Bio


Our lab seeks to develop and deploy novel tools for optical imaging and sensing at the microscale and nanoscale. Our work finds applications both in the clinic and for basic science research; we also have particular interest in the development of low-cost, portable technologies suited for use in poorly resourced environments.

Academic Appointments


Honors & Awards


  • Young Investigator Award, Air Force (2013)
  • Hellman Faculty Scholar, Hellman Fellowship Program (2013)
  • Diversity Postdoctoral Fellowship, Ford Foundation (2013)
  • Arthur H. Guenther Congressional Fellow, Arthur H. Guenther Congressional Fellowship Program (2013)
  • Golden Torch Award, National Society of Black Engineers (2013)

Professional Education


  • PhD, Duke University, Biomedical Engineering
  • BS, Princeton University, Electrical Engineering

Journal Articles


  • Three-dimensional, distendable bladder phantom for optical coherence tomography and white light cystoscopy. Journal of biomedical optics Lurie, K. L., Smith, G. T., Khan, S. A., Liao, J. C., Ellerbee, A. K. 2014; 19 (3): 36009-?

    Abstract

    ABSTRACT. We describe a combination of fabrication techniques and a general process to construct a three-dimensional (3-D) phantom that mimics the size, macroscale structure, microscale surface topology, subsurface microstructure, optical properties, and functional characteristics of a cancerous bladder. The phantom also includes features that are recognizable in white light (i.e., the visual appearance of blood vessels), making it suitable to emulate the bladder for emerging white light+optical coherence tomography (OCT) cystoscopies and other endoscopic procedures of large, irregularly shaped organs. The fabrication process has broad applicability and can be generalized to OCT phantoms for other tissue types or phantoms for other imaging modalities. To this end, we also enumerate the nuances of applying known fabrication techniques (e.g., spin coating) to contexts (e.g., nonplanar, 3-D shapes) that are essential to establish their generalizability and limitations. We anticipate that this phantom will be immediately useful to evaluate innovative OCT systems and software being developed for longitudinal bladder surveillance and early cancer detection.

    View details for DOI 10.1117/1.JBO.19.3.036009

    View details for PubMedID 24623158

  • Interleaved optical coherence tomography OPTICS EXPRESS Lee, H. Y., Sudkamp, H., Marvdashti, T., Ellerbee, A. K. 2013; 21 (22): 26542-26556

    Abstract

    We present a novel and cost-effective technique--interleaved optical coherence tomography (iOCT)--to enhance the imaging speed of swept source OCT systems by acquiring data from multiple lateral positions simultaneously during a single wavelength sweep, using a single detector and a virtually imaged phase array (VIPA) as a multi-band demultiplexer. This technique uses spectral encoding to convert coherence length into higher imaging speed; the speed enhancement factor is independent of the source speed or center wavelength, and the effective A-scan rate scales linearly with sweep speed. The optical configuration requires only a change in the sample arm of a traditional OCT system and preserves the axial resolution and fall-off characteristic of a traditional SS-OCT using the same light source. Using 10 kHz, 20 kHz and 100 kHz sources we provide a first demonstration of image speed enhancement factors of up to 12, 6 and 10, respectively, which yield effective A-scan rates of 120 kHz, 120 kHz and 1 MHz for B-scan imaging, with a sensitivity of up to 82.5 dB. We also show that iOCT can image faster dynamics than traditional OCT B-scan imaging and is capable of 3D biological imaging. The iOCT concept suggests a new route to high-speed OCT imaging for laser developers: that is, by focusing on improving the coherence length and linewidth of existing and emerging sources. Hence, iOCT is a nice complement to ongoing research and commercial efforts to enable faster imaging through development of lasers with faster sweep rates, and offers new hope for existing sources with slow sweep rates and potential for enhancement of coherence length to compete with faster sources to achieve high-speed OCT.

    View details for DOI 10.1364/OE.21.026542

    View details for Web of Science ID 000327007800111

    View details for PubMedID 24216876

  • Air Force test chart-like phantom for measuring axial and lateral resolution in optical coherence tomography DESIGN AND PERFORMANCE VALIDATION OF PHANTOMS USED IN CONJUNCTION WITH OPTICAL MEASUREMENT OF TISSUE V Gu, R. Y., Lurie, K. L., Ellerbee, A. K. 2013; 8583

    View details for DOI 10.1117/12.2003189

    View details for Web of Science ID 000322903900006

  • The magnitude of lift forces acting on drops and bubbles in liquids flowing inside microchannels LAB ON A CHIP Stan, C. A., Ellerbee, A. K., Guglielmini, L., Stone, H. A., Whitesides, G. M. 2013; 13 (3): 365-376

    Abstract

    Hydrodynamic lift forces offer a convenient way to manipulate particles in microfluidic applications, but there is little quantitative information on how non-inertial lift mechanisms act and compete with each other in the confined space of microfluidic channels. This paper reports measurements of lift forces on nearly spherical drops and bubbles, with diameters from one quarter to one half of the width of the channel, flowing in microfluidic channels, under flow conditions characterized by particle capillary numbers Ca(P) = 0.0003-0.3 and particle Reynolds numbers Re(P) = 0.0001-0.1. For Ca(P) < 0.01 and Re(P) < 0.01 the measured lift forces were much larger than predictions of deformation-induced and inertial lift forces found in the literature, probably due to physicochemical hydrodynamic effects at the interface of drops and bubbles, such as the presence of surfactants. The measured forces could be fit with good accuracy using an empirical formula given herein. The empirical formula describes the power-law dependence of the lift force on hydrodynamic parameters (velocity and viscosity of the carrier phase; sizes of channel and drop or bubble), and includes a numerical lift coefficient that depends on the fluids used. The empirical formula using an average lift coefficient of ~500 predicted, within one order of magnitude, all lift force measurements in channels with cross-sectional dimensions below 1 mm.

    View details for DOI 10.1039/c2lc41035d

    View details for Web of Science ID 000312947300007

    View details for PubMedID 23212283

  • Single-shot interpixel shifting for optical coherence tomography by oblique incidence spectroscopy OPTICAL COHERENCE TOMOGRAPHY AND COHERENCE DOMAIN OPTICAL METHODS IN BIOMEDICINE XVII Lee, H. Y., Ellerbee, A. K. 2013; 8571

    View details for DOI 10.1117/12.2007197

    View details for Web of Science ID 000322744300009

  • Interleaved Optical Coherence Tomography Opt. Exp Lee, H., H., Sudkamp, Marvdashti, T., Ellerbee, A., K. 2013; 22 (21): 26542-26556
  • Variable-sized bar targets for characterizing three-dimensional resolution in OCT BIOMEDICAL OPTICS EXPRESS Gu, R. Y., Lurie, K. L., Pipes, M., Ellerbee, A. K. 2012; 3 (9): 2317-2325

    Abstract

    Resolution is an important figure of merit for imaging systems. We designed, fabricated and tested an optical phantom that mimics the simplicity of an Air Force Test Chart but can characterize both the axial and lateral resolution of optical coherence tomography systems. The phantom is simple to fabricate, simple to use and functions in versatile environments.

    View details for Web of Science ID 000308861100032

    View details for PubMedID 23024923

  • Design considerations for polarization-sensitive optical coherence tomography with a single input polarization state BIOMEDICAL OPTICS EXPRESS Lurie, K. L., Moritz, T. J., Ellerbee, A. K. 2012; 3 (9): 2273-2287

    Abstract

    Using a generalized design for a polarization-sensitive optical coherence tomography (PS-OCT) system with a single input polarization state (SIPS), we prove the existence of an infinitely large design space over which it is possible to develop simple PS-OCT systems that yield closed form expressions for birefringence. Through simulation and experiment, we validate this analysis by demonstrating new configurations for PS-OCT systems, and present guidelines for the general design of such systems in light of their inherent inaccuracies. After accounting for systemic errors, alternative designs exhibit similar performance on average to the traditional SIPS PS-OCT system. This analysis could be extended to systems with multiple input polarization states and could usher in a new generation of PS-OCT systems optimally designed to probe specific birefringent samples with high accuracy.

    View details for Web of Science ID 000308861100028

    View details for PubMedID 23024919

  • The effects of reduced bit depth on optical coherence tomography phase data OPTICS EXPRESS Ling, W. A., Ellerbee, A. K. 2012; 20 (14): 15654-15668

    Abstract

    Past studies of the effects of bit depth on OCT magnitude data concluded that 8 bits of digitizer resolution provided nearly the same image quality as a 14-bit digitizer. However, such studies did not assess the effects of bit depth on the accuracy of phase data. In this work, we show that the effects of bit depth on phase data and magnitude data can differ significantly. This finding has an important impact on the design of phase-resolved OCT systems, such as those measuring motion and the birefringence of samples, particularly as one begins to consider the tradeoff between bit depth and digitizer speed.

    View details for Web of Science ID 000306176100100

    View details for PubMedID 22772258

  • The Effects of Different Gold Standards on the Accuracy of Optical Coherence Tomography IMAGING, MANIPULATION, AND ANALYSIS OF BIOMOLECULES, CELLS, AND TISSUES X Copeland, C. N., Ellerbee, A. K. 2012; 8225

    View details for DOI 10.1117/12.909328

    View details for Web of Science ID 000302555800015

  • Analysis of the Effects of Different Resampling Techniques for Optical Coherence Tomography THREE-DIMENSIONAL AND MULTIDIMENSIONAL MICROSCOPY: IMAGE ACQUISITION AND PROCESSING XIX Copeland, C. N., Ellerbee, A. K. 2012; 8227

    View details for DOI 10.1117/12.909268

    View details for Web of Science ID 000302561200018

  • Sheathless hydrodynamic positioning of buoyant drops and bubbles inside microchannels PHYSICAL REVIEW E Stan, C. A., Guglielmini, L., Ellerbee, A. K., Caviezel, D., Stone, H. A., Whitesides, G. M. 2011; 84 (3)

    Abstract

    Particles, bubbles, and drops carried by a fluid in a confined environment such as a pipe can be subjected to hydrodynamic lift forces, i.e., forces that are perpendicular to the direction of the flow. We investigated the positioning effect of lift forces acting on buoyant drops and bubbles suspended in a carrier fluid and flowing in a horizontal microchannel. We report experiments on drops of water in fluorocarbon liquid, and on bubbles of nitrogen in hydrocarbon liquid and silicone oil, inside microchannels with widths on the order of 0.1-1 mm. Despite their buoyancy, drops and bubbles could travel without contacting with the walls of channels; the most important parameters for reaching this flow regime in our experiments were the viscosity and the velocity of the carrier fluid, and the sizes of drops and bubbles. The dependencies of the transverse position of drops and bubbles on these parameters were investigated. At steady state, the trajectories of drops and bubbles approached the center of the channel for drops and bubbles almost as large as the channel, carried by rapidly flowing viscous liquids; among our experiments, these flow conditions were characterized by larger capillary numbers and smaller Reynolds numbers. Analytical models of lift forces developed for the flow of drops much smaller than the width of the channel failed to predict their transverse position, while computational fluid dynamic simulations of the experiments agreed better with the experimental measurements. The degrees of success of these predictions indicate the importance of confinement on generating strong hydrodynamic lift forces. We conclude that, inside microfluidic channels, it is possible to support and position buoyant drops and bubbles simply by flowing a single-stream (i.e., "sheathless") carrier liquid that has appropriate velocity and hydrodynamic properties.

    View details for DOI 10.1103/PhysRevE.84.036302

    View details for Web of Science ID 000294945500005

    View details for PubMedID 22060487

  • Using magnetic levitation for three-dimentional self assembly Adv. Mat. Mirica, K., A., Ilievski, F., Ellerbee, A., K., Shevkoplyas, S., S., Whitesides, G., M. 2011; 36 (23): 4134-4140
  • Templated three-dimensional self-assembly using magnetic levitation Soft Matter Ilievski, F., Mirica, K., A., Ellerbee, A., K., Whitesides, G., M. 2011; 19 (7): 9113-9118
  • Bubbles navigating through networks of microchannels Lab Chip Choi, W., Hashimoto, M., Ellerbee, A., K., Chen, Bishop, X., M., K., J., Garstecki, P. 2011; 23 (8): 3970-3978
  • Quantifying colorimetric assays in paper-based microfluidic devices by measuring the transmission of light through paper Anal. Chem. Ellerbee, A., K., Phillips, S., T., Siegel, A., C., Mirica, K., A., Martinez, A., W., Striehl, P. 2009; 20 (81): 8447-8452
  • Infochemistry: Encoding information as optical pulses using droplets in a microfluidic device J. Am. Chem. Soc. Hashimoto, M., Feng, J., York, R., L., Ellerbee, A., K., Morrison, G., Thomas III, S., W. 2009; 34 (131): 12420-12429
  • Spectral domain phase microscopy for local measurements of cytoskeletal rheology in cells J. Biomed. Opt. McDowell, E., J., Ellerbee, A., K., Choma, M., A., Applegate, B., E., Izatt, J., A. 2007; 4 (12): 044008
  • Investigating nanoscale cellular dynamics with cross-sectional spectral domain phase microscopy Opt. Exp. Ellerbee, A., K., Creazzo, T., L., Izatt, J., A. 2007; 13 (15): 8115-8124
  • Phase retrieval in low-coherence interference microscopy Opt. Lett. Ellerbee, A., K., Izatt, J., A. 2007; 4 (32): 388-390
  • Doppler flow imaging of cytoplasmic flow using spectral domain phase microscopy J. Biomed. Opt. Choma, M., A., Ellerbee, A., K., Yazdanfar, S., Izatt, J., A. 2006; 11: 024014
  • Spectral-domain phase microscopy Opt. Lett. Choma, M., A., Ellerbee, A., K., Yang, C., Creazzo, T., L., Izatt, J., A. 2005; 30: 1162-1164

Conference Proceedings


  • High-resolution spectrometer: solution to the axial resolution and imaging depth tradeoff of SD-OCT Marvdashti, T., Lee, H., Ellerbee, A., K. 2013
  • Full-field Optical Coherence Tomography of Early Embryonic Development Zarnescu, L., Sudkamp, H., Baer, T., Ellerbee, A., K. 2013
  • Combined Polarization Sensitive OCT (PS-OCT) and Raman Spectroscopy (RS) for Label-free Assessment of Molecular and Structural Abnormalities for Point-of-Care Skin Cancer Diagnostics Marvdashti, T., Duan, L., Ellerbee, A., K. 2013
  • Non-contact, label-free 3D imaging of developing embryos Zarnescu, L., Sudkamp, H., Behr, B., Baer, T., Ellerbee, A., K. 2013
  • Full-field Optical Coherence Tomography of Early Embryonic Development Zarnescu, L., Sudkamp, H., Baer, T., Ellerbee 2013
  • Enhanced Speed in Swept-Source OCT with a Multi-band Demultiplexer Lee, H., Y., Sudkamp, H., Marvdashti, T., Ellerbee, A., K. 2013
  • Co-registration of OCT volumes for 3D bladder mosaicing Lurie, K., L., Ellerbee, A., K. 2013
  • Measuring Performance of Different Compression Algorithms for Fourier Domain OCT Data Su, N., Lurie, K., L., Ellerbee, A., K. 2012
  • High-Resolution Spectrometer for Spectral-Domain Optical Coherence Tomography Marvdashti, T., Ellerbee, A., K. 2012
  • Extend Imaging Depth in Spectral-domain Optical Coherence Tomography by Oblique Incidence Lee, H., Ellerbee, A., K. 2012
  • New Design Options for Polarization-Sensitive Optical Coherence Tomography Lurie, K., L., Ellerbee, A., K. 2012
  • Extend Imaging Depth in Spectral-domain Optical Coherence Tomography by Oblique Incidence Lee, H., Ellerbee, A., K. 2012
  • Effects of Reduced Bit-Depth on Phase Data in Common-Path Optical Coherence Tomography Ling, W., A., Ellerbee, A., K. 2012
  • Considerations for Polarization-sensitive optical coherence tomography design Lurie, K., L., Moritz, T., J., Ellerbee, A., K. 2012
  • A Spectral Encoding-Based Approach to Real-time Volumetric Imaging with Optical Coherence Tomography Lee, H., Y., Ellerbee, A., K. 2011
  • Towards Polarization-Sensitive OCT for Non-Invasive Blood Glucose Monitoring Lurie, K., L., Ellerbee, A., K. 2011
  • Optical Coherence Tomography: Paradoxical Problem Solving Cohen, N., Gebru, T., Lee, H., Y., Lurie, K., L., Marvdashti, T., Ellerbee, A., K. 2011
  • Optical Coherence Tomography: Advancing Technology, Impacting Disease Cohen, N., Gebru, T., Lee, H., Y., Lurie, K., L., Marvdashti, T., Ellerbee, A., K. 2011
  • Towards Polarization-Sensitive OCT for Non-Invasive Blood Glucose Monitoring Lurie, K., L., Ellerbee, A., K. 2011
  • Flows of Bubbles in Microfluidic Networks Choi, W., Hashimoto, M., Ellerbee, A., K., Bishop, Chen, X., M., K., J., Garstecki, P. 2011
  • Using magnetic levitation for meso-scale self-assembly Mirica, K., A., Ilievski, F., Ellerbee, A., K., Whitesides, G., M. 2010
  • Programmable Self-Assembly of Complex Shapes in Three Dimensions Mirica, K., A., Ellerbee, A., K., Ilievski, F., Whitesides, G., M. 2009
  • Quantifying colorimetric assays in paper-based microfluidic devices by measuring the transmission of light through paper Ellerbee, A., K., Phillips, S., T., Siegel, A., C., Mirica, K., A., Martinez, A., W., Striehl, P. 2009
  • Extension of Spectral Domain Phase Microscopy to Three-Dimensional Nanoscale Displacement Mapping in Cardiomyocytes Ellerbee, A., K., Hendargo, H., Motomora, A., R., Izatt, J., A. 2008
  • Examining Cardiomyocyte Development with Spectral Domain Phase Microscopy Ellerbee, A., K., Choma, M., A., Creazzo, T., L., Izatt, J., A. 2007
  • Full-field swept-source phase microscopy Sarunic, M., Weinberg, S., Ellerbee, A., Applegate, B., Izatt., J., A. 2006
  • High Speed Spectral Domain Phase Microscopy for Quantitative Cell Surface and Cytoplasmic Flow Measurements Ellerbee, A., K. 2006
  • High Speed Multidimensional Spectral Domain Phase Microscopy Ellerbee, A., K. 2006
  • Spectral domain phase microscopy: a new tool for measuring cellular dynamics and cytoplasmic flow McDowell, E., J., Choma, M., A., Ellerbee, A., K., Izatt, J., A. 2005
  • Characterizing Cellular Contractility and Cytoplasmic Flow Using Spectral Domain Phase Microscopy Ellerbee, A., K., Choma, M., A., McDowell, E., J., Yang, C., Creazzo, A., L., Izatt, J., A. 2005
  • Spectral domain phase microscopy: a new tool for investigating nanoscale and cellular dynamics Ellerbee, A., K. 2005
  • Spectral domain phase microscopy Choma, M., A., Ellerbee, A., K., Yang, C., Izatt, J., A. 2004
  • Exploring heart cell dynamics using spectral domain phase microscopy Ellerbee, A., K., Choma, M., A., Izatt, J., A. 2004
  • Spectral domain phase microscopy Choma, M., A., Ellerbee, A., K., Yang, C., Izatt, J., A. 2004
  • Temperature and Fish Immunology: Assumptions, Truths, and New Data Ellerbee, A., K., Perrotti, L., I., Landsman, R., E. 1997