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1.  Swept source optical coherence microscopy using a 1310 nm VCSEL light source 
Optics Express  2013;21(15):18021-18033.
We demonstrate high speed, swept source optical coherence microscopy (OCM) using a MEMS tunable vertical cavity surface-emitting laser (VCSEL) light source. The light source had a sweep rate of 280 kHz, providing a bidirectional axial scan rate of 560 kHz. The sweep bandwidth was 117 nm centered at 1310 nm, corresponding to an axial resolution of 13.1 µm in air, corresponding to 8.1 µm (9.6 µm spectrally shaped) in tissue. Dispersion mismatch from different objectives was compensated numerically, enabling magnification and field of view to be easily changed. OCM images were acquired with transverse resolutions between 0.86 µm - 3.42 µm using interchangeable 40X, 20X and 10X objectives with ~600 µm x 600 µm, ~1 mm x 1 mm and ~2 mm x 2 mm field-of-view (FOV), respectively. Parasitic variations in path length with beam scanning were corrected numerically. These features enable swept source OCM to be integrated with a wide range of existing scanning microscopes. Large FOV mosaics were generated by serially acquiring adjacent overlapping microscopic fields and combining them in post-processing. Fresh human colon, thyroid and kidney specimens were imaged ex vivo and compared to matching histology sections, demonstrating the ability of OCM to image tissue specimens.
doi:10.1364/OE.21.018021
PMCID: PMC3756222  PMID: 23938673
(110.4500) Optical coherence tomography; (140.3600) Lasers, tunable; (170.3880) Medical and biological imaging; (180.1790) Confocal microscopy; (180.6900) Three-dimensional microscopy
2.  Enhanced Vitreous Imaging in Healthy Eyes Using Swept Source Optical Coherence Tomography 
PLoS ONE  2014;9(7):e102950.
Purpose
To describe enhanced vitreous imaging for visualization of anatomic features and microstructures within the posterior vitreous and vitreoretinal interface in healthy eyes using swept-source optical coherence tomography (SS-OCT). The study hypothesis was that long-wavelength, high-speed, volumetric SS-OCT with software registration motion correction and vitreous window display or high-dynamic-range (HDR) display improves detection sensitivity of posterior vitreous and vitreoretinal features compared to standard OCT logarithmic scale display.
Design
Observational prospective cross-sectional study.
Methods
Multiple wide-field three-dimensional SS-OCT scans (500×500A-scans over 12×12 mm2) were obtained using a prototype instrument in 22 eyes of 22 healthy volunteers. A registration motion-correction algorithm was applied to compensate motion and generate a single volumetric dataset. Each volumetric dataset was displayed in three forms: (1) standard logarithmic scale display, enhanced vitreous imaging using (2) vitreous window display and (3) HDR display. Each dataset was reviewed independently by three readers to identify features of the posterior vitreous and vitreoretinal interface. Detection sensitivities for these features were measured for each display method.
Results
Features observed included the bursa premacularis (BPM), area of Martegiani, Cloquet's/BPM septum, Bergmeister papilla, posterior cortical vitreous (hyaloid) detachment, papillomacular hyaloid detachment, hyaloid attachment to retinal vessel(s), and granular opacities within vitreous cortex, Cloquet's canal, and BPM. The detection sensitivity for these features was 75.0% (95%CI: 67.8%–81.1%) using standard logarithmic scale display, 80.6% (95%CI: 73.8%–86.0%) using HDR display, and 91.9% (95%CI: 86.6%–95.2%) using vitreous window display.
Conclusions
SS-OCT provides non-invasive, volumetric and measurable in vivo visualization of the anatomic microstructural features of the posterior vitreous and vitreoretinal interface. The vitreous window display provides the highest sensitivity for posterior vitreous and vitreoretinal interface analysis when compared to HDR and standard OCT logarithmic scale display. Enhanced vitreous imaging with SS-OCT may help assess the natural history and treatment response in vitreoretinal interface diseases.
doi:10.1371/journal.pone.0102950
PMCID: PMC4103882  PMID: 25036044
3.  Analysis of the Short Term Change in Subfoveal Choroidal Thickness in Eyes With Age Related Macular Degeneration Using Optical Coherence Tomography 
Background and Objective
To measure the subfoveal choroidal thickness in patients with age-related macular degeneration (AMD) over 6 months.
Study Design/Patients and Methods
A retrospective, observational study of patients with AMD followed for 6 months at the New England Eye Center. Baseline and 6 month subfoveal choroidal thickness was measured using spectral domain OCT and compared.
Results
For the entire cohort there was statistically significant thinning of the subfoveal choroidal thickness at 6 months compared to baseline, which was driven by the cohort of patients with neovascular AMD [181.2 +/− 75 μm to 173.4 +/− 63 μm] p=0.049. (Figure and Table 1).
Conclusions
There was a statistically significant decrease in subfoveal choroidal thickness observed in this cohort of patients with AMD over 6 months, but it was driven by one subgroup, those patients with neovascular age related macular degeneration.
doi:10.3928/23258160-20131220-04
PMCID: PMC4069121  PMID: 24392909
4.  Choroidal Haller's and Sattler's Layer Thickness Measurement Using 3-Dimensional 1060-nm Optical Coherence Tomography 
PLoS ONE  2014;9(6):e99690.
Objectives
To examine the feasibility of automatically segmented choroidal vessels in three-dimensional (3D) 1060-nmOCT by testing repeatability in healthy and AMD eyes and by mapping Haller's and Sattler's layer thickness in healthy eyes
Methods
Fifty-five eyes (from 45 healthy subjects and 10 with non-neovascular age-related macular degeneration (AMD) subjects) were imaged by 3D-1060-nmOCT over a 36°x36° field of view. Haller's and Sattler's layer were automatically segmented, mapped and averaged across the Early Treatment Diabetic Retinopathy Study grid. For ten AMD eyes and ten healthy eyes, imaging was repeated within the same session and on another day. Outcomes were the repeatability agreement of Haller's and Sattler's layer thicknesses in healthy and AMD eyes, the validation with ICGA and the statistical analysis of the effect of age and axial eye length (AL) on both healthy choroidalsublayers.
Results
The coefficients of repeatability for Sattler's and Haller's layers were 35% and 21% in healthy eyes and 44% and 31% in AMD eyes, respectively. The mean±SD healthy central submacular field thickness for Sattler's and Haller's was 87±56 µm and 141±50 µm, respectively, with a significant relationship for AL (P<.001).
Conclusions
Automated Sattler's and Haller's thickness segmentation generates rapid 3D measurements with a repeatability correspondingto reported manual segmentation. Sublayers in healthy eyes thinnedsignificantly with increasing AL. In the presence of the thinned Sattler's layer in AMD, careful measurement interpretation is needed. Automatic choroidal vascular layer mapping may help to explain if pathological choroidal thinning affects medium and large choroidal vasculature in addition to choriocapillaris loss.
doi:10.1371/journal.pone.0099690
PMCID: PMC4050051  PMID: 24911446
5.  In Vivo Lamina Cribrosa Micro-Architecture in Healthy and Glaucomatous Eyes as Assessed by Optical Coherence Tomography 
Purpose.
The lamina cribrosa (LC) is a prime location of glaucomatous damage. The purpose of this study was to compare LC 3-dimensional micro-architecture between healthy and glaucomatous eyes in vivo by using optical coherence tomography (OCT).
Methods.
Sixty-eight eyes (19 healthy and 49 glaucomatous) from 47 subjects were scanned in a 3.5 × 3.5 × 3.64-mm volume (400 × 400 × 896 pixels) at the optic nerve head by using swept-source OCT. The LC micro-architecture parameters were measured on the visible LC by an automated segmentation algorithm. The LC parameters were compared to diagnosis and visual field mean deviation (VF MD) by using a linear mixed effects model accounting for age.
Results.
The average VF MD for the healthy and glaucomatous eyes was −0.50 ± 0.80 dB and −7.84 ± 8.75 dB, respectively. Beam thickness to pore diameter ratio (P = 0.04) and pore diameter standard deviation (P < 0.01) were increased in glaucomatous eyes. With worse MD, beam thickness to pore diameter ratio (P < 0.01), pore diameter standard deviation (P = 0.05), and beam thickness (P < 0.01) showed a statistically significant increase while pore diameter (P = 0.02) showed a significant decrease. There were no significant interactions between any of the parameters and age (all P > 0.05).
Conclusions.
Glaucomatous micro-architecture changes in the LC, detected by OCT analysis, reflect beams remodeling and axonal loss leading to reduction in pore size and increased pore size variability.
Using swept-source OCT we demonstrated in vivo significant differences in the lamina cribrosa micro-architecture between healthy and glaucomatous eyes. These changes reflect beams remodeling and axonal loss leading to reduction in pore size and increased pore size variability.
doi:10.1167/iovs.13-13109
PMCID: PMC3869422  PMID: 24302585
lamina cribrosa; optical coherence tomography; glaucoma
6.  Reproducibility of In-Vivo OCT Measured Three-Dimensional Human Lamina Cribrosa Microarchitecture 
PLoS ONE  2014;9(4):e95526.
Purpose
To determine the reproducibility of automated segmentation of the three-dimensional (3D) lamina cribrosa (LC) microarchitecture scanned in-vivo using optical coherence tomography (OCT).
Methods
Thirty-nine eyes (8 healthy, 19 glaucoma suspects and 12 glaucoma) from 49 subjects were scanned twice using swept-source (SS−) OCT in a 3.5×3.5×3.64 mm (400×400×896 pixels) volume centered on the optic nerve head, with the focus readjusted after each scan. The LC was automatically segmented and analyzed for microarchitectural parameters, including pore diameter, pore diameter standard deviation (SD), pore aspect ratio, pore area, beam thickness, beam thickness SD, and beam thickness to pore diameter ratio. Reproducibility of the parameters was assessed by computing the imprecision of the parameters between the scans.
Results
The automated segmentation demonstrated excellent reproducibility. All LC microarchitecture parameters had an imprecision of less or equal to 4.2%. There was little variability in imprecision with respect to diagnostic category, although the method tends to show higher imprecision amongst healthy subjects.
Conclusion
The proposed automated segmentation of the LC demonstrated high reproducibility for 3D LC parameters. This segmentation analysis tool will be useful for in-vivo studies of the LC.
doi:10.1371/journal.pone.0095526
PMCID: PMC3991692  PMID: 24747957
7.  Handheld ultrahigh speed swept source optical coherence tomography instrument using a MEMS scanning mirror 
Biomedical Optics Express  2013;5(1):293-311.
We developed an ultrahigh speed, handheld swept source optical coherence tomography (SS-OCT) ophthalmic instrument using a 2D MEMS mirror. A vertical cavity surface-emitting laser (VCSEL) operating at 1060 nm center wavelength yielded a 350 kHz axial scan rate and 10 µm axial resolution in tissue. The long coherence length of the VCSEL enabled a 3.08 mm imaging range with minimal sensitivity roll-off in tissue. Two different designs with identical optical components were tested to evaluate handheld OCT ergonomics. An iris camera aided in alignment of the OCT beam through the pupil and a manual fixation light selected the imaging region on the retina. Volumetric and high definition scans were obtained from 5 undilated normal subjects. Volumetric OCT data was acquired by scanning the 2.4 mm diameter 2D MEMS mirror sinusoidally in the fast direction and linearly in the orthogonal slow direction. A second volumetric sinusoidal scan was obtained in the orthogonal direction and the two volumes were processed with a software algorithm to generate a merged motion-corrected volume. Motion-corrected standard 6 x 6 mm2 and wide field 10 x 10 mm2 volumetric OCT data were generated using two volumetric scans, each obtained in 1.4 seconds. High definition 10 mm and 6 mm B-scans were obtained by averaging and registering 25 B-scans obtained over the same position in 0.57 seconds. One of the advantages of volumetric OCT data is the generation of en face OCT images with arbitrary cross sectional B-scans registered to fundus features. This technology should enable screening applications to identify early retinal disease, before irreversible vision impairment or loss occurs. Handheld OCT technology also promises to enable applications in a wide range of settings outside of the traditional ophthalmology or optometry clinics including pediatrics, intraoperative, primary care, developing countries, and military medicine.
doi:10.1364/BOE.5.000293
PMCID: PMC3891340  PMID: 24466495
(170.4460) Ophthalmic optics and devices; (170.5755) Retina scanning; (170.3880) Medical and biological imaging; (170.4500) Optical coherence tomography; (170.4470) Ophthalmology
8.  Choriocapillaris and Choroidal Microvasculature Imaging with Ultrahigh Speed OCT Angiography 
PLoS ONE  2013;8(12):e81499.
We demonstrate in vivo choriocapillaris and choroidal microvasculature imaging in normal human subjects using optical coherence tomography (OCT). An ultrahigh speed swept source OCT prototype at 1060 nm wavelengths with a 400 kHz A-scan rate is developed for three-dimensional ultrahigh speed imaging of the posterior eye. OCT angiography is used to image three-dimensional vascular structure without the need for exogenous fluorophores by detecting erythrocyte motion contrast between OCT intensity cross-sectional images acquired rapidly and repeatedly from the same location on the retina. En face OCT angiograms of the choriocapillaris and choroidal vasculature are visualized by acquiring cross-sectional OCT angiograms volumetrically via raster scanning and segmenting the three-dimensional angiographic data at multiple depths below the retinal pigment epithelium (RPE). Fine microvasculature of the choriocapillaris, as well as tightly packed networks of feeding arterioles and draining venules, can be visualized at different en face depths. Panoramic ultra-wide field stitched OCT angiograms of the choriocapillaris spanning ∼32 mm on the retina show distinct vascular structures at different fundus locations. Isolated smaller fields at the central fovea and ∼6 mm nasal to the fovea at the depths of the choriocapillaris and Sattler's layer show vasculature structures consistent with established architectural morphology from histological and electron micrograph corrosion casting studies. Choriocapillaris imaging was performed in eight healthy volunteers with OCT angiograms successfully acquired from all subjects. These results demonstrate the feasibility of ultrahigh speed OCT for in vivo dye-free choriocapillaris and choroidal vasculature imaging, in addition to conventional structural imaging.
doi:10.1371/journal.pone.0081499
PMCID: PMC3859478  PMID: 24349078
9.  Parafoveal Retinal Vascular Response to Pattern Visual Stimulation Assessed with OCT Angiography 
PLoS ONE  2013;8(12):e81343.
We used optical coherence tomography (OCT) angiography with a high-speed swept-source OCT system to investigate retinal blood flow changes induced by visual stimulation with a reversing checkerboard pattern. The split-spectrum amplitude-decorrelation angiography (SSADA) algorithm was used to quantify blood flow as measured with parafoveal flow index (PFI), which is proportional to the density of blood vessels and the velocity of blood flow in the parafoveal region of the macula. PFI measurements were taken in 15 second intervals during a 4 minute period consisting of 1 minute of baseline, 2 minutes with an 8 Hz reversing checkerboard pattern stimulation, and 1 minute without stimulation. PFI measurements increased 6.1±4.7% (p = .001) during the first minute of stimulation, with the most significant increase in PFI occurring 30 seconds into stimulation (p<0.001). These results suggest that pattern stimulation induces a change to retinal blood flow that can be reliably measured with OCT angiography.
doi:10.1371/journal.pone.0081343
PMCID: PMC3846672  PMID: 24312549
10.  High-precision, high-accuracy ultralong-range swept-source optical coherence tomography using vertical cavity surface emitting laser light source 
Optics letters  2013;38(5):673-675.
We demonstrate ultralong-range swept-source optical coherence tomography (OCT) imaging using vertical cavity surface emitting laser technology. The ability to adjust laser parameters and high-speed acquisition enables imaging ranges from a few centimeters up to meters using the same instrument. We discuss the challenges of long-range OCT imaging. In vivo human-eye imaging and optical component characterization are presented. The precision and accuracy of OCT-based measurements are assessed and are important for ocular biometry and reproducible intraocular distance measurement before cataract surgery. Additionally, meter-range measurement of fiber length and multicentimeter-range imaging are reported. 3D visualization supports a class of industrial imaging applications of OCT.
PMCID: PMC3836603  PMID: 23455261
11.  Extracting and compensating dispersion mismatch in ultrahigh-resolution Fourier domain OCT imaging of the retina 
Optics Express  2012;20(23):25357-25368.
We present a numerical approach to extract the dispersion mismatch in ultrahigh-resolution Fourier domain optical coherence tomography (OCT) imaging of the retina. The method draws upon an analogy with a Shack-Hartmann wavefront sensor. By exploiting mathematical similarities between the expressions for aberration in optical imaging and dispersion mismatch in spectral / Fourier domain OCT, Shack-Hartmann principles can be extended from the two-dimensional paraxial wavevector space (or the x-y plane in the spatial domain) to the one-dimensional wavenumber space (or the z-axis in the spatial domain). For OCT imaging of the retina, different retinal layers, such as the retinal nerve fiber layer (RNFL), the photoreceptor inner and outer segment junction (IS/OS), or all the retinal layers near the retinal pigment epithelium (RPE) can be used as point source beacons in the axial direction, analogous to point source beacons used in conventional two-dimensional Shack-Hartman wavefront sensors for aberration characterization. Subtleties regarding speckle phenomena in optical imaging, which affect the Shack-Hartmann wavefront sensor used in adaptive optics, also occur analogously in this application. Using this approach and carefully suppressing speckle, the dispersion mismatch in spectral / Fourier domain OCT retinal imaging can be successfully extracted numerically and used for numerical dispersion compensation to generate sharper, ultrahigh-resolution OCT images.
doi:10.1364/OE.20.025357
PMCID: PMC3601734  PMID: 23187353
(170.3880) Medical and biological imaging; (170.4500) Optical coherence tomography; (170.4470) Ophthalmology; (260.2030) Dispersion
12.  Automated lamina cribrosa microstructural segmentation in optical coherence tomography scans of healthy and glaucomatous eyes 
Biomedical Optics Express  2013;4(11):2596-2608.
We demonstrate an automated segmentation method for in-vivo 3D optical coherence tomography (OCT) imaging of the lamina cribrosa (LC). Manual segmentations of coronal slices of the LC were used as a gold standard in parameter selection and evaluation of the automated technique. The method was validated using two prototype OCT devices; each had a subject cohort including both healthy and glaucomatous eyes. Automated segmentation of in-vivo 3D LC OCT microstructure performed comparably to manual segmentation and is useful for investigative research and in clinical quantification of the LC.
doi:10.1364/BOE.4.002596
PMCID: PMC3829553  PMID: 24298418
(100.2000) Digital image processing; (170.4470) Ophthalmology; (110.4500) Optical coherence tomography; (170.1610) Clinical applications; (330.4460) Ophthalmic optics and devices
14.  EXERCISE-INDUCED ACUTE CHANGES IN SYSTOLIC BLOOD PRESSURE DO NOT ALTER CHOROIDAL THICKNESS AS MEASURED BY A PORTABLE SPECTRAL-DOMAIN OPTICAL COHERENCE TOMOGRAPHY DEVICE 
Retina (Philadelphia, Pa.)  2013;33(1):160-165.
Purpose
To measure choroidal thickness in patients manifesting an acute change in systemic arterial blood pressure using a portable spectral-domain optical coherence tomography device (iVue).
Methods
Fifteen patients (15 eyes) undergoing cardiac exercise stress testing were scanned using a portable spectral-domain optical coherence tomography system (iVue). Two scan protocols were used: cross line scan for measuring choroidal thickness and the retina map scan to measure retinal thickness. Each patient was scanned before and within 3 minutes after the stress test. Blood pressure was measured at the same time as the acquisition of the scans. Choroidal thickness was measured from the posterior edge of the retinal pigment epithelium to the choroid–sclera junction at 500-μm intervals up to 1,000 μm temporal and nasal to the fovea. Retinal thickness was measured by an automated software. All choroidal thickness measurements were performed by two independent observers.
Results
Fifteen patients (15 eyes) with a mean age of 60.6 (±10.4 years) were scanned. There was a significant increase in systolic but not diastolic pressure after stress testing (P < 0.05). The mean choroidal thickness measurements showed no significant difference before and after exercise stress testing (P > 0.05). In addition, there was no significant difference in retinal thickness before and after stress testing measurements (P > 0.05).
Conclusion
There was no change in choroidal thickness or retinal thickness, despite an acute change in the systemic systolic blood pressure induced by exercise.
doi:10.1097/IAE.0b013e3182618c22
PMCID: PMC3758128  PMID: 22869027
choroid; choroidal thickness; optical coherence tomography (OCT); retinal thickness; stress test; choroidal blood flow; blood pressure
15.  Phase-sensitive swept source OCT imaging of the human retina with a VCSEL light source 
Optics letters  2013;38(3):338-340.
Despite the challenges in achieving high phase stability, Doppler swept source / Fourier domain OCT has advantages of less fringe washout and faster imaging speeds compared to spectral / Fourier domain detection. This manuscript demonstrates swept source OCT with a VCSEL light source at 400kHz sweep rate for phase-sensitive Doppler imaging, measuring pulsatile total retinal blood flow with high sensitivity and phase stability. A robust, simple, and computationally efficient phase stabilization approach for phase-sensitive swept source imaging is also presented.
PMCID: PMC3721635  PMID: 23381430
16.  Ultrahigh speed spectral-domain optical coherence microscopy 
Biomedical Optics Express  2013;4(8):1236-1254.
We demonstrate a compact, ultrahigh speed spectral-domain optical coherence microscopy (SD-OCM) system for multiscale imaging of specimens at 840 nm. Using a high speed 512-pixel line scan camera, an imaging speed of 210,000 A-scans per second was demonstrated. Interchangeable water immersion objectives with magnifications of 10×, 20×, and 40× provided co-registered en face cellular-resolution imaging over several size scales. Volumetric OCM data sets and en face OCM images were demonstrated on both normal and pathological human colon and kidney specimens ex vivo with an axial resolution of ~4.2 µm, and transverse resolutions of ~2.9 µm (10×), ~1.7 µm (20×), and ~1.1 µm (40×) in tissue. In addition, en face OCM images acquired with high numerical aperture over an extended field-of-view (FOV) were demonstrated using image mosaicking. Comparison between en face OCM images among different transverse and axial resolutions was demonstrated, which promises to help the design and evaluation of imaging performance of Fourier domain OCM systems at different resolution regimes.
doi:10.1364/BOE.4.001236
PMCID: PMC3756571  PMID: 24009989
(170.4500) Optical coherence tomography; (170.3880) Medical and biological imaging; (170.6900) Three-dimensional microscopy; (180.1790) Confocal microscopy
17.  Ultrahigh speed endoscopic optical coherence tomography using micromotor imaging catheter and VCSEL technology 
Biomedical Optics Express  2013;4(7):1119-1132.
We developed a micromotor based miniature catheter with an outer diameter of 3.2 mm for ultrahigh speed endoscopic swept source optical coherence tomography (OCT) using a vertical cavity surface-emitting laser (VCSEL) at a 1 MHz axial scan rate. The micromotor can rotate a micro-prism at several hundred frames per second with less than 5 V drive voltage to provide fast and stable scanning, which is not sensitive to the bending of the catheter. The side-viewing probe can be pulled back to acquire a three-dimensional (3D) data set covering a large area on the specimen. The VCSEL provides a high axial scan rate to support dense sampling under high frame rate operation. Using a high speed data acquisition system, in vivo 3D-OCT imaging in the rabbit GI tract and ex vivo imaging of a human colon specimen with 8 μm axial resolution, 8 μm lateral resolution and 1.2 mm depth range in tissue at a frame rate of 400 fps was demonstrated.
doi:10.1364/BOE.4.001119
PMCID: PMC3704093  PMID: 23847737
(170.4500) Optical coherence tomography; (170.3880) Medical and biological imaging; (170.2150) Endoscopic imaging; (170.2680) Gastrointestinal; (140.3600) Three-dimensional image acquisition; (110.2350) Fiber optics imaging; (120.5800) Scanners; (120.3890) Medical optics instrumentation
18.  Cervical inlet patch-optical coherence tomography imaging and clinical significance 
AIM: To demonstrate the feasibility of optical coherence tomography (OCT) imaging in differentiating cervical inlet patch (CIP) from normal esophagus, Barrett’s esophagus (BE), normal stomach and duodenum.
METHODS: This study was conducted at the Veterans Affairs Boston Healthcare System (VABHS). Patients undergoing standard esophagogastroduodenoscopy at VABHS, including one patient with CIP, one representative patient with BE and three representative normal subjects were included. White light video endoscopy was performed and endoscopic 3D-OCT images were obtained in each patient using a prototype OCT system. The OCT imaging probe passes through the working channel of the endoscope to enable simultaneous video endoscopy and 3D-OCT examination of the human gastrointestinal (GI) tract. Standard hematoxylin and eosin (H and E) histology was performed on biopsy or endoscopic mucosal resection specimens in order to compare and validate the 3D-OCT data.
RESULTS: CIP was observed from a 68-year old male with gastroesophageal reflux disease. The CIP region appeared as a pink circular lesion in the upper esophagus under white light endoscopy. OCT imaging over the CIP region showed columnar epithelium structure, which clearly contrasted the squamous epithelium structure from adjacent normal esophagus. 3D-OCT images obtained from other representative patients demonstrated distinctive patterns of the normal esophagus, BE, normal stomach, and normal duodenum bulb. Microstructures, such as squamous epithelium, lamina propria, muscularis mucosa, muscularis propria, esophageal glands, Barrett’s glands, gastric mucosa, gastric glands, and intestinal mucosal villi were clearly observed with OCT and matched with H and E histology. These results demonstrated the feasibility of using OCT to evaluate GI tissue morphology in situ and in real-time.
CONCLUSION: We demonstrate in situ evaluation of CIP microstructures using 3D-OCT, which may be a useful tool for future diagnosis and follow-up of patients with CIP.
doi:10.3748/wjg.v18.i20.2502
PMCID: PMC3360448  PMID: 22654447
Cervical inlet patch; Heterotopic gastric mucosa; Optical coherence tomography; Optical biopsy; Barrett’s esophagus
19.  Swept source / Fourier domain polarization sensitive optical coherence tomography with a passive polarization delay unit 
Optics Express  2012;20(9):10229-10241.
Polarization sensitive optical coherence tomography (PS-OCT) is a functional imaging method that provides additional contrast using the light polarizing properties of a sample. This manuscript describes PS-OCT based on ultrahigh speed swept source / Fourier domain OCT operating at 1050nm at 100kHz axial scan rates using single mode fiber optics and a multiplexing approach. Unlike previously reported PS-OCT multiplexing schemes, the method uses a passive polarization delay unit and does not require active polarization modulating devices. This advance decreases system cost and avoids complex synchronization requirements. The polarization delay unit was implemented in the sample beam path in order to simultaneously illuminate the sample with two different polarization states. The orthogonal polarization components for the depth-multiplexed signals from the two input states were detected using dual balanced detection. PS-OCT images were computed using Jones calculus. 3D PS-OCT imaging was performed in the human and rat retina. In addition to standard OCT images, PS-OCT images were generated using contrast form birefringence and depolarization. Enhanced tissue discrimination as well as quantitative measurements of sample properties was demonstrated using the additional contrast and information contained in the PS-OCT images.
doi:10.1364/OE.20.010229
PMCID: PMC3366588  PMID: 22535114
(170.4500) Optical coherence tomography; (230.5440) Polarization-selective devices; (170.4580) Optical diagnostics for medicine; (170.4470) Ophthalmology
20.  Variation in optical coherence tomography signal quality as an indicator of retinal nerve fibre layer segmentation error 
Purpose
Commercial optical coherence tomography (OCT) systems use global signal quality indices to quantify scan quality. Signal quality can vary throughout a scan, contributing to local retinal nerve fibre layer segmentation errors (SegE). The purpose of this study was to develop an automated method, using local scan quality, to predict SegE.
Methods
Good-quality (global signal strength (SS)≥6; manufacturer specification) peripapillary circular OCT scans (fast retinal nerve fibre layer scan protocol; Stratus OCT; Carl Zeiss Meditec, Dublin, California, USA) were obtained from 6 healthy, 19 glaucoma-suspect and 43 glaucoma subjects. Scans were grouped based on SegE. Quality index (QI) values were computed for each A-scan using software of our own design. Logistic mixed-effects regression modelling was applied to evaluate SS, global mean and SD of QI, and the probability of SegE.
Results
The difference between local mean QI in SegE regions and No-SegE regions was −5.06 (95% CI −6.38 to 3.734) (p<0.001). Using global mean QI, QI SD and their interaction term resulted in the model of best fit (Akaike information criterion=191.8) for predicting SegE. Global mean QI≥20 or SS≥8 shows little chance for SegE. Once mean QI<20 or SS<8, the probability of SegE increases as QI SD increases.
Conclusions
When combined with a signal quality parameter, the variation of signal quality between A-scans provides significant information about the quality of an OCT scan and can be used as a predictor of segmentation error.
doi:10.1136/bjophthalmol-2011-300044
PMCID: PMC3375178  PMID: 21900227
21.  Split-spectrum amplitude-decorrelation angiography with optical coherence tomography 
Optics Express  2012;20(4):4710-4725.
Amplitude decorrelation measurement is sensitive to transverse flow and immune to phase noise in comparison to Doppler and other phase-based approaches. However, the high axial resolution of OCT makes it very sensitive to the pulsatile bulk motion noise in the axial direction. To overcome this limitation, we developed split-spectrum amplitude-decorrelation angiography (SSADA) to improve the signal-to-noise ratio (SNR) of flow detection. The full OCT spectrum was split into several narrower bands. Inter-B-scan decorrelation was computed using the spectral bands separately and then averaged. The SSADA algorithm was tested on in vivo images of the human macula and optic nerve head. It significantly improved both SNR for flow detection and connectivity of microvascular network when compared to other amplitude-decorrelation algorithms.
doi:10.1364/OE.20.004710
PMCID: PMC3381646  PMID: 22418228
(170.4500) Optical coherence tomography; (170.3880) Medical and biological imaging; (170.4470) Ophthalmology; (999.999) Optical angiography
22.  In vivo imaging of the rodent eye with swept source/Fourier domain OCT 
Biomedical Optics Express  2013;4(2):351-363.
Swept source/Fourier domain OCT is demonstrated for in vivo imaging of the rodent eye. Using commercial swept laser technology, we developed a prototype OCT imaging system for small animal ocular imaging operating in the 1050 nm wavelength range at an axial scan rate of 100 kHz with ~6 µm axial resolution. The high imaging speed enables volumetric imaging with high axial scan densities, measuring high flow velocities in vessels, and repeated volumetric imaging over time. The 1050 nm wavelength light provides increased penetration into tissue compared to standard commercial OCT systems at 850 nm. The long imaging range enables multiple operating modes for imaging the retina, posterior eye, as well as anterior eye and full eye length. A registration algorithm using orthogonally scanned OCT volumetric data sets which can correct motion on a per A-scan basis is applied to compensate motion and merge motion corrected volumetric data for enhanced OCT image quality. Ultrahigh speed swept source OCT is a promising technique for imaging the rodent eye, proving comprehensive information on the cornea, anterior segment, lens, vitreous, posterior segment, retina and choroid.
doi:10.1364/BOE.4.000351
PMCID: PMC3567721  PMID: 23412778
(170.3880) Medical and biological imaging; (170.4500) Optical coherence tomography; (170.4470) Ophthalmology
23.  Reproducibility of Choroidal Thickness Measurements Across Three Spectral Domain Optical Coherence Tomography Systems 
Ophthalmology  2011;119(1):119-123.
Purpose
To investigate the reproducibility of choroidal thickness measurements in normal subjects on three Spectral Domain Optical Coherence Tomography (SDOCT) instruments, Zeiss Cirrus HD-OCT (Carl Zeiss Meditec Inc, Dublin, California, USA), Heidelberg Spectralis (Heidelberg Engineering, Heidelberg, Germany) and Optovue RTVue (Optovue Inc., Fremont, CA).
Design
Cross-sectional non-interventional study
Participants
Images were obtained in 28 eyes of 28 healthy undilated volunteers without ocular pathology in a clinical setting.
Methods
All subjects were imaged on the fovea using Cirrus HD 1-line raster, Spectralis enhanced depth imaging and RTVue retina-cross.
Main Outcome Measures
The choroid was measured subfoveally, 750 μm temporal and 750 μm nasal to the fovea. All measurements were performed by 2 independent observers. Two way analysis of variance (ANOVA) with Bonferroni's post-test, Pearson correlation and the Bland-Altman analysis were used to compare measurements.
Results
The group of 28 subjects consisted of 7 men and 21 women, with an average age of 35.2 years (range, 23 to 64 years). A two way ANOVA with Bonferroni's post-test revealed no significant difference in the average subfoveal choroidal thickness (P >0.05) between systems for any location: subfoveally, 750μm temporal and 750 μm nasal to the fovea. The measurements of choroidal thickness from any pair of three instruments (Cirrus vs. Spectralis, Cirrus vs. RTVue, Spectralis vs. RTVue) were also strongly correlated. The Pearson correlation between all two system pairs of the three systems was greater than 0.9 p <0.0001. The 95% limits of agreement between four choroidal thickness measurements between Cirrus and RTVue were +11.21% to -13.57% (Bias -1.17), between Spectralis and RTVue +10.85% to -12.45% (Bias -0.80) and between Cirrus and Spectralis +12.81% to -13.33% (Bias -0.25).
Conclusions
In our population of young healthy adults with normal vision, there was good reproducibility between choroidal thickness measurements of images acquired with Cirrus, Spectralis and RTVue.
doi:10.1016/j.ophtha.2011.07.002
PMCID: PMC3251715  PMID: 21943786
24.  Automated three-dimensional choroidal vessel segmentation of 3D 1060 nm OCT retinal data 
Biomedical Optics Express  2012;4(1):134-150.
A fully automated, robust vessel segmentation algorithm has been developed for choroidal OCT, employing multiscale 3D edge filtering and projection of “probability cones” to determine the vessel “core”, even in the tomograms with low signal-to-noise ratio (SNR). Based on the ideal vessel response after registration and multiscale filtering, with computed depth related SNR, the vessel core estimate is dilated to quantify the full vessel diameter. As a consequence, various statistics can be computed using the 3D choroidal vessel information, such as ratios of inner (smaller) to outer (larger) choroidal vessels or the absolute/relative volume of choroid vessels. Choroidal vessel quantification can be displayed in various forms, focused and averaged within a special region of interest, or analyzed as the function of image depth. In this way, the proposed algorithm enables unique visualization of choroidal watershed zones, as well as the vessel size reduction when investigating the choroid from the sclera towards the retinal pigment epithelium (RPE). To the best of our knowledge, this is the first time that an automatic choroidal vessel segmentation algorithm is successfully applied to 1060 nm 3D OCT of healthy and diseased eyes.
doi:10.1364/BOE.4.000134
PMCID: PMC3539191  PMID: 23304653
(170.4500) Optical coherence tomography; (100.0100) Image processing; (100.3008) Image recognition, algorithms and filters; (170.4580) Optical diagnostics for medicine
25.  Structural Markers Observed with Endoscopic Three-dimensional Optical Coherence Tomography Correlating with Barrett's Esophagus Radiofrequency Ablation Treatment Response 
Gastrointestinal endoscopy  2012;76(6):1104-1112.
Background
Radiofrequency ablation (RFA) is effective for treating Barrett's esophagus (BE) but often involves multiple endoscopy sessions over several months to achieve complete response.
Objective
Identify structural markers using three-dimensional optical coherence tomography (3D-OCT) that correlate with treatment response.
Design
Cross-sectional.
Setting
Single teaching hospital.
Patients
Thirty-two male and one female Caucasians with short-segment BE (<3cm) undergoing RFA treatment.
Interventions
Patients were treated with focal RFA and 3D-OCT was performed at the gastroesophageal junction before and immediately after the RFA treatment. Patients were re-examined with standard endoscopy 6-8 weeks later and biopsied to rule out BE if not visibly evident.
Main outcome measurement
The thickness of BE epithelium before RFA and the presence of residual-gland-like structures immediately after RFA were determined using 3D-OCT. The presence of BE at follow-up was assessed endoscopically.
Results
BE mucosa was significantly thinner in patients who achieved complete eradication of intestinal metaplasia (CE-IM) than in patients who did not achieve CE-IM at follow-up [257±60μm vs. 403±86μm, p<0.0001]. A threshold thickness of 333μm derived from receiver-operator characteristics corresponds to a 92.3% sensitivity, 85% specificity and 87.9% accuracy in predicting the presence of BE at follow-up. The presence of OCT-visible glands immediately after RFA also correlated with the presence residual BE at follow-up (83.3% Sensitivity, 95% specificity, and 90.6% accuracy).
Limitations
Single center, cross sectional study and only patients with short-segment BE were examined.
Conclusions
3D-OCT assessment of BE thickness and residual glands during RFA sessions correlated with treatment response. 3D-OCT may predict response to RFA or make real-time RFA retreatment decisions in the future.
doi:10.1016/j.gie.2012.05.024
PMCID: PMC3485415  PMID: 22831857
Optical Coherence Tomography; Optical Biopsy; Barrett's Esophagus; Radiofrequency Ablation; Epithelial depth

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