dark-field microscopy of human breast lumpectomy samples for tumor margin detection

Helen Zhang, Philip Cheney, Stephan Kanick, Hanh Le, David McClatchy, Nian Liu, John Lu, Tae Joon Cho, Kimberly Briggman, David Allen, Wendy Wells, Brian Pogue, Jeeseong Hwang

Proceedings Volume PC12833, PC128330M (2024) https://doi.org/10.1117/12.3023601

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Proceedings Article | 13 March 2024 Poster

Poster

Development of optical medical imaging standards at the National Institute of Standards and Technology

Jeeseong Hwang, Alexis Lee, Kimberly Briggman, Nikki Rentz, David Allen, Lee Richter, John Lu

Proceedings Volume PC12833, PC128330L (2024) https://doi.org/10.1117/12.3009503

KEYWORDS: Optical resolution, Optical medical imaging, Image resolution, Optical coherence tomography, Optical calibration, Tissues, Tissue optics, Surface plasmons, Refraction, Optical coherence

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Proceedings Article | 14 June 2023 Presentation

Presentation

Characterization of hyperspectral imagers utilizing color tile standards traceable to NIST

David Allen, Clarence Zarobila, Steven Grantham

Proceedings Volume PC12519, PC1251903 (2023) https://doi.org/10.1117/12.2664008

KEYWORDS: Imaging systems, Hyperspectral imaging, Spectrometers, Reflectivity, Colorimetry

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SPIE Journal Paper | 18 November 2021 Open Access

Open Access

Polydimethylsiloxane tissue-mimicking phantoms with tunable optical properties

Aaron Goldfain, Paul Lemaillet, David Allen, Kimberly Briggman, Jeeseong Hwang

JBO, Vol. 27, Issue 07, 074706, (November 2021) https://doi.org/10.1117/12.10.1117/1.JBO.27.7.074706

KEYWORDS: Scattering, Absorption, Tissues, Light scattering, Particles, Optical properties, Tissue optics, Integrating spheres, Rayleigh scattering, Picosecond phenomena

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Significance: The polymer, polydimethylsiloxane (PDMS), has been increasingly used to make tissue simulating phantoms due to its excellent processability, durability, flexibility, and limited tunability of optical, mechanical, and thermal properties. We report on a robust technique to fabricate PDMS-based tissue-mimicking phantoms where the broad range of scattering and absorption properties are independently adjustable in the visible- to near-infrared wavelength range from 500 to 850 nm. We also report on an analysis method to concisely quantify the phantoms’ broadband characteristics with four parameters. Aim: We report on techniques to manufacture and characterize solid tissue-mimicking phantoms of PDMS polymers. Tunability of the absorption (μa ( λ ) ) and reduced scattering coefficient spectra (μs′(λ)) in the wavelength range of 500 to 850 nm is demonstrated by adjusting the concentrations of light absorbing carbon black powder (CBP) and light scattering titanium dioxide powder (TDP) added into the PDMS base material. Approach: The μa ( λ ) and μs′(λ) of the phantoms were obtained through measurements with a broadband integrating sphere system and by applying an inverse adding doubling algorithm. Analyses of μa ( λ ) and μs′(λ) of the phantoms, by fitting them to linear and power law functions, respectively, demonstrate that independent control of μa ( λ ) and μs′(λ) is possible by systematically varying the concentrations of CBP and TDP. Results: Our technique quantifies the phantoms with four simple fitting parameters enabling a concise tabulation of their broadband optical properties as well as comparisons to the optical properties of biological tissues. We demonstrate that, to a limited extent, the scattering properties of our phantoms mimic those of human tissues of various types. A possible way to overcome this limitation is demonstrated with phantoms that incorporate polystyrene microbead scatterers. Conclusions: Our manufacturing and analysis techniques may further promote the application of PDMS-based tissue-mimicking phantoms and may enable robust quality control and quality checks of the phantoms.

Proceedings Article | 4 October 2020 Presentation

Presentation

IEEE P4001: Towards a standard for push-broom hyperspectral imagers

John Gilchrist, Christopher Durell, David Allen

Proceedings Volume 11576, 115760E (2020) https://doi.org/10.1117/12.2585141

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Proceedings Article | 24 April 2020 Presentation

Presentation

IEEE P4001-update on progress towards a hyperspectral standard (Conference Presentation)

John Gilchrist, Chris Durell, David Allen

Proceedings Volume 11392, 113920A (2020) https://doi.org/10.1117/12.2560149

KEYWORDS: Standards development, Hyperspectral systems, Diagnostics, Roads

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Proceedings Article | 9 March 2020 Presentation

Presentation

Tumor margin analysis in resected breast tissue using hyperspectral dark-field microscopy (Conference Presentation)

Hanh Le, David McClatchy, David Allen, Kimberly Briggman, Brian Pogue, Wendy Wells, Jeeseong Hwang

Proceedings Volume 11231, 112310F (2020) https://doi.org/10.1117/12.2561804

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Proceedings Article | 27 July 2019 Presentation

Presentation

Hyperspectral imager calibration using ceramic color tiles (Conference Presentation)

Matti Eskelinen, Clarence Zarobila, David Allen

Proceedings Volume 11057, 110570Y (2019) https://doi.org/10.1117/12.2525966

KEYWORDS: Imaging systems, Calibration, Ceramics, Hyperspectral imaging, Instrument modeling, Reflectivity, Spectrophotometry, Colorimetry, Integrating spheres, Spectral calibration

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Proceedings Article | 14 May 2019 Presentation

Presentation

Hyperspectral imaging microscopy with a tunable laser illumination source (Conference Presentation)

Ronald Resmini, David Allen, E. Slonecker

Proceedings Volume 10986, 109861E (2019) https://doi.org/10.1117/12.2519082

KEYWORDS: Tunable lasers, Hyperspectral imaging, Microscopy, Data acquisition, Short wave infrared radiation, Imaging systems, Cameras, Sensors, Shortwaves, Infrared sensors

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Proceedings Article | 14 May 2019 Paper

Paper

Stray light characterization in a high-resolution imaging spectrometer designed for solar-induced fluorescence

Loren Albert, K. C. Cushman, David Allen, Yuqin Zong, Luis Alonso, James Kellner

Proceedings Volume 10986, 109860G (2019) https://doi.org/10.1117/12.2519395

KEYWORDS: Stray light, Spectroscopy, Photosynthesis, Optical parametric oscillators, Calibration, Sensors, Spectrometer engineering, Optical testing

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Proceedings Article | 14 May 2019 Paper

Paper

IEEE P4001: Progress towards a hyperspectral standard

John Gilchrist, David Allen, Chris Durell

Proceedings Volume 10986, 1098602 (2019) https://doi.org/10.1117/12.2520190

KEYWORDS: Standards development, Imaging systems, Hyperspectral imaging, Remote sensing, Sensors, Manufacturing, Calibration, Optical filters, Data storage, Imaging spectroscopy, Multispectral imaging

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Proceedings Article | 14 May 2019 Presentation + Paper

Presentation + Paper

Unraveling low abundance intimate mixtures with deep learning

Ronald Resmini, Kevin Christiansen, David Allen

Proceedings Volume 10986, 109860W (2019) https://doi.org/10.1117/12.2518487

KEYWORDS: Neodymium, Neural networks, Hyperspectral imaging, Remote sensing, MATLAB, Short wave infrared radiation, Sensors, Reflectivity, Spectroscopy

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Proceedings Article | 14 May 2019 Paper

Paper

Solar-induced fluorescence retrievals in the context of physiological, environmental, and hardware-based sources of uncertainty

Julia Marrs, Lucy Hutyra, David Allen

Proceedings Volume 10986, 109860F (2019) https://doi.org/10.1117/12.2520457

KEYWORDS: Spectroscopy, Signal to noise ratio, Absorption, Luminescence, Calibration, Vegetation, Sensors, Carbon, Signal detection, Atmospheric corrections

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SPIE Journal Paper | 4 September 2018 Open Access

Open Access

Optical characterization of two cyanobacteria genera, Aphanizomenon and Microcystis, with hyperspectral microscopy

Emily Paine, E. Terrence Slonecker, Nancy S. Simon, Barry H. Rosen, Ronald Resmini, David Allen

JARS, Vol. 12, Issue 03, 036013, (September 2018) https://doi.org/10.1117/12.10.1117/1.JRS.12.036013

KEYWORDS: Microscopes, Microscopy, Remote sensing, Hyperspectral imaging, Algorithm development, Reflectivity, Absorption, Image classification, Shape analysis, Water

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SPIE Journal Paper | 5 June 2018 Open Access

Open Access

Full-range, solar-reflected hyperspectral microscopy to support earth remote sensing research

E. Terrence Slonecker, David Allen, Ronald Resmini, Robert Rand, Emily Paine

JARS, Vol. 12, Issue 02, 026024, (June 2018) https://doi.org/10.1117/12.10.1117/1.JRS.12.026024

KEYWORDS: Microscopy, Reflectivity, Sensors, Microscopes, Remote sensing, Hyperspectral imaging, Feldspar, Spectrometers, Imaging spectroscopy, Minerals

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Proceedings Article | 16 March 2017 Paper

Paper

Broadband spectral measurements of diffuse optical properties by an integrating sphere instrument at the National Institute of Standards and Technology

Paul Lemaillet, Jeeseong Hwang, Heidrun Wabnitz, Dirk Grosenick, Lin Yang, David Allen

Proceedings Volume 10056, 1005604 (2017) https://doi.org/10.1117/12.2263338

KEYWORDS: Indium oxide, Scattering, Optical properties, Integrating spheres, Reflectivity, Transmittance, Standards development, Optical testing, Optical spheres, Solids

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Proceedings Article | 15 March 2017 Paper

Paper

Polydimethylsiloxane tissue-mimicking phantoms for quantitative optical medical imaging standards

Jeeseong Hwang, Hyun-Jin Kim, Paul Lemaillet, Heidrun Wabnitz, Dirk Grosenick, Lin Yang, Thomas Gladytz, David McClatchy, David Allen, Kimberly Briggman, Brian Pogue

Proceedings Volume 10056, 1005603 (2017) https://doi.org/10.1117/12.2263379

KEYWORDS: Scattering, Particles, Confocal microscopy, Tissue optics, Light scattering, Integrating spheres, Tissues, Reflectivity, Standards development, Backscatter

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Proceedings Article | 15 March 2017 Paper

Paper

Label-free hyperspectral dark-field microscopy for quantitative scatter imaging

Philip Cheney, David McClatchy, Stephen Kanick, Paul Lemaillet, David Allen, Daniel Samarov, Brian Pogue, Jeeseong Hwang

Proceedings Volume 10056, 1005602 (2017) https://doi.org/10.1117/12.2263336

KEYWORDS: Scattering, Monte Carlo methods, Reflectivity, Optical spheres, Microscopy, Tissues, Microscopes, Distributed interactive simulations, Objectives, Transmittance

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SPIE Journal Paper | 11 January 2017 Open Access

Open Access

Modeling linear and intimate mixtures of materials in hyperspectral imagery with single-scattering albedo and kernel approaches

Robert Rand, Ronald Resmini, David Allen

JARS, Vol. 11, Issue 01, 016005, (January 2017) https://doi.org/10.1117/12.10.1117/1.JRS.11.016005

KEYWORDS: Reflectivity, Hyperspectral imaging, RGB color model, Vegetation, Composites, Data modeling, Sensors, Diagnostics, Glasses, Error analysis

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Proceedings Article | 19 September 2016 Presentation + Paper

Presentation + Paper

Abundance estimation of solid and liquid mixtures in hyperspectral imagery with albedo-based and kernel-based methods

Robert Rand, Ronald Resmini, David Allen

Proceedings Volume 9976, 99760M (2016) https://doi.org/10.1117/12.2239253

KEYWORDS: Solids, Liquids, Scattering, Reflectivity, Data modeling, Hyperspectral imaging, Sensors, Statistical analysis, RGB color model, Glasses

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Proceedings Article | 24 March 2016 Presentation + Paper

Presentation + Paper

National Institute of Standards and Technology measurement service of the optical properties of biomedical phantoms: current status

Paul Lemaillet, Catherine Cooksey, Zachary Levine, Adam Pintar, Jeeseong Hwang, David Allen

Proceedings Volume 9700, 970002 (2016) https://doi.org/10.1117/12.2214569

KEYWORDS: Bidirectional reflectance transmission function, Optical properties, Indium oxide, Biomedical optics, Polarization, Monte Carlo methods, Standards development, Scattering, Transmittance, Solids

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Proceedings Article | 18 March 2016 Presentation + Paper

Presentation + Paper

Optical characterization of tissue mimicking phantoms by a vertical double integrating sphere system

Yilin Han, Qiumin Jia, Shuwei Shen, Guangli Liu, Yuwei Guo, Ximing Zhou, Jiaru Chu, Gang Zhao, Erbao Dong, David Allen, Paul Lemaillet, Ronald Xu

Proceedings Volume 9700, 97000A (2016) https://doi.org/10.1117/12.2212287

KEYWORDS: Tissue optics, Integrating spheres, System integration, Absorption, Scattering, 3D printing, Tissues, Integrated optics, Optical properties, Biomedical optics, Titanium dioxide, Optical testing, Liquids, Solids

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SPIE Journal Paper | 28 December 2015 Open Access

Open Access

Special Section Guest Editorial:Optical Medical Imaging Standards

David Allen, Jeeseong Hwang, Maritoni Litorja

JBO, Vol. 20, Issue 12, 121301, (December 2015) https://doi.org/10.1117/12.10.1117/1.JBO.20.12.121301

KEYWORDS: Standards development, Optical medical imaging, Medical imaging, Sensor technology, Sensors, Climatology, Electromagnetism, Optical benches, Diagnostics, Imaging technologies

SPIE Journal Paper | 27 October 2015 Open Access

Open Access

Double-integrating-sphere system at the National Institute of Standards and Technology in support of measurement standards for the determination of optical properties of tissue-mimicking phantoms

Paul Lemaillet, Jean-Pierre Bouchard, Jeeseong Hwang, David Allen

JBO, Vol. 20, Issue 12, 121310, (October 2015) https://doi.org/10.1117/12.10.1117/1.JBO.20.12.121310

KEYWORDS: Optical properties, Reflectivity, Indium oxide, Optical spheres, Scattering, Transmittance, Standards development, Absorption, Tissue optics, Biomedical optics

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SPIE Journal Paper | 11 September 2015 Open Access

Open Access

Digital phantoms generated by spectral and spatial light modulators

Bonghwan Chon, Fuyuki Tokumasu, Ji Youn Lee, David Allen, Joseph Rice, Jeeseong Hwang

JBO, Vol. 20, Issue 12, 121309, (September 2015) https://doi.org/10.1117/12.10.1117/1.JBO.20.12.121309

KEYWORDS: Spatial light modulators, Hyperspectral imaging, Absorption, Scattering, Liquid crystal on silicon, Image sensors, Image quality, Calibration, Reflectivity, Image analysis

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Proceedings Article | 1 September 2015 Paper

Paper

Characterizing intimate mixtures of materials in hyperspectral imagery with albedo-based and kernel-based approaches

Robert Rand, Ronald Resmini, David Allen

Proceedings Volume 9611, 961112 (2015) https://doi.org/10.1117/12.2190067

KEYWORDS: Reflectivity, RGB color model, Hyperspectral imaging, Scattering, Composites, Data modeling, Glasses, Sensors, Remote sensing, Diagnostics

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Proceedings Article | 21 May 2015 Paper

Paper

Spectral reflectance variability of skin and attributing factors

Catherine Cooksey, Benjamin Tsai, David Allen

Proceedings Volume 9461, 94611M (2015) https://doi.org/10.1117/12.2184485

KEYWORDS: Reflectivity, Skin, Absorption, Spectrophotometry, Ultraviolet radiation, Visible radiation, Human subjects, Short wave infrared radiation, Infrared signatures, Near infrared

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Proceedings Article | 6 March 2015 Paper

Paper

Measurement of the optical properties of solid biomedical phantoms at the National Institute of Standards and Technology

Paul Lemaillet, David Allen, Jeeseong Hwang

Proceedings Volume 9325, 932504 (2015) https://doi.org/10.1117/12.2085110

KEYWORDS: Indium oxide, Optical properties, Solids, Optical testing, Reflectivity, Biomedical optics, Optical spheres, Transmittance, Standards development, Scattering

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Proceedings Article | 6 March 2015 Paper

Paper

Making digital phantoms with spectral and spatial light modulators for quantitative applications of hyperspectral optical medical imaging devices

Bonghwan Chon, Fuyuki Tokumasu, Ji Youn Lee, David Allen, Joseph Rice, Jeeseong Hwang

Proceedings Volume 9325, 93250C (2015) https://doi.org/10.1117/12.2085237

KEYWORDS: Spatial light modulators, Hyperspectral imaging, Liquid crystal on silicon, Image sensors, Calibration, Reflectivity, Absorption, Imaging systems, Imaging devices, Standards development

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Proceedings Article | 13 June 2014 Paper

Paper

An analysis of the nonlinear spectral mixing of didymium and soda-lime glass beads using hyperspectral imagery (HSI) microscopy

Ronald Resmini, Robert Rand, David Allen, Christopher Deloye

Proceedings Volume 9088, 90880Z (2014) https://doi.org/10.1117/12.2051434

KEYWORDS: Reflectivity, Glasses, Hyperspectral imaging, Microscopy, Remote sensing, Soda-lime glass, Spectroscopy, Sensors, Particles, Microscopes

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Nonlinear spectral mixing occurs when materials are intimately mixed. Intimate mixing is a common characteristic of granular materials such as soils. A linear spectral unmixing inversion applied to a nonlinear mixture will yield subpixel abundance estimates that do not equal the true values of the mixture's components. These aspects of spectral mixture analysis theory are well documented. Several methods to invert (and model) nonlinear spectral mixtures have been proposed. Examples include Hapke theory, the extended endmember matrix method, and kernel-based methods. There is, however, a relative paucity of real spectral image data sets that contain well characterized intimate mixtures. To address this, special materials were custom fabricated, mechanically mixed to form intimate mixtures, and measured with a hyperspectral imaging (HSI) microscope. The results of analyses of visible/near-infrared (VNIR; 400 nm to 900 nm) HSI microscopy image cubes (in reflectance) of intimate mixtures of the two materials are presented. The materials are spherical beads of didymium glass and soda-lime glass both ranging in particle size from 63 m to 125 m. Mixtures are generated by volume and thoroughly mixed mechanically. Three binary mixtures (and the two endmembers) are constructed and emplaced in the wells of a 96-well sample plate: 0%/100%, 25%/75%, 50%/50%, 80%/20%, and 100%/0% didymium/soda-lime. Analysis methods are linear spectral unmixing (LSU), LSU applied to reflectance converted to single-scattering albedo (SSA) using Hapke theory, and two kernel-based methods. The first kernel method uses a generalized kernel with a gamma parameter that gauges non-linearity, applying the well-known kernel trick to the least squares formulation of the constrained linear model. This method attempts to determine if each pixel in a scene is linear or non-linear, and adapts to compute a mixture model at each pixel accordingly. The second method uses 'K-hype' with a polynomial (quadratic) kernel. LSU applied to the reflectance spectra of the mixtures produced poor abundance estimates regardless of the constraints applied in the inversion. The 'K-hype' kernel-based method also produced poor fraction estimates. The best performers are LSU applied to the reflectance spectra converted to SSA using Hapke theory and the gamma parameter kernel-based method.

Proceedings Article | 4 June 2014 Paper

Paper

A collection and statistical analysis of skin reflectance signatures for inherent variability over the 250 nm to 2500 nm spectral range

Catherine Cooksey, Benjamin Tsai, David Allen

Proceedings Volume 9082, 908206 (2014) https://doi.org/10.1117/12.2053604

KEYWORDS: Reflectivity, Skin, Principal component analysis, Statistical analysis, Human subjects, Spectrophotometry, Short wave infrared radiation, Ultraviolet radiation, Photography, Solids

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Proceedings Article | 23 May 2013 Paper

Paper

Reflectance measurements of human skin from the ultraviolet to the shortwave infrared (250 nm to 2500 nm)

Catherine Cooksey, David Allen

Proceedings Volume 8734, 87340N (2013) https://doi.org/10.1117/12.2015821

KEYWORDS: Reflectivity, Skin, Spectrophotometry, Short wave infrared radiation, Ultraviolet radiation, Infrared radiation, Shortwaves, Visible radiation, Imaging spectroscopy, Sensors

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Proceedings Article | 18 May 2013 Paper

Paper

A microscene approach to the evaluation of hyperspectral system level performance

David Allen, Ronald Resmini, Christopher Deloye, Jeffrey Stevens

Proceedings Volume 8743, 87431M (2013) https://doi.org/10.1117/12.2015834

KEYWORDS: Sensors, Remote sensing, Hyperspectral imaging, Fractal analysis, Reflectivity, Data modeling, Principal component analysis, Imaging systems, Scene classification, Radiative transfer

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Assessing the ability of a hyperspectral imaging (HSI) system to detect the presence of a substance or to quantify abundance requires an understanding of the many factors in the end-to-end remote sensing scenario from scene to sensor to data exploitation. While there are methods which attempt to model such an overall scenario, they are necessarily implemented with assumptions and approximations that do not completely capture the true complexity of the actual radiative transfer processes nor do they capture the range of variability that materials display in a natural setting. We propose one alternative to numerical data models that generate hyperspectral image cubes for system trade studies and for algorithm development and testing. This approach makes use of compact hyperspectral imagers that can be used in the laboratory to measure materials in a 'microscene' specific to one’s application. The key to acceptance of this approach is quantifying the distributions of spectra as points in n-D space so that one can compare the spectral complexity of laboratory generated microscene data to that of an earth remote sensing scene. The spectral complexity of the microscene generated in the lab is thus compared to airborne remotely sensed HSI. We produce and measure a microscene, estimate its data dimensionality, and compare that to similar estimates of dimensionality of airborne HSI data sets. Signal-to-clutter ratios (SCR) of the microscene are also compared to those derived from airborne HSI data. The results suggest the microscene is capable of producing a scene that is as complex, if not more so, than that of a hyperspectral scene collected from an airborne sensor. A scene classification analysis and a system trade study are conducted to illustrate the utility of the microscene for assessing system-level performance. This simple, low-cost method can provide proxy data with a distribution of points in n-dimensional (n-D) hyperspace that are indistinguishable from an earth remote sensing scene.

Proceedings Article | 18 May 2013 Paper

Paper

An analysis of the probability distribution of spectral angle and Euclidean distance in hyperspectral remote sensing using microspectroscopy

Ronald Resmini, Christopher Deloye, David Allen

Proceedings Volume 8743, 87431I (2013) https://doi.org/10.1117/12.2015701

KEYWORDS: Microscopy, Reflectivity, Ruby, Minerals, Statistical analysis, Imaging spectroscopy, Remote sensing, Data acquisition, Detection and tracking algorithms, Sensors

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Determining the probability distribution of hyperspectral imagery (HSI) data and of the results of algorithms applied to those data, is critical to understanding algorithm performance and for establishing performance metrics such as probability of detection, false alarm rate, and minimum detectable and identifiable quantities. The results of analyses of visible/near-infrared (VNIR; 400 nm to 900 nm) HSI microscopy data of small fragments (~1.25 cm in size) of minerals are presented. HSI microscopy, also known as microspectroscopy, is the acquisition of HSI data cubes of fields of view ranging from centimeters to millimeters in size. It is imaging spectrometry but at a small spatial scale. With HSI microspectroscopy, several thousand spectral signatures may be easily acquired of individual target materials—samples of which may be quite small. With such data, probability distributions may be very precisely determined. For faceted/irregularly shaped samples and mixtures (checkerboard, intimate, or microscopic), HSI microscopy data readily facilitate a detailed assessment of the contribution of the materials, their morphology, spectral mixing interactions, radiative transfer processes, view/illumination geometry contributions, etc., to the observed probability distribution(s) of the HSI data and of algorithm output. Here, spectral angle, the individual components of spectral angle (e.g., the inner product or numerator of the spectral angle equation), Euclidean distance, and L1 norm values are calculated. Regions of interest (ROI) on the fragments are easily defined that contain thousands of spectra far from the fragments' edges though translucency sometimes remains a factor impacting spectral signatures. The aforementioned metrics are derived for the spectra in an ROI of individual mineral fragments; across ROIs of different minerals; and with an ROI of an inert background. The resulting probability distributions of the various populations of the metrics are decidedly non-Gaussian though the precise probability distribution is difficult to determine. Spectral angle values appear to be most closely related to beta distributed. The HSI microscopy method is described as are the results of the analyses applied to the data of the mineral fragments. The interpretation of the microspectroscopy data is considered within the ongoing investigation into determining how the spectral variability on the ~10 micrometer spatial scale relates to the spectral variability on larger scales such as those acquired by airborne remote sensing systems.

Proceedings Article | 11 May 2012 Paper

Paper

The evaluation of hyperspectral imaging for the detection of person-borne threat objects over the 400nm to 1700nm spectral region

Catherine Cooksey, Jorge Neira, David Allen

Proceedings Volume 8357, 83570O (2012) https://doi.org/10.1117/12.919432

KEYWORDS: Hyperspectral imaging, Tissues, Short wave infrared radiation, Imaging systems, Reflectivity, Transmittance, Improvised explosive devices, Skin, Image analysis, Natural surfaces

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Proceedings Article | 13 February 2012 Paper

Paper

Hyperspectral image projector applications

Joseph Rice, Steven Brown, David Allen, Howard Yoon, Maritoni Litorja, Jeeseong Hwang

Proceedings Volume 8254, 82540R (2012) https://doi.org/10.1117/12.907898

KEYWORDS: Digital micromirror devices, Hyperspectral imaging, Projection systems, Sensors, Calibration, Remote sensing, Photovoltaics, Imaging systems, Prototyping, Short wave infrared radiation

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Proceedings Article | 3 February 2012 Paper

Paper

Validating the LASSO algorithm by unmixing spectral signatures in multicolor phantoms

Daniel Samarov, Matthew Clarke, Ji Yoon Lee, David Allen, Maritoni Litorja, Jeeseong Hwang

Proceedings Volume 8229, 82290Z (2012) https://doi.org/10.1117/12.908133

KEYWORDS: Autoregressive models, Hyperspectral imaging, Printing, Calibration, Biomedical optics, Statistical analysis, Image analysis, Feature selection, Absorbance, Standards development

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As hyperspectral imaging (HSI) sees increased implementation into the biological and medical elds it becomes increasingly important that the algorithms being used to analyze the corresponding output be validated. While certainly important under any circumstance, as this technology begins to see a transition from benchtop to bedside ensuring that the measurements being given to medical professionals are accurate and reproducible is critical. In order to address these issues work has been done in generating a collection of datasets which could act as a test bed for algorithms validation. Using a microarray spot printer a collection of three food color dyes, acid red 1 (AR), brilliant blue R (BBR) and erioglaucine (EG) are mixed together at dierent concentrations in varying proportions at dierent locations on a microarray chip. With the concentration and mixture proportions known at each location, using HSI an algorithm should in principle, based on estimates of abundances, be able to determine the concentrations and proportions of each dye at each location on the chip. These types of data are particularly important in the context of medical measurements as the resulting estimated abundances will be used to make critical decisions which can have a serious impact on an individual's health. In this paper we present a novel algorithm for processing and analyzing HSI data based on the LASSO algorithm (similar to "basis pursuit"). The LASSO is a statistical method for simultaneously performing model estimation and variable selection. In the context of estimating abundances in an HSI scene these so called "sparse" representations provided by the LASSO are appropriate as not every pixel will be expected to contain every endmember. The algorithm we present takes the general framework of the LASSO algorithm a step further and incorporates the rich spatial information which is available in HSI to further improve the estimates of abundance. We show our algorithm's improvement over the standard LASSO using the dye mixture data as the test bed.

Proceedings Article | 3 February 2012 Paper

Paper

Hyperspectral imaging of ischemic wounds

Surya Gnyawali, Haytham Elgharably, James Melvin, Kun Huang, Valerie Bergdall, David Allen, Jeeseong Hwang, Maritoni Litorja, Eric Shirley, Chandan Sen, Ronald Xu

Proceedings Volume 8229, 822910 (2012) https://doi.org/10.1117/12.907107

KEYWORDS: Tissues, Skin, Hyperspectral imaging, Oxygen, Surgery, Reflectivity, Calibration, Wound healing, Optical imaging, Image fusion

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Proceedings Article | 23 May 2011 Paper

Paper

Investigation of the potential use of hyperspectral imaging for stand-off detection of person-borne IEDs

Catherine Cooksey, David Allen

Proceedings Volume 8017, 80171W (2011) https://doi.org/10.1117/12.883502

KEYWORDS: Reflectivity, Transmittance, Skin, Hyperspectral imaging, Improvised explosive devices, Short wave infrared radiation, Tissues, Sensors, Ultraviolet radiation, Imaging systems

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Proceedings Article | 22 February 2011 Paper

Paper

Characterization of hyperspectral imaging and analysis via microarray printing of dyes

Matthew Clarke, Maritoni Litorja, David Allen, Daniel Samarov, Jeeseong Hwang

Proceedings Volume 7891, 78910W (2011) https://doi.org/10.1117/12.875521

KEYWORDS: Hyperspectral imaging, Microscopes, Calibration, Transmittance, Printing, Optical filters, Cameras, Reflectivity, Image processing, Image analysis

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Proceedings Article | 15 February 2011 Paper

Paper

An examination of spectral diversity of medical scenes for hyperspectral projection

David Allen, Joseph Rice, Eleanor Wehner, Robert McMahon, Edward Livingston, Jonathan White, Rafael Ufret-Vincenty, Karel Zuzak

Proceedings Volume 7932, 793205 (2011) https://doi.org/10.1117/12.877188

KEYWORDS: Hyperspectral imaging, Imaging systems, Digital Light Processing, Digital micromirror devices, Projection systems, Tissues, Mirrors, Tissue optics, Eye, Cameras

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Proceedings Article | 11 February 2011 Paper

Paper

Hyperspectral image projection of a pig kidney for the evaluation of imagers used for oximetry

David Allen, Stephen Maxwell, Joseph Rice, Robert Chang, Maritoni Litorja, Jeeseong Hwang, Jeffrey Cadeddu, Edward Livingston, Eleanor Wehner, Karel Zuzak

Proceedings Volume 7906, 79060V (2011) https://doi.org/10.1117/12.875498

KEYWORDS: Imaging systems, Kidney, Hyperspectral imaging, Tissues, Reflectivity, Tissue optics, Medical imaging, Surgery, Laparoscopy, Oximetry

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Proceedings Article | 18 February 2010 Paper

Paper

The robustness of DLP hyperspectral imaging for clinical and surgical utility

Karel Zuzak, Eleanor Wehner, Shekar Rao, Maritoni Litorja, David Allen, Mike Singer, Gary Purdue, Rafael Ufret-Vincenty, Jonathan White, Jeffrey Cadeddu, Edward Livingston

Proceedings Volume 7596, 759604 (2010) https://doi.org/10.1117/12.845564

KEYWORDS: Hyperspectral imaging, Kidney, Surgery, Tissues, Imaging systems, Retina, Digital Light Processing, Brain, Laparoscopy, Eye

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Proceedings Article | 21 August 2009 Paper

Paper

The extension of the NIST BRDF scale from 1100 nm to 2500 nm

Howard Yoon, David Allen, George Eppeldauer, Benjamin Tsai

Proceedings Volume 7452, 745204 (2009) https://doi.org/10.1117/12.827293

KEYWORDS: Reflectivity, Radiometry, Sensors, Calibration, Monochromators, Radio optics, Polarization, Infrared radiation, Indium gallium arsenide, Lamps

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Proceedings Article | 30 April 2009 Paper

Paper

Hyperspectral projection of a coral reef scene using the NIST hyperspectral image projector

David Allen, Joseph Rice, James Goodman

Proceedings Volume 7334, 733415 (2009) https://doi.org/10.1117/12.818809

KEYWORDS: Image processing, Hyperspectral imaging, Remote sensing, Projection systems, Sensors, Spectroscopy, Imaging systems, Algorithm development, Sensing systems, Reflectivity

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Proceedings Article | 27 April 2009 Paper

Paper

Hyperspectral image compressive projection algorithm

Joseph Rice, David Allen

Proceedings Volume 7334, 733414 (2009) https://doi.org/10.1117/12.818844

KEYWORDS: Spectroscopy, Calibration, Charge-coupled devices, Hyperspectral imaging, Image compression, Algorithm development, Digital micromirror devices, Projection systems, Collimators, Polysomnography

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Proceedings Article | 14 February 2009 Paper

Paper

DLP hyperspectral imaging for surgical and clinical utility

Karel Zuzak, Robert Francis, Eleanor Wehner, Jack Smith, Maritoni Litorja, David Allen, Chad Tracy, Jeffrey Cadeddu, Edward Livingston

Proceedings Volume 7210, 721006 (2009) https://doi.org/10.1117/12.810068

KEYWORDS: Hyperspectral imaging, Digital Light Processing, Imaging systems, Kidney, Image processing, Spectroscopy, Tissues, Reflectivity, Sensors, Surgery

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SPIE Journal Paper | 1 September 2008 Open Access

Open Access

Light scattering of semitransparent sintered polytetrafluoroethylene films

Qinghe Li, Bong-Jae Lee, Zhuomin Zhang, David Allen

JBO, Vol. 13, Issue 05, 054064, (September 2008) https://doi.org/10.1117/12.10.1117/1.2992485

KEYWORDS: Scattering, Light scattering, Bidirectional reflectance transmission function, Transmittance, Laser scattering, Reflectivity, Monte Carlo methods, Sensors, Photons, Absorption

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Proceedings Article | 29 August 2008 Paper

Paper

A comparison of optical properties between high density and low density sintered PTFE

Benjamin Tsai, David Allen, Leonard Hanssen, Boris Wilthan, Jinan Zeng

Proceedings Volume 7065, 70650Y (2008) https://doi.org/10.1117/12.798138

KEYWORDS: Bidirectional reflectance transmission function, Transmittance, FT-IR spectroscopy, Reflectivity, Optical properties, Ultraviolet radiation, Sensors, Infrared radiation, Diffusers, Particles

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Proceedings Article | 21 February 2008 Paper

Paper

Dynamically programmable digital tissue phantoms

Steven Brown, Joseph Rice, David Allen, Karel Zuzak, Edward Livingston, Maritoni Litorja

Proceedings Volume 6870, 687003 (2008) https://doi.org/10.1117/12.762292

KEYWORDS: Digital micromirror devices, Tissue optics, Calibration, Mirrors, Projection systems, Imaging systems, Hyperspectral imaging, Tissues, Sensors, Spatial light modulators

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Proceedings Article | 2 October 2007 Paper

Paper

Evaluation of a portable hyperspectral imager for medical imaging applications

David Allen, Maritoni Litorja, Steven Brown, Yuqin Zong

Proceedings Volume 6765, 67650F (2007) https://doi.org/10.1117/12.733189

KEYWORDS: Imaging systems, Hyperspectral imaging, Stray light, Relays, Cameras, Optical filters, Medical imaging, Sensors, Calibration, Near infrared

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Proceedings Article | 10 November 2003 Paper

Paper

Calibration and characterization of trap detector filter radiometers

David Allen, George Eppeldauer, Steven Brown, Edward Early, B. Carol Johnson, Keith Lykke

Proceedings Volume 5151, (2003) https://doi.org/10.1117/12.507995

KEYWORDS: Radiometry, Sensors, Calibration, Optical filters, Lamps, Silicon, Remote sensing, Integrating spheres, Radio optics, Photodiodes

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Proceedings Article | 18 January 2002 Paper

Paper

Radiometric calibration of the Scripps Earth Polychromatic Imaging Camera

Edward Early, Brett Bush, Steven Brown, David Allen, B. Carol Johnson

Proceedings Volume 4483, (2002) https://doi.org/10.1117/12.453474

KEYWORDS: Calibration, Radiometry, Charge-coupled devices, Temperature metrology, Lamps, Radio optics, Camera shutters, Sensors, Telescopes, Ocean optics

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Showing 5 of 54 publications

Proceedings Volume Editor (2)

SPIE Conference Volume | 31 March 2015

Design and Performance Validation of Phantoms Used in Conjunction with Optical Measurement of Tissue VII

SPIE Conference Volume | 14 March 2014

Design and Performance Validation of Phantoms Used in Conjunction with Optical Measurement of Tissue VI

Conference Committee Involvement (19)

Design and Quality for Biomedical Technologies XVIII

25 January 2025 | San Francisco, California, United States

Design and Quality for Biomedical Technologies XVII

27 January 2024 | San Francisco, California, United States

Design and Quality for Biomedical Technologies XVI

28 January 2023 | San Francisco, California, United States

Design and Quality for Biomedical Technologies XV

22 January 2022 | San Francisco, California, United States

Design and Quality for Biomedical Technologies XIV

6 March 2021 | Online Only, California, United States

Design and Quality for Biomedical Technologies XIII

1 February 2020 | San Francisco, California, United States

Design and Quality for Biomedical Technologies XII

2 February 2019 | San Francisco, California, United States

Design and Quality for Biomedical Technologies XI

27 January 2018 | San Francisco, California, United States

Hyperspectral Imaging Sensors: Innovative Applications and Sensor Standards 2017

12 April 2017 | Anaheim, CA, United States

Design and Quality for Biomedical Technologies X

28 January 2017 | San Francisco, California, United States

Hyperspectral Imaging Sensors: Innovative Applications and Sensor Standards 2016

20 April 2016 | Baltimore, MD, United States

Design and Quality for Biomedical Technologies IX

13 February 2016 | San Francisco, California, United States

Active and Passive Signatures VI

22 April 2015 | Baltimore, MD, United States

Design and Quality for Biomedical Technologies VIII

7 February 2015 | San Francisco, California, United States

Design and Performance Validation of Phantoms Used in Conjunction with Optical Measurement of Tissue VII

7 February 2015 | San Francisco, California, United States

Active and Passive Signatures V

7 May 2014 | Baltimore, MD, United States

Design and Quality for Biomedical Technologies VII

1 February 2014 | San Francisco, California, United States

Design and Performance Validation of Phantoms Used in Conjunction with Optical Measurement of Tissue VI

1 February 2014 | San Francisco, California, United States

Design and Quality for Biomedical Technologies VI

2 February 2013 | San Francisco, California, United States

Showing 5 of 19 Conference Committees

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