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


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

Professional Education


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

All Publications


  • Two-Dimensional Cochlear Micromechanics Measured In Vivo Demonstrate Radial Tuning within the Mouse Organ of Corti. journal of neuroscience Lee, H. Y., Raphael, P. D., Xia, A., Kim, J., Grillet, N., Applegate, B. E., Ellerbee Bowden, A. K., Oghalai, J. S. 2016; 36 (31): 8160-8173

    Abstract

    The exquisite sensitivity and frequency discrimination of mammalian hearing underlie the ability to understand complex speech in noise. This requires force generation by cochlear outer hair cells (OHCs) to amplify the basilar membrane traveling wave; however, it is unclear how amplification is achieved with sharp frequency tuning. Here we investigated the origin of tuning by measuring sound-induced 2-D vibrations within the mouse organ of Corti in vivo Our goal was to determine the transfer function relating the radial shear between the structures that deflect the OHC bundle, the tectorial membrane and reticular lamina, to the transverse motion of the basilar membrane. We found that, after normalizing their responses to the vibration of the basilar membrane, the radial vibrations of the tectorial membrane and reticular lamina were tuned. The radial tuning peaked at a higher frequency than transverse basilar membrane tuning in the passive, postmortem condition. The radial tuning was similar in dead mice, indicating that this reflected passive, not active, mechanics. These findings were exaggerated in Tecta(C1509G/C1509G) mice, where the tectorial membrane is detached from OHC stereocilia, arguing that the tuning of radial vibrations within the hair cell epithelium is distinct from tectorial membrane tuning. Together, these results reveal a passive, frequency-dependent contribution to cochlear filtering that is independent of basilar membrane filtering. These data argue that passive mechanics within the organ of Corti sharpen frequency selectivity by defining which OHCs enhance the vibration of the basilar membrane, thereby tuning the gain of cochlear amplification.Outer hair cells amplify the traveling wave within the mammalian cochlea. The resultant gain and frequency sharpening are necessary for speech discrimination, particularly in the presence of background noise. Here we measured the 2-D motion of the organ of Corti in mice and found that the structures that stimulate the outer hair cell stereocilia, the tectorial membrane and reticular lamina, were sharply tuned in the radial direction. Radial tuning was similar in dead mice and in mice lacking a tectorial membrane. This suggests that radial tuning comes from passive mechanics within the hair cell epithelium, and that these mechanics, at least in part, may tune the gain of cochlear amplification.

    View details for DOI 10.1523/JNEUROSCI.1157-16.2016

    View details for PubMedID 27488636

  • Enhanced depolarization contrast in polarization-sensitive optical coherence tomography OPTICS LETTERS Ortega-Quijano, N., Marvdashti, T., Bowden, A. K. 2016; 41 (10): 2350-2353

    Abstract

    We demonstrate the first application of the differential depolarization index (DDI) for depolarization imaging in polarization-sensitive optical coherence tomography (PS-OCT). Unlike the widely used degree of polarization uniformity (DOPU), the DDI is independent of the incident polarization state and, therefore, more robust to varying system and sample parameters. Moreover, it can be applied to single-input-polarization-state PS-OCT systems, and it overcomes several limitations of the emerging depolarization index used in multiple-input-polarization-state systems. Our results on tissue phantoms and human skin prove that DDI yields significant depolarization contrast improvements compared to DOPU, which highlights its potential for depolarization imaging in PS-OCT.

    View details for DOI 10.1364/OL.41.002350

    View details for Web of Science ID 000375747600056

    View details for PubMedID 27177000

  • Colloidal Quantum Dots for Cost-effective, Miniaturized, and Simple Spectrometers. Clinical chemistry Khan, S. A., Ellerbee Bowden, A. K. 2016; 62 (4): 548-550

    View details for DOI 10.1373/clinchem.2015.247999

    View details for PubMedID 26832936

  • Iterative re-weighted approach to high-resolution optical coherence tomography with narrow-band sources OPTICS EXPRESS Mousavi, M., Duan, L., Javidi, T., Bowden, A. K. 2016; 24 (2): 1781-1793

    Abstract

    Optical coherence tomography (OCT) is a non-invasive optical imaging modality capable of high resolution imaging of internal tissue structures. It is widely believed that the high axial resolution in OCT systems requires a wide-bandwidth light source. As a result, often the potential advantages of narrow-bandwidth sources (in terms of cost and/or imaging speed) are understood to come at the cost of significant reduction in imaging resolution. In this paper, we argue that this trade-off between resolution and speed is a shortcoming imposed by the-state-of-the-art A-scan reconstruction algorithm, Fast Fourier Transform, and can be circumvented through use of alternative processing methods. In particular, we investigate the shortcomings of the FFT as well as previously proposed alternatives and demonstrate the first application of an iterative regularized re-weighted l(2) norm method to improve the axial resolution of fast scan rate OCT systems in the narrow-bandwidth imaging conditions. We validate our claims via experimental results generated from a home-built OCT system used to image layered phantom and in vivo data. Our results rely on new, sophisticated signal processing algorithms to generate higher precision (i.e., higher resolution) OCT images at correspondingly fast scan rates. In other words, our work demonstrates the feasibility of simultaneously more reliable and more comfortable medical imaging systems for patients by reducing the overall scan time, without sacrificing image quality.

    View details for DOI 10.1364/OE.24.001781

    View details for Web of Science ID 000369066300139

    View details for PubMedID 26832556

  • Metal-insulator-metal waveguides for particle trapping and separation LAB ON A CHIP Khan, S. A., Chang, C., Zaidi, Z., Shin, W., Shi, Y., Bowden, A. K., Solgaard, O. 2016; 16 (12): 2302-2308

    Abstract

    Optical particle trapping and separation are essential techniques in the fields of biology and chemistry. In many applications, it is important to identify passive separation techniques that only rely on intrinsic forces in a system with a fixed device geometry. We present a dual-waveguide sorter that utilizes the loss of metal-insulator-metal (MIM) waveguides for completely passive particle trapping and separation and is created using a unique angle sidewall deposition process. Our experiments show that an inner Au-Si3N4-Au waveguide is able to trap particles within the propagation distance of its dominant modes and release the particles into an outer Au-H2O-Au waveguide. The outer waveguide then propels the particles and separates them by size. The separation results are accurately modeled by a first-principles, analytical model.

    View details for DOI 10.1039/c6lc00366d

    View details for Web of Science ID 000378944800016

    View details for PubMedID 27216706

  • Robust dipstick urinalysis using a low-cost, micro-volume slipping manifold and mobile phone platform LAB ON A CHIP Smith, G. T., Dwork, N., Khan, S. A., Millet, M., Magar, K., Javanmard, M., Bowden, A. K. 2016; 16 (11): 2069-2078

    Abstract

    We introduce a novel manifold and companion software for dipstick urinalysis that eliminate many of the aspects that are traditionally plagued by user error: precise sample delivery, accurate readout timing, and controlled lighting conditions. The proposed all-acrylic slipping manifold is reusable, reliable, and low in cost. A simple timing mechanism ensures results are read out at the appropriate time. Results are obtained by capturing videos using a mobile phone and by analyzing them using custom-designed software. We show that the results obtained with the proposed device are as accurate and consistent as a properly executed dip-and-wipe method, the industry gold-standard, suggesting the potential for this strategy to enable confident urinalysis testing in home environments.

    View details for DOI 10.1039/c6lc00340k

    View details for Web of Science ID 000377087000010

    View details for PubMedID 27166097

  • Label-free characterization of vitrification-induced morphology changes in single-cell embryos with full-field optical coherence tomography. Journal of biomedical optics Zarnescu, L., Leung, M. C., Abeyta, M., Sudkamp, H., Baer, T., Behr, B., Ellerbee, A. K. 2015; 20 (9): 096004-?

    View details for DOI 10.1117/1.JBO.20.9.096004

    View details for PubMedID 26334977

  • Fabrication of healthy and disease-mimicking retinal phantoms with tapered foveal pits for optical coherence tomography. Journal of biomedical optics Lee, G. C., Smith, G. T., Agrawal, M., Leng, T., Ellerbee, A. K. 2015; 20 (8): 85004-?

    View details for DOI 10.1117/1.JBO.20.8.085004

    View details for PubMedID 26287985

  • Rapid scanning catheterscope for expanded forward-view volumetric imaging with optical coherence tomography OPTICS LETTERS Lurie, K. L., Gurjarpadhye, A. A., Seibel, E. J., Ellerbee, A. K. 2015; 40 (13): 3165-3168

    Abstract

    We demonstrate a novel catheterscope, based on scanning fiber endoscopy, for volumetric imaging with optical coherence tomography (OCT), which possesses a high resonance frequency (>2  kHz) and a small outer diameter (OD) (1.07 mm). Our design is the fastest volumetric-scanning, forward-viewing catheterscope for OCT, and the scanning package has the smallest OD of any such OCT package published to date. Using a proof-of-operation catheterscope with commercial lenses, we demonstrate high-quality in vivo and ex vivo volumetric imaging and extend the 1.1 mm diameter field of view more than 200-fold by mosaicking. Due to its small OD, short rigid tip length, and fast scan rate, this scope is the leading candidate design to enable early detection and staging of bladder cancer during flexible white light cystoscopy.

    View details for DOI 10.1364/OL.40.003165

    View details for Web of Science ID 000357486800059

    View details for PubMedID 26125393

  • Polarization-sensitive interleaved optical coherence tomography OPTICS EXPRESS Duan, L., Marvdashti, T., Ellerbee, A. K. 2015; 23 (10): 13693-13703

    Abstract

    We introduce a new strategy for single-mode fiber based polarization-sensitive (PS-) optical coherence tomography (OCT) using orthogonally polarized optical frequency combs (OFC) in the sample arm. The two OFCs are tuned to be interleaved in the spectral domain, permitting simultaneous measurement of both polarization states from the same spatial region C close to the location of zero pathlength delay. The two polarization states of the beam in the sample arm are demultiplexed by interpolation after performing wavelength stabilization via a two-mirror calibration method. The system uses Jones matrix methods to measure quantitatively the round-trip phase retardation B-scans in the sample. A glass plate and quarter-wave plate were measured to validate the accuracy of the birefringence measurement. Further, we demonstrated the potential of this system for biomedical applications by measurement of chicken breast muscle.

    View details for DOI 10.1364/OE.23.013693

    View details for Web of Science ID 000354706800116

    View details for PubMedID 26074618

  • Optical separation of heterogeneous size distributions of microparticles on silicon nitride strip waveguides OPTICS EXPRESS Khan, S. A., Shi, Y., Chang, C., Jan, C., Fan, S., Ellerbee, A. K., Solgaard, O. 2015; 23 (7): 8855-8866

    Abstract

    We demonstrate two complementary optical separation techniques of dielectric particles on the surface of silicon nitride waveguides. Glass particles ranging from 2 μm to 10 μm in diameter are separated at guided powers below 40 mW. The effects of optical, viscous, and frictional forces on the particles are modeled and experimentally shown to enable separation. Particle interactions are investigated and shown to decrease measured particle velocity without interfering with the overall particle separation distribution. The demonstrated separation techniques have the potential to be integrated with microfluidic structures for cell sorting.

    View details for DOI 10.1364/OE.23.008855

    View details for Web of Science ID 000352290000088

    View details for PubMedID 25968723

  • Noninvasive in vivo imaging reveals differences between tectorial membrane and basilar membrane traveling waves in the mouse cochlea PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Lee, H. Y., Raphael, P. D., Park, J., Ellerbee, A. K., Applegate, B. E., Oghalai, J. S. 2015; 112 (10): 3128-3133

    Abstract

    Sound is encoded within the auditory portion of the inner ear, the cochlea, after propagating down its length as a traveling wave. For over half a century, vibratory measurements to study cochlear traveling waves have been made using invasive approaches such as laser Doppler vibrometry. Although these studies have provided critical information regarding the nonlinear processes within the living cochlea that increase the amplitude of vibration and sharpen frequency tuning, the data have typically been limited to point measurements of basilar membrane vibration. In addition, opening the cochlea may alter its function and affect the findings. Here we describe volumetric optical coherence tomography vibrometry, a technique that overcomes these limitations by providing depth-resolved displacement measurements at 200 kHz inside a 3D volume of tissue with picometer sensitivity. We studied the mouse cochlea by imaging noninvasively through the surrounding bone to measure sound-induced vibrations of the sensory structures in vivo, and report, to our knowledge, the first measures of tectorial membrane vibration within the unopened cochlea. We found that the tectorial membrane sustains traveling wave propagation. Compared with basilar membrane traveling waves, tectorial membrane traveling waves have larger dynamic ranges, sharper frequency tuning, and apically shifted positions of peak vibration. These findings explain discrepancies between previously published basilar membrane vibration and auditory nerve single unit data. Because the tectorial membrane directly overlies the inner hair cell stereociliary bundles, these data provide the most accurate characterization of the stimulus shaping the afferent auditory response available to date.

    View details for DOI 10.1073/pnas.1500038112

    View details for Web of Science ID 000350646500059

    View details for PubMedID 25737536

  • Label-free and non-contact optical biosensing of glucose with quantum dots. Biosensors & bioelectronics Khan, S. A., Smith, G. T., Seo, F., Ellerbee, A. K. 2015; 64: 30-35

    Abstract

    We present a label-free, optical sensor for biomedical applications based on changes in the visible photoluminescence (PL) of quantum dots in a thin polymer film. Using glucose as the target molecule, the screening of UV excitation due to pre-absorption by the product of an enzymatic assay leads to quenching of the PL of quantum dots (QDs) in a non-contact scheme. The irradiance changes in QD PL indicate quantitatively the level of glucose present. The non-contact nature of the assay prevents surface degradation of the QDs, which yields an efficient, waste-free, cost-effective, portable, and sustainable biosensor with attractive market features. The limit of detection of the demonstrated biosensor is ~3.5 µm, which is competitive with existing contact-based bioassays. In addition, the biosensor operates over the entire clinically relevant range of glucose concentrations of biological fluids including urine and whole blood. The comparable results achieved across a range of cost-affordable detectors, including a spectrophotometer, portable spectrometer, and iPhone camera, suggest that label-free and visible quantification of glucose with QD films can be applied to low-cost, point-of-care biomedical sensing as well as scientific applications in the laboratory for characterizing glucose or other analytes.

    View details for DOI 10.1016/j.bios.2014.08.035

    View details for PubMedID 25189097

  • Fabrication of Anatomically Tapered Foveal Pits in Retinal Phantoms for Optical Coherence Tomography DESIGN AND PERFORMANCE VALIDATION OF PHANTOMS USED IN CONJUNCTION WITH OPTICAL MEASUREMENT OF TISSUE VII Lee, G. C., Smith, G. T., Agrawal, M., Ellerbee, A. K. 2015; 9325

    View details for DOI 10.1117/12.2079730

    View details for Web of Science ID 000353883600003

  • Perspectives of the optical coherence tomography community on code and data sharing OPTICAL COHERENCE TOMOGRAPHY AND COHERENCE DOMAIN OPTICAL METHODS IN BIOMEDICINE XIX Lurie, K. L., Mistree, B. F., Ellerbee, A. K. 2015; 9312

    View details for DOI 10.1117/12.2082412

    View details for Web of Science ID 000353885800019

  • Single-shot speckle noise reduction by interleaved optical coherence tomography JOURNAL OF BIOMEDICAL OPTICS Duan, L., Lee, H. Y., Lee, G., Agrawal, M., Smith, G. T., Ellerbee, A. K. 2014; 19 (12)

    Abstract

    Speckle noise is one of the dominant factors that degrade image quality in optical coherence tomography (OCT). Here, we propose a new strategy, interleaved OCT (iOCT), for spatial compounding and angular compounding. We demonstrate the efficiency of compounding with iOCT to restrain speckle noise without compromising imaging speed in phantoms and tissue samples.

    View details for DOI 10.1117/1.JBO.19.12.120501

    View details for Web of Science ID 000347442600001

    View details for PubMedID 25486093

  • Automated identification of basal cell carcinoma by polarization-sensitive optical coherence tomography BIOMEDICAL OPTICS EXPRESS Duan, L., Marvdashti, T., Lee, A., Tang, J. Y., Ellerbee, A. K. 2014; 5 (10): 3717-3729
  • Automated identification of basal cell carcinoma by polarization-sensitive optical coherence tomography. Biomedical optics express Duan, L., Marvdashti, T., Lee, A., Tang, J. Y., Ellerbee, A. K. 2014; 5 (10): 3717-3729

    Abstract

    We report an automated classifier to detect the presence of basal cell carcinoma in images of mouse skin tissue samples acquired by polarization-sensitive optical coherence tomography (PS-OCT). The sensitivity and specificity of the classifier based on combined information of the scattering intensity and birefringence properties of the samples are significantly higher than when intensity or birefringence information are used alone. The combined information offers a sensitivity of 94.4% and specificity of 92.5%, compared to 78.2% and 82.2% for intensity-only information and 85.5% and 87.9% for birefringence-only information. These results demonstrate that analysis of the combination of complementary optical information obtained by PS-OCT has great potential for accurate skin cancer diagnosis.

    View details for DOI 10.1364/BOE.5.003717

    View details for PubMedID 25360384

  • Quantitative measurements of strain and birefringence with common-path polarization-sensitive optical coherence tomography OPTICS LETTERS Marvdashti, T., Duan, L., Lurie, K. L., Smith, G. T., Ellerbee, A. K. 2014; 39 (19): 5507-5510
  • Scalable multiplexing for parallel imaging with interleaved optical coherence tomography. Biomedical optics express Lee, H. Y., Marvdashti, T., Duan, L., Khan, S. A., Ellerbee, A. K. 2014; 5 (9): 3192-3203

    Abstract

    We demonstrate highly parallel imaging with interleaved optical coherence tomography (iOCT) using an in-house-fabricated, air-spaced virtually-imaged phased array (VIPA). The air-spaced VIPA performs spectral encoding of the interferograms from multiple lateral points within a single sweep of the source and allows us to tune and balance several imaging parameters: number of multiplexed points, ranging depth, and sensitivity. In addition to a thorough discussion of the parameters and operating principles of the VIPA, we experimentally demonstrate the effect of different VIPA designs on the multiplexing potential of iOCT. Using a 200-kHz light source, we achieve an effective A-scan rate of 3.2-MHz by multiplexing 16 lateral points onto a single wavelength sweep. The improved sensitivity of this system is demonstrated for 3D imaging of biological samples such as a human finger and a fruit fly.

    View details for DOI 10.1364/BOE.5.003192

    View details for PubMedID 25401031

  • Scalable multiplexing for parallel imaging with interleaved optical coherence tomography BIOMEDICAL OPTICS EXPRESS Lee, H. Y., Marvdashti, T., Duan, L., Khan, S. A., Ellerbee, A. K. 2014; 5 (9): 3192-3203
  • Automated Mosaicing of Feature-Poor Optical Coherence Tomography Volumes With an Integrated White Light Imaging System IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING Lurie, K. L., Angst, R., Ellerbee, A. K. 2014; 61 (7): 2141-2153
  • 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

  • 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)
  • Multilayered disease-mimicking bladder phantom with realistic surface topology for optical coherence tomography DESIGN AND PERFORMANCE VALIDATION OF PHANTOMS USED IN CONJUNCTION WITH OPTICAL MEASUREMENT OF TISSUE VI Smith, G. T., Lurie, K. L., Khan, S. A., Liao, J. C., Ellerbee, A. K. 2014; 8945

    View details for DOI 10.1117/12.2036402

    View details for Web of Science ID 000334097200012

  • Assessment of imaging parameters correlated with the effects of cryopreservation on embryo development OPTICAL METHODS IN DEVELOPMENTAL BIOLOGY II Zarnescu, L., Abeyta, M., Baer, T. M., Behr, B., Ellerbee, A. K. 2014; 8953

    View details for DOI 10.1117/12.2040487

    View details for Web of Science ID 000336049000006

  • Volumetric mosaicing for optical coherence tomography for large area bladder wall visualization PHOTONIC THERAPEUTICS AND DIAGNOSTICS X Lurie, K. L., Ellerbee, A. K. 2014; 8926

    View details for DOI 10.1117/12.2036325

    View details for Web of Science ID 000337574500033

  • Label-free assay for the detection of glucose mediated by the effects of narrowband absorption on quantum dot photoluminescence FRONTIERS IN BIOLOGICAL DETECTION: FROM NANOSENSORS TO SYSTEMS VI Khan, S. A., Smith, G. T., Ellerbee, A. K. 2014; 8933

    View details for DOI 10.1117/12.2039963

    View details for Web of Science ID 000336738600007

  • Evaluation of fingerprint deformation using optical coherence tomography OPTICAL ELASTOGRAPHY AND TISSUE BIOMECHANICS Gutierrez da Costa, H. S., Maxey, J. R., Silva, L., Ellerbee, A. K. 2014; 8946

    View details for DOI 10.1117/12.2038694

    View details for Web of Science ID 000334343200009

  • Telemedicine plus OCT: toward design of optimized algorithms for high-quality compressed images DESIGN AND QUALITY FOR BIOMEDICAL TECHNOLOGIES VII Mousavi, M., Lurie, K., Land, J., Javidi, T., Ellerbee, A. K. 2014; 8936

    View details for DOI 10.1117/12.2038530

    View details for Web of Science ID 000334099600005

  • 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

  • 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

  • High-resolution spectrometer: solution to the axial resolution and ranging depth trade-off of SD-OCT ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC SYSTEMS XI Marvdashti, T., Lee, H. Y., Ellerbee, A. K. 2013; 8572

    View details for DOI 10.1117/12.2003865

    View details for Web of Science ID 000337082600009

  • 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
  • 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

  • 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
  • Interleaved Optical Coherence Tomography Opt. Exp Lee, H., H., Sudkamp, Marvdashti, T., Ellerbee, A., K. 2013; 22 (21): 26542-26556
  • 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

  • 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

  • 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
  • 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

  • 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
  • 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
  • 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
  • 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
  • Programmable Self-Assembly of Complex Shapes in Three Dimensions Mirica, K., A., Ellerbee, A., K., Ilievski, F., Whitesides, G., M. 2009
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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