Browsing by Subject "Imaging, Three-Dimensional"
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Item Open Access A digital collection of rare and endangered lemurs and other primates from the Duke Lemur Center.(PloS one, 2019-01) Yapuncich, Gabriel S; Kemp, Addison D; Griffith, Darbi M; Gladman, Justin T; Ehmke, Erin; Boyer, Doug MScientific study of lemurs, a group of primates found only on Madagascar, is crucial for understanding primate evolution. Unfortunately, lemurs are among the most endangered animals in the world, so there is a strong impetus to maximize as much scientific data as possible from available physical specimens. MicroCT scanning efforts at Duke University have resulted in scans of more than 100 strepsirrhine cadavers representing 18 species from the Duke Lemur Center. An error study of the microCT scanner recovered less than 0.3% error at multiple resolution levels. Scans include specimen overviews and focused, high-resolution selections of complex anatomical regions (e.g., cranium, hands, feet). Scans have been uploaded to MorphoSource, an online digital repository for 3D data. As captive (but free ranging) individuals, these specimens have a wealth of associated information that is largely unavailable for wild populations, including detailed life history data. This digital collection maximizes the information obtained from rare and endangered animals with minimal degradation of the original specimens.Item Open Access A low-cost, portable, and quantitative spectral imaging system for application to biological tissues.(Opt Express, 2010-06-07) Fu, Henry L; Yu, Bing; Lo, Justin Y; Palmer, Greg M; Kuech, Thomas F; Ramanujam, NimmiThe ability of diffuse reflectance spectroscopy to extract quantitative biological composition of tissues has been used to discern tissue types in both pre-clinical and clinical cancer studies. Typically, diffuse reflectance spectroscopy systems are designed for single-point measurements. Clinically, an imaging system would provide valuable spatial information on tissue composition. While it is feasible to build a multiplexed fiber-optic probe based spectral imaging system, these systems suffer from drawbacks with respect to cost and size. To address these we developed a compact and low cost system using a broadband light source with an 8-slot filter wheel for illumination and silicon photodiodes for detection. The spectral imaging system was tested on a set of tissue mimicking liquid phantoms which yielded an optical property extraction accuracy of 6.40 +/- 7.78% for the absorption coefficient (micro(a)) and 11.37 +/- 19.62% for the wavelength-averaged reduced scattering coefficient (micro(s)').Item Open Access A new fully automated approach for aligning and comparing shapes.(Anatomical record (Hoboken, N.J. : 2007), 2015-01) Boyer, Doug M; Puente, Jesus; Gladman, Justin T; Glynn, Chris; Mukherjee, Sayan; Yapuncich, Gabriel S; Daubechies, IngridThree-dimensional geometric morphometric (3DGM) methods for placing landmarks on digitized bones have become increasingly sophisticated in the last 20 years, including greater degrees of automation. One aspect shared by all 3DGM methods is that the researcher must designate initial landmarks. Thus, researcher interpretations of homology and correspondence are required for and influence representations of shape. We present an algorithm allowing fully automatic placement of correspondence points on samples of 3D digital models representing bones of different individuals/species, which can then be input into standard 3DGM software and analyzed with dimension reduction techniques. We test this algorithm against several samples, primarily a dataset of 106 primate calcanei represented by 1,024 correspondence points per bone. Results of our automated analysis of these samples are compared to a published study using a traditional 3DGM approach with 27 landmarks on each bone. Data were analyzed with morphologika(2.5) and PAST. Our analyses returned strong correlations between principal component scores, similar variance partitioning among components, and similarities between the shape spaces generated by the automatic and traditional methods. While cluster analyses of both automatically generated and traditional datasets produced broadly similar patterns, there were also differences. Overall these results suggest to us that automatic quantifications can lead to shape spaces that are as meaningful as those based on observer landmarks, thereby presenting potential to save time in data collection, increase completeness of morphological quantification, eliminate observer error, and allow comparisons of shape diversity between different types of bones. We provide an R package for implementing this analysis.Item Open Access A positioning QA procedure for 2D/2D (kV/MV) and 3D/3D (CT/CBCT) image matching for radiotherapy patient setup.(Journal of applied clinical medical physics, 2009-10-06) Guan, Huaiqun; Hammoud, Rabih; Yin, Fang-FangA positioning QA procedure for Varian's 2D/2D (kV/MV) and 3D/3D (planCT/CBCT) matching was developed. The procedure was to check: (1) the coincidence of on-board imager (OBI), portal imager (PI), and cone beam CT (CBCT)'s isocenters (digital graticules) to a linac's isocenter (to a pre-specified accuracy); (2) that the positioning difference detected by 2D/2D (kV/MV) and 3D/3D(planCT/CBCT) matching can be reliably transferred to couch motion. A cube phantom with a 2 mm metal ball (bb) at the center was used. The bb was used to define the isocenter. Two additional bbs were placed on two phantom surfaces in order to define a spatial location of 1.5 cm anterior, 1.5 cm inferior, and 1.5 cm right from the isocenter. An axial scan of the phantom was acquired from a multislice CT simulator. The phantom was set at the linac's isocenter (lasers); either AP MV/R Lat kV images or CBCT images were taken for 2D/2D or 3D/3D matching, respectively. For 2D/2D, the accuracy of each device's isocenter was obtained by checking the distance between the central bb and the digital graticule. Then the central bb in orthogonal DRRs was manually moved to overlay to the off-axis bbs in kV/MV images. For 3D/3D, CBCT was first matched to planCT to check the isocenter difference between the two CTs. Manual shifts were then made by moving CBCT such that the point defined by the two off-axis bbs overlay to the central bb in planCT. (PlanCT can not be moved in the current version of OBI1.4.) The manual shifts were then applied to remotely move the couch. The room laser was used to check the accuracy of the couch movement. For Trilogy (or Ix-21) linacs, the coincidence of imager and linac's isocenter was better than 1 mm (or 1.5 mm). The couch shift accuracy was better than 2 mm.Item Open Access A three dimensional nerve map of human bladder trigone.(Neurourology and urodynamics, 2017-04) Purves, J Todd; Spruill, Laura; Rovner, Eric; Borisko, Elyse; McCants, Alden; Mugo, Elizabeth; Wingard, Ainsley; Trusk, Thomas C; Bacro, Thierry; Hughes, Francis MCentral efferent and afferent neural pathways to and from the human urinary bladder are well-characterized, but the location and arborization of these nerves as they traverse the serosa, muscularis, and urothelial layers are not clearly defined. The purpose of this study was to create a three dimensional map of the innervation of the human bladder trigone from the extrinsic perivesical adventitial nerve trunks to the urothelium.A male and a female human bladder were harvested from fresh frozen cadavers and fixed in formalin. The bladder neck and trigone region were serially sectioned (5 μm) and every 20th slide was stained (S100), scanned and aligned to create 3D maps.Nerve penetration into the detrusor muscle occurs with the highest frequency at the bladder neck and interureteric ridge. Nerves traveling parallel to the bladder lumen do so in the adventitia, beyond the outer border of detrusor. In females, the depth of these nerve bands is uniform at 0.7-1.7 cm below the luminal surface, the outer limits of which include the anterior vaginal wall. In the male, depth is more variable owing to detrusor hypertrophy with the minimum depth of nerves approximately 0.5 cm near the interureteric ridge and over 1 cm near the bladder neck.Myelinated neural pathways traversing in the human bladder in the region of the trigone have a discreet regional density. This 3D map of trigonal innervation may provide guidance to more precisely direct therapies for urinary incontinence or pelvic pain. Neurourol. Urodynam. 36:1015-1019, 2017. © 2016 Wiley Periodicals, Inc.Item Open Access An enteroendocrine cell-enteric glia connection revealed by 3D electron microscopy.(PLoS One, 2014) Bohórquez, Diego V; Samsa, Leigh A; Roholt, Andrew; Medicetty, Satish; Chandra, Rashmi; Liddle, Rodger AThe enteroendocrine cell is the cornerstone of gastrointestinal chemosensation. In the intestine and colon, this cell is stimulated by nutrients, tastants that elicit the perception of flavor, and bacterial by-products; and in response, the cell secretes hormones like cholecystokinin and peptide YY--both potent regulators of appetite. The development of transgenic mice with enteroendocrine cells expressing green fluorescent protein has allowed for the elucidation of the apical nutrient sensing mechanisms of the cell. However, the basal secretory aspects of the enteroendocrine cell remain largely unexplored, particularly because a complete account of the enteroendocrine cell ultrastructure does not exist. Today, the fine ultrastructure of a specific cell can be revealed in the third dimension thanks to the invention of serial block face scanning electron microscopy (SBEM). Here, we bridged confocal microscopy with SBEM to identify the enteroendocrine cell of the mouse and study its ultrastructure in the third dimension. The results demonstrated that 73.5% of the peptide-secreting vesicles in the enteroendocrine cell are contained within an axon-like basal process. We called this process a neuropod. This neuropod contains neurofilaments, which are typical structural proteins of axons. Surprisingly, the SBEM data also demonstrated that the enteroendocrine cell neuropod is escorted by enteric glia--the cells that nurture enteric neurons. We extended these structural findings into an in vitro intestinal organoid system, in which the addition of glial derived neurotrophic factors enhanced the development of neuropods in enteroendocrine cells. These findings open a new avenue of exploration in gastrointestinal chemosensation by unveiling an unforeseen physical relationship between enteric glia and enteroendocrine cells.Item Open Access Automatic segmentation of seven retinal layers in SDOCT images congruent with expert manual segmentation.(Opt Express, 2010-08-30) Chiu, SJ; Li, XT; Nicholas, P; Toth, CA; Izatt, JA; Farsiu, SSegmentation of anatomical and pathological structures in ophthalmic images is crucial for the diagnosis and study of ocular diseases. However, manual segmentation is often a time-consuming and subjective process. This paper presents an automatic approach for segmenting retinal layers in Spectral Domain Optical Coherence Tomography images using graph theory and dynamic programming. Results show that this method accurately segments eight retinal layer boundaries in normal adult eyes more closely to an expert grader as compared to a second expert grader.Item Open Access CLARITY and PACT-based imaging of adult zebrafish and mouse for whole-animal analysis of infections.(Dis Model Mech, 2015-12) Cronan, Mark R; Rosenberg, Allison F; Oehlers, Stefan H; Saelens, Joseph W; Sisk, Dana M; Jurcic Smith, Kristen L; Lee, Sunhee; Tobin, David MVisualization of infection and the associated host response has been challenging in adult vertebrates. Owing to their transparency, zebrafish larvae have been used to directly observe infection in vivo; however, such larvae have not yet developed a functional adaptive immune system. Cells involved in adaptive immunity mature later and have therefore been difficult to access optically in intact animals. Thus, the study of many aspects of vertebrate infection requires dissection of adult organs or ex vivo isolation of immune cells. Recently, CLARITY and PACT (passive clarity technique) methodologies have enabled clearing and direct visualization of dissected organs. Here, we show that these techniques can be applied to image host-pathogen interactions directly in whole animals. CLARITY and PACT-based clearing of whole adult zebrafish and Mycobacterium tuberculosis-infected mouse lungs enables imaging of mycobacterial granulomas deep within tissue to a depth of more than 1 mm. Using established transgenic lines, we were able to image normal and pathogenic structures and their surrounding host context at high resolution. We identified the three-dimensional organization of granuloma-associated angiogenesis, an important feature of mycobacterial infection, and characterized the induction of the cytokine tumor necrosis factor (TNF) within the granuloma using an established fluorescent reporter line. We observed heterogeneity in TNF induction within granuloma macrophages, consistent with an evolving view of the tuberculous granuloma as a non-uniform, heterogeneous structure. Broad application of this technique will enable new understanding of host-pathogen interactions in situ.Item Open Access Compressive holography.(2012) Lim, Se HoonCompressive holography estimates images from incomplete data by using sparsity priors. Compressive holography combines digital holography and compressive sensing. Digital holography consists of computational image estimation from data captured by an electronic focal plane array. Compressive sensing enables accurate data reconstruction by prior knowledge on desired signal. Computational and optical co-design optimally supports compressive holography in the joint computational and optical domain. This dissertation explores two examples of compressive holography : estimation of 3D tomographic images from 2D data and estimation of images from under sampled apertures. Compressive holography achieves single shot holographic tomography using decompressive inference. In general, 3D image reconstruction suffers from underdetermined measurements with a 2D detector. Specifically, single shot holographic tomography shows the uniqueness problem in the axial direction because the inversion is ill-posed. Compressive sensing alleviates the ill-posed problem by enforcing some sparsity constraints. Holographic tomography is applied for video-rate microscopic imaging and diffuse object imaging. In diffuse object imaging, sparsity priors are not valid in coherent image basis due to speckle. So incoherent image estimation is designed to hold the sparsity in incoherent image basis by support of multiple speckle realizations. High pixel count holography achieves high resolution and wide field-of-view imaging. Coherent aperture synthesis can be one method to increase the aperture size of a detector. Scanning-based synthetic aperture confronts a multivariable global optimization problem due to time-space measurement errors. A hierarchical estimation strategy divides the global problem into multiple local problems with support of computational and optical co-design. Compressive sparse aperture holography can be another method. Compressive sparse sampling collects most of significant field information with a small fill factor because object scattered fields are locally redundant. Incoherent image estimation is adopted for the expanded modulation transfer function and compressive reconstruction.Item Open Access Dietary inference from upper and lower molar morphology in platyrrhine primates.(PLoS One, 2015) Allen, Kari L; Cooke, Siobhán B; Gonzales, Lauren A; Kay, Richard FThe correlation between diet and dental topography is of importance to paleontologists seeking to diagnose ecological adaptations in extinct taxa. Although the subject is well represented in the literature, few studies directly compare methods or evaluate dietary signals conveyed by both upper and lower molars. Here, we address this gap in our knowledge by comparing the efficacy of three measures of functional morphology for classifying an ecologically diverse sample of thirteen medium- to large-bodied platyrrhines by diet category (e.g., folivore, frugivore, hard object feeder). We used Shearing Quotient (SQ), an index derived from linear measurements of molar cutting edges and two indices of crown surface topography, Occlusal Relief (OR) and Relief Index (RFI). Using SQ, OR, and RFI, individuals were then classified by dietary category using Discriminate Function Analysis. Both upper and lower molar variables produce high classification rates in assigning individuals to diet categories, but lower molars are consistently more successful. SQs yield the highest classification rates. RFI and OR generally perform above chance. Upper molar RFI has a success rate below the level of chance. Adding molar length enhances the discriminatory power for all variables. We conclude that upper molar SQs are useful for dietary reconstruction, especially when combined with body size information. Additionally, we find that among our sample of platyrrhines, SQ remains the strongest predictor of diet, while RFI is less useful at signaling dietary differences in absence of body size information. The study demonstrates new ways for inferring the diets of extinct platyrrhine primates when both upper and lower molars are available, or, for taxa known only from upper molars. The techniques are useful in reconstructing diet in stem representatives of anthropoid clade, who share key aspects of molar morphology with extant platyrrhines.Item Open Access Footprint evidence of early hominin locomotor diversity at Laetoli, Tanzania.(Nature, 2021-12) McNutt, Ellison J; Hatala, Kevin G; Miller, Catherine; Adams, James; Casana, Jesse; Deane, Andrew S; Dominy, Nathaniel J; Fabian, Kallisti; Fannin, Luke D; Gaughan, Stephen; Gill, Simone V; Gurtu, Josephat; Gustafson, Ellie; Hill, Austin C; Johnson, Camille; Kallindo, Said; Kilham, Benjamin; Kilham, Phoebe; Kim, Elizabeth; Liutkus-Pierce, Cynthia; Maley, Blaine; Prabhat, Anjali; Reader, John; Rubin, Shirley; Thompson, Nathan E; Thornburg, Rebeca; Williams-Hatala, Erin Marie; Zimmer, Brian; Musiba, Charles M; DeSilva, Jeremy MBipedal trackways discovered in 1978 at Laetoli site G, Tanzania and dated to 3.66 million years ago are widely accepted as the oldest unequivocal evidence of obligate bipedalism in the human lineage1-3. Another trackway discovered two years earlier at nearby site A was partially excavated and attributed to a hominin, but curious affinities with bears (ursids) marginalized its importance to the paleoanthropological community, and the location of these footprints fell into obscurity3-5. In 2019, we located, excavated and cleaned the site A trackway, producing a digital archive using 3D photogrammetry and laser scanning. Here we compare the footprints at this site with those of American black bears, chimpanzees and humans, and we show that they resemble those of hominins more than ursids. In fact, the narrow step width corroborates the original interpretation of a small, cross-stepping bipedal hominin. However, the inferred foot proportions, gait parameters and 3D morphologies of footprints at site A are readily distinguished from those at site G, indicating that a minimum of two hominin taxa with different feet and gaits coexisted at Laetoli.Item Restricted Global view of the functional molecular organization of the avian cerebrum: mirror images and functional columns.(J Comp Neurol, 2013-11) Jarvis, Erich D; Yu, Jing; Rivas, Miriam V; Horita, Haruhito; Feenders, Gesa; Whitney, Osceola; Jarvis, Syrus C; Jarvis, Electra R; Kubikova, Lubica; Puck, Ana EP; Siang-Bakshi, Connie; Martin, Suzanne; McElroy, Michael; Hara, Erina; Howard, Jason; Pfenning, Andreas; Mouritsen, Henrik; Chen, Chun-Chun; Wada, KazuhiroBased on quantitative cluster analyses of 52 constitutively expressed or behaviorally regulated genes in 23 brain regions, we present a global view of telencephalic organization of birds. The patterns of constitutively expressed genes revealed a partial mirror image organization of three major cell populations that wrap above, around, and below the ventricle and adjacent lamina through the mesopallium. The patterns of behaviorally regulated genes revealed functional columns of activation across boundaries of these cell populations, reminiscent of columns through layers of the mammalian cortex. The avian functionally regulated columns were of two types: those above the ventricle and associated mesopallial lamina, formed by our revised dorsal mesopallium, hyperpallium, and intercalated hyperpallium; and those below the ventricle, formed by our revised ventral mesopallium, nidopallium, and intercalated nidopallium. Based on these findings and known connectivity, we propose that the avian pallium has four major cell populations similar to those in mammalian cortex and some parts of the amygdala: 1) a primary sensory input population (intercalated pallium); 2) a secondary intrapallial population (nidopallium/hyperpallium); 3) a tertiary intrapallial population (mesopallium); and 4) a quaternary output population (the arcopallium). Each population contributes portions to columns that control different sensory or motor systems. We suggest that this organization of cell groups forms by expansion of contiguous developmental cell domains that wrap around the lateral ventricle and its extension through the middle of the mesopallium. We believe that the position of the lateral ventricle and its associated mesopallium lamina has resulted in a conceptual barrier to recognizing related cell groups across its border, thereby confounding our understanding of homologies with mammals.Item Restricted Hyperpolarized Xe MR imaging of alveolar gas uptake in humans.(PLoS One, 2010-08-16) Cleveland, Zackary I; Cofer, Gary P; Metz, Gregory; Beaver, Denise; Nouls, John; Kaushik, S Sivaram; Kraft, Monica; Wolber, Jan; Kelly, Kevin T; McAdams, H Page; Driehuys, BastiaanBACKGROUND: One of the central physiological functions of the lungs is to transfer inhaled gases from the alveoli to pulmonary capillary blood. However, current measures of alveolar gas uptake provide only global information and thus lack the sensitivity and specificity needed to account for regional variations in gas exchange. METHODS AND PRINCIPAL FINDINGS: Here we exploit the solubility, high magnetic resonance (MR) signal intensity, and large chemical shift of hyperpolarized (HP) (129)Xe to probe the regional uptake of alveolar gases by directly imaging HP (129)Xe dissolved in the gas exchange tissues and pulmonary capillary blood of human subjects. The resulting single breath-hold, three-dimensional MR images are optimized using millisecond repetition times and high flip angle radio-frequency pulses, because the dissolved HP (129)Xe magnetization is rapidly replenished by diffusive exchange with alveolar (129)Xe. The dissolved HP (129)Xe MR images display significant, directional heterogeneity, with increased signal intensity observed from the gravity-dependent portions of the lungs. CONCLUSIONS: The features observed in dissolved-phase (129)Xe MR images are consistent with gravity-dependent lung deformation, which produces increased ventilation, reduced alveolar size (i.e., higher surface-to-volume ratios), higher tissue densities, and increased perfusion in the dependent portions of the lungs. Thus, these results suggest that dissolved HP (129)Xe imaging reports on pulmonary function at a fundamental level.Item Open Access Identification of fluorescent beads using a coded aperture snapshot spectral imager.(Appl Opt, 2010-04-01) Cull, Christy Fernandez; Choi, Kerkil; Brady, David J; Oliver, TimWe apply a coded aperture snapshot spectral imager (CASSI) to fluorescence microscopy. CASSI records a two-dimensional (2D) spectrally filtered projection of a three-dimensional (3D) spectral data cube. We minimize a convex quadratic function with total variation (TV) constraints for data cube estimation from the 2D snapshot. We adapt the TV minimization algorithm for direct fluorescent bead identification from CASSI measurements by combining a priori knowledge of the spectra associated with each bead type. Our proposed method creates a 2D bead identity image. Simulated fluorescence CASSI measurements are used to evaluate the behavior of the algorithm. We also record real CASSI measurements of a ten bead type fluorescence scene and create a 2D bead identity map. A baseline image from filtered-array imaging system verifies CASSI's 2D bead identity map.Item Open Access Image Quality and Dose Comparison of 3 Mobile Intraoperative Three-Dimensional Imaging Systems in Spine Surgery.(World neurosurgery, 2022-04) Foster, Norah; Shaffrey, Christopher; Buchholz, Avery; Turner, Raymond; Yang, Lexie Zidanyue; Niedzwiecki, Donna; Goode, AllenObjective
To evaluate radiation exposure and image quality (IQ) for 3 intraoperative imaging systems (Airo TruCT, Cios Spin, O-arm) using varying radiation dose settings in a single cadaveric model.Methods
Axial images of L4-5 instrumentation were obtained using 3 manufacturer dose protocols for each system. Measurements included scattered radiation dose, subjective and objective IQ, and estimates of patient effective dose (ED). Four images per system were selected at each dose level. Using the Likert scale (1 = best, 5 = worst), 9 reviewers rated the same 36 images. Objective IQ measures included the degree of streak artifacts (lines with incorrect data from metal objects) in each image. A composite figure of merit was derived based on ED and subjective and objective scores.Results
The best subjective IQ scores were 1.44 (Cios Spin medium dose), 1.78 (Cios Spin high dose) and 2.22 (Airo TruCT low dose). The best objective IQ scores were 87.3 (Airo TruCT) and 89.1 (Cios Spin). ED low-dose results in mSv included 1.6 (Airo TruCT), 1.9 (Cios Spin), and 3.3 (O-arm). ED high-dose results in mSv included 4.6 (Cios Spin), 9.7 (Airo TruCT), and 9.9 (O-arm). Scatter radiation measurements for low dose in μGy included 21.9 (Cios Spin), 31.8 (Airo TruCT), and 33.9 (O-arm). Scatter radiation for high dose in μGy included 55.9 (Cios Spin), 104.5 (O-arm), and 200 (Airo TruCT). The best figure of merit score was for the Airo TruCT low dose, followed by Cios Spin medium dose and high dose.Conclusions
Selection of intraoperative imaging systems requires a greater understanding of the risks and benefits of radiation exposure and IQ.Item Open Access Improved delineation of short cortical association fibers and gray/white matter boundary using whole-brain three-dimensional diffusion tensor imaging at submillimeter spatial resolution.(Brain Connect, 2014-11) Song, Allen W; Chang, Hing-Chiu; Petty, Christopher; Guidon, Arnaud; Chen, Nan-KueiRecent emergence of human connectome imaging has led to a high demand on angular and spatial resolutions for diffusion magnetic resonance imaging (MRI). While there have been significant growths in high angular resolution diffusion imaging, the improvement in spatial resolution is still limited due to a number of technical challenges, such as the low signal-to-noise ratio and high motion artifacts. As a result, the benefit of a high spatial resolution in the whole-brain connectome imaging has not been fully evaluated in vivo. In this brief report, the impact of spatial resolution was assessed in a newly acquired whole-brain three-dimensional diffusion tensor imaging data set with an isotropic spatial resolution of 0.85 mm. It was found that the delineation of short cortical association fibers is drastically improved as well as the definition of fiber pathway endings into the gray/white matter boundary-both of which will help construct a more accurate structural map of the human brain connectome.Item Open Access Intraoperative spectral domain optical coherence tomography for vitreoretinal surgery.(Opt Lett, 2010-10-15) Tao, Yuankai K; Ehlers, Justis P; Toth, Cynthia A; Izatt, Joseph AWe demonstrate in vivo human retinal imaging using an intraoperative microscope-mounted optical coherence tomography system (MMOCT). Our optomechanical design adapts an Oculus Binocular Indirect Ophthalmo Microscope (BIOM3), suspended from a Leica ophthalmic surgical microscope, with spectral domain optical coherence tomography (SD-OCT) scanning and relay optics. The MMOCT enables wide-field noncontact real-time cross-sectional imaging of retinal structure, allowing for SD-OCT augmented intrasurgical microscopy for intraocular visualization. We experimentally quantify the axial and lateral resolution of the MMOCT and demonstrate fundus imaging at a 20Hz frame rate.Item Open Access Investigation of sliced body volume (SBV) as respiratory surrogate.(Journal of applied clinical medical physics, 2013-01-07) Cai, Jing; Chang, Zheng; O'Daniel, Jennifer; Yoo, Sua; Ge, Hong; Kelsey, Christopher; Yin, Fang-FangThe purpose of this study was to evaluate the sliced body volume (SBV) as a respiratory surrogate by comparing with the real-time position management (RPM) in phantom and patient cases. Using the SBV surrogate, breathing signals were extracted from unsorted 4D CT images of a motion phantom and 31 cancer patients (17 lung cancers, 14 abdominal cancers) and were compared to those clinically acquired using the RPM system. Correlation coefficient (R), phase difference (D), and absolute phase difference (D(A)) between the SBV-derived breathing signal and the RPM signal were calculated. 4D CT reconstructed based on the SBV surrogate (4D CT(SBV)) were compared to those clinically generated based on RPM (4D CT(RPM)). Image quality of the 4D CT were scored (S(SBV) and S(RPM), respectively) from 1 to 5 (1 is the best) by experienced evaluators. The comparisons were performed for all patients, and for the lung cancer patients and the abdominal cancer patients separately. RPM box position (P), breathing period (T), amplitude (A), period variability (V(T)), amplitude variability (V(A)), and space-dependent phase shift (F) were determined and correlated to S(SBV). The phantom study showed excellent match between the SBV-derived breathing signal and the RPM signal (R = 0.99, D= -3.0%, D(A) = 4.5%). In the patient study, the mean (± standard deviation (SD)) R, D, D(A), T, V(T), A, V(A), and F were 0.92 (± 0.05), -3.3% (± 7.5%), 11.4% (± 4.6%), 3.6 (± 0.8) s, 0.19 (± 0.10), 6.6 (± 2.8) mm, 0.20 (± 0.08), and 0.40 (± 0.18) s, respectively. Significant differences in R and D(A) (p = 0.04 and 0.001, respectively) were found between the lung cancer patients and the abdominal cancer patients. 4D CT(RPM) slightly outperformed 4D CT(SBV): the mean (± SD) S(RPM) and S(SBV) were 2.6 (± 0.6) and 2.9 (± 0.8), respectively, for all patients, 2.5 (± 0.6) and 3.1 (± 0.8), respectively, for the lung cancer patients, and 2.6 (± 0.7) and 2.8 (± 0.9), respectively, for the abdominal cancer patients. The difference between S(RPM) and S(SBV) was insignificant for the abdominal patients (p = 0.59). F correlated moderately with S(SBV) (r = 0.72). The correlation between SBV-derived breathing signal and RPM signal varied between patients and was significantly better in the abdomen than in the thorax. Space-dependent phase shift is a limiting factor of the accuracy of the SBV surrogate.Item Open Access Magnetic resonance microscopy.(Anal Cell Pathol (Amst), 2012) Badea, Alexandra; Johnson, G AllanItem Open Access Optical-CT 3D Dosimetry Using Fresnel Lenses with Minimal Refractive-Index Matching Fluid.(PLoS One, 2016) Bache, Steven; Malcolm, Javian; Adamovics, John; Oldham, MarkTelecentric optical computed tomography (optical-CT) is a state-of-the-art method for visualizing and quantifying 3-dimensional dose distributions in radiochromic dosimeters. In this work a prototype telecentric system (DFOS-Duke Fresnel Optical-CT Scanner) is evaluated which incorporates two substantial design changes: the use of Fresnel lenses (reducing lens costs from $10-30K t0 $1-3K) and the use of a 'solid tank' (which reduces noise, and the volume of refractively matched fluid from 1 ltr to 10 cc). The efficacy of DFOS was evaluated by direct comparison against commissioned scanners in our lab. Measured dose distributions from all systems were compared against the predicted dose distributions from a commissioned treatment planning system (TPS). Three treatment plans were investigated including a simple four-field box treatment, a multiple small field delivery, and a complex IMRT treatment. Dosimeters were imaged within 2 h post irradiation, using consistent scanning techniques (360 projections acquired at 1 degree intervals, reconstruction at 2mm). DFOS efficacy was evaluated through inspection of dose line-profiles, and 2D and 3D dose and gamma maps. DFOS/TPS gamma pass rates with 3%/3mm dose difference/distance-to-agreement criteria ranged from 89.3% to 92.2%, compared to from 95.6% to 99.0% obtained with the commissioned system. The 3D gamma pass rate between the commissioned system and DFOS was 98.2%. The typical noise rates in DFOS reconstructions were up to 3%, compared to under 2% for the commissioned system. In conclusion, while the introduction of a solid tank proved advantageous with regards to cost and convenience, further work is required to improve the image quality and dose reconstruction accuracy of the new DFOS optical-CT system.