Dr. Matthew Clarke Profile

Dr. Matthew Clarke

Guest Researcher at National Institute of Standards and Technology

SPIE Involvement:

Author

Publications (6)

Proceedings Article | 3 February 2012 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

Read Abstract +

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 | 28 February 2011 Paper

Real-time fluorescence polarization microscopy for probing local distributions of biomolecules

Ji Youn Lee, John Lesoine, Jeffrey Krogmeier, Hyeonggon Kang, Matthew Clarke, Robert Chang, Dan Sackett, Ralph Nossal, Jeeseong Hwang

Proceedings Volume 7891, 78910Z (2011) https://doi.org/10.1117/12.875612

KEYWORDS: Polarization, Luminescence, Analog electronics, Molecules, Absorption, Wave plates, Microscopy, Calibration, Liquid crystals, Microscopes

Read Abstract +

Proceedings Article | 22 February 2011 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

Read Abstract +

Proceedings Article | 12 February 2008 Paper

Thermal properties of gold nanoshells in lipid vesicles studied by single particle tracking measurements

Matthew Clarke, HyeongGon Kang, Peter Yim, Rani Kishore, Kristian Helmerson, Jeeseong Hwang

Proceedings Volume 6849, 68490H (2008) https://doi.org/10.1117/12.766415

KEYWORDS: Gold, Near infrared, Particles, Digital image correlation, Diffusion, Luminescence, Nanoparticles, Microscopy, Temperature metrology, Biomedical optics

Read Abstract +

Proceedings Article | 7 February 2007 Paper

Fluorescence intermittency and spectral shifts of single bio-conjugated nanocrystals studied by single molecule confocal fluorescence microscopy and spectroscopy

HyeongGon Kang, Mathew Maye, Dmytro Nykypanchuk, Matthew Clarke, Peter Yim, Jeffrey Krogmeier, Kimberly Briggman, Oleg Gang, Jeeseong Hwang

Proceedings Volume 6430, 643024 (2007) https://doi.org/10.1117/12.713934

KEYWORDS: Luminescence, Confocal microscopy, Molecules, Nanocrystals, Fluorescence spectroscopy, Diffusion, Optical properties, Spectroscopy, Singular optics, Linear filtering

Read Abstract +

Proceedings Article | 6 February 2007 Paper

Nanocrystal-based biomimetic system for quantitative flow cytometry

Peter Yim, Marina Dobrovolskaia, HyeongGon Kang, Matthew Clarke, Anil Patri, Jeeseong Hwang

Proceedings Volume 6430, 64301T (2007) https://doi.org/10.1117/12.714138

KEYWORDS: Luminescence, Flow cytometry, Biomimetics, Silica, Standards development, Microscopy, Quantum dots, Sensors, Scattering, Microfluidics

Read Abstract +

Flow cytometry has been instrumental in rapid analysis of single cells since the 1970s. One of the common approaches is the immunofluorescence study involving labeling of cells with antibodies conjugated to organic fluorophores. More recently, as the application of flow cytometry extended from simple cell detection to single-cell proteomic analysis, the need of determining the actual number of antigens in a single cell has driven the flow cytomery technique towards a quantitative methodology. However, organic fluorophores are challenging to use as probes for quantitative detection due to the lack of photostability and of quantitative fluorescence standards. National Institute of Standards and Technologies (NIST) provides a set of fluorescein isothiocyanate (FITC) labeled beads, RM 8640, which is the only nationally recognized fluorescent particle standard. On the other hand, optical characteristics of semiconductor nanocrystals or quantum dots or QDs are superior to traditional dye molecules for the use as tags for biological and chemical fluorescent sensors and detectors. Compelling advantages of QDs include long photostability, broad spectral coverage, easy excitation, and suitability for multiplexed sensing. Recently, novel surface coatings have been developed to render QDs water soluble and bio-conjugation ready, leading to their use as fluorescent tags and sensors for a variety of biological applications including immunolabeling of cells. Here, we describe our approach of using fluorescent semiconductor QDs as a novel tool for quantitative flow cytometry detection. Our strategy involves the development of immuno-labeled QD-conjugated silica beads as "biomimetic cells." In addition to flow cytometry, the QD-conjugated silica beads were characterized by fluorescence microscopy to quantitate the number of QDs attached to a single silica bead. Our approach enables flow cytometry analysis to be highly sensitive, quantitative, and encompass a wide dynamic range of fluorescence detection. Quantitative aspects of the proposed flow cytometery-based approach for measurement of the QD-based biomimetic samples are discussed.

Showing 5 of 6 publications

View contact details

UPDATE YOUR PROFILE

Is this your profile? Update it now.

Sign into your SPIE.org account

Don’t have a profile and want one?

Create an account on SPIE.org

Keywords/Phrases

Search In:

Publication Years