通过光学相干断层扫描图像进行自动视网膜分割评估黄斑水肿的投影面积

在本文中,我们提出了一种自动视网膜分割方法,以评估光学相干断层扫描（OCT）图像中黄斑水肿（ME）在视网膜特定层上的投影面积。首先使用基于权重矩阵的优化的最短路径最快算法对十个视网膜层边界进行分割,这有效降低了算法对血管阴影的敏感性。然而,ME的存在将导致水肿区域的分割不准确。因此,我们使用强度阈值方法提取每个OCT图像中的水肿区域,并将该区域中的值设置为零,并确保获得的分割边界可以自动穿过而不是绕过水肿区域。我们使用最小值投影来计算ME在不同层的投影面积。为了测试我们的方法,我们使用了从Topcon的OCT机器收集的数据。在轴向和B扫描方向上测得的黄斑区域分辨率分别为11.7微米和46.8微米。与手动分割相比,视网膜层边界分割的平均绝对误差和标准偏差为4.5±3.2微米。因此,所提出的方法为评估水肿提供了一种自动,无创和定量的工具。     

A new high‐resolution computed tomography (CT) segmentation method for trabecular bone architectural analysis

In the last decade, high‐resolution computed tomography (CT) and microcomputed tomography (micro‐CT) have been increasingly used in anthropological studies and as a complement to traditional histological techniques. This is due in large part to the ability of CT techniques to nondestructively extract three‐dimensional representations of bone structures. Despite prior studies employing CT techniques, no completely reliable method of bone segmentation has been established. Accurate preprocessing of digital data is crucial for measurement accuracy, especially when subtle structures such as trabecular bone are investigated. The research presented here is a new, reproducible, accurate, and fully automated computerized segmentation method for high‐resolution CT datasets of fossil and recent cancellous bone: the Ray Casting Algorithm (RCA). We compare this technique with commonly used methods of image thresholding (i.e., the half‐maximum height protocol and the automatic, adaptive iterative thresholding procedure). While the quality of the input images is crucial for conventional image segmentation, the RCA method is robust regarding the signal to noise ratio, beam hardening, ring artifacts, and blurriness. Tests with data of extant and fossil material demonstrate the superior quality of RCA compared with conventional thresholding procedures, and emphasize the need for careful consideration of optimal CT scanning parameters. Am J Phys Anthropol 2009. © 2009 Wiley‐Liss, Inc.     

Retinal imaging with optical coherence tomography and low‐loss adaptive optics using a 2.8‐mm beam size

As data acquisition for retinal imaging with optical coherence tomography (OCT) becomes faster, efficient collection of photons becomes more important to maintain image quality. One approach is to use a larger aperture at the eye's pupil to collect more photons that have been reflected from the retina. A 2.8‐mm beam diameter system with only seven reflecting surfaces was developed for low‐loss retinal imaging. The larger beam size requires defocus and astigmatism correction, which was done in a closed loop adaptive optics method using a Shack‐Hartmann wavefront sensor and a deformable mirror (DM) with 140 actuators and a ±2.75 μm stroke. This DM facilitates defocus correction ranging from approximately ?3 D to +3 D. Comparing the new system with a standard 1.2‐mm system on a model eye, a signal‐to‐noise gain of 4.5 dB and a 2.3 times smaller speckle size were measured. Measurements on the retinas of five subjects showed even better results, with increases in dynamic range up to 13 dB. Note that the new sample arm only occupies 30 cm × 60 cm, which makes it highly suitable for imaging in a clinical environment. Figure: B‐scan images obtained over a width of 8 deg from the right eye of a 31‐year‐old Caucasian male. While the left side was imaged with a standard 1.2‐mm OCT system, the right side was imaged with the 2.8‐mm system. Both images were collected with the same integration time and incident power, after correction of aberrations. Using the dynamic range within the images, which is determined by comparing the highest pixel value to the noise floor, a difference in dynamic range of 10.8 dB was measured between the two systems.      

Comparison of the Iowa Reference Algorithm to the Heidelberg Spectralis optical coherence tomography segmentation algorithm

For spectral‐domain optical coherence tomography (SD‐OCT) studies of neurodegeneration, it is important to understand how segmentation algorithms differ in retinal layer thickness measurements, segmentation error locations and the impact of manual correction. Using macular SD‐OCT images of frontotemporal degeneration patients and controls, we compare the individual and aggregate retinal layer thickness measurements provided by two commonly used algorithms, the Iowa Reference Algorithm and Heidelberg Spectralis, with manual correction of significant segmentation errors. We demonstrate small differences of most retinal layer thickness measurements between these algorithms. Outer sectors of the Early Treatment Diabetic Retinopathy Study grid require a greater percent of eyes to be corrected than inner sectors of the retinal nerve fiber layer (RNFL). Manual corrections affect thickness measurements mildly, resulting in at most a 5% change in RNFL thickness. Our findings can inform researchers how to best use different segmentation algorithms when comparing retinal layer thicknesses.     

Multicontrast endomyocardial imaging by single‐channel high‐resolution cross‐polarization optical coherence tomography

A single‐channel high‐resolution cross‐polarization (CP) optical coherence tomography (OCT) system is presented for multicontrast imaging of human myocardium in one‐shot measurement. The intensity and functional contrasts, including the ratio between the cross‐ and co‐polarization channels as well as the cumulative retardation, are reconstructed from the CP‐OCT readout. By comparing the CP‐OCT results with histological analysis, it is shown that the system can successfully delineate microstructures in the myocardium and differentiate the fibrotic myocardium from normal or ablated myocardium based on the functional contrasts provided by the CP‐OCT system. The feasibility of using A‐line profiles from the 2 orthogonal polarization channels to identify fibrotic myocardium, normal myocardium and ablated lesion is also discussed.      

Pixel classification method in optical coherence tomography for tumor segmentation and its complementary usage with OCT microangiography

A novel machine‐learning method to distinguish between tumor and normal tissue in optical coherence tomography (OCT) has been developed. Pre‐clinical murine ear model implanted with mouse colon carcinoma CT‐26 was used. Structural‐image‐based feature sets were defined for each pixel and machine learning classifiers were trained using “ground truth” OCT images manually segmented by comparison with histology. The accuracy of the OCT tumor segmentation method was then quantified by comparing with fluorescence imaging of tumors expressing genetically encoded fluorescent protein KillerRed that clearly delineates tumor borders. Because the resultant 3D tumor/normal structural maps are inherently co‐registered with OCT derived maps of tissue microvasculature, the latter can be color coded as belonging to either tumor or normal tissue. Applications to radiomics‐based multimodal OCT analysis are envisioned.      

Super‐achromatic optical coherence tomography capsule for ultrahigh‐resolution imaging of esophagus

Endoscopic optical coherence tomography (OCT) is a noninvasive technology allowing for imaging of tissue microanatomies of luminal organs in real time. Conventional endoscopic OCT operates at 1300 nm wavelength region with a suboptimal axial resolution limited to 8‐20 μm. In this paper, we present the first ultrahigh‐resolution tethered OCT capsule operating at 800 nm and offering about 3‐ to 4‐fold improvement of axial resolution (plus enhanced imaging contrast). The capsule uses diffractive optics to manage chromatic aberration over a full ~200 nm spectral bandwidth centering around 830 nm, enabling to achieve super‐achromaticity and an axial resolution of ~2.6 μm in air. The performance of the OCT capsule is demonstrated by volumetric imaging of swine esophagus ex vivo and sheep esophagus in vivo, where fine anatomic structures including the sub‐epithelial layers are clearly identified. The ultrahigh resolution and excellent imaging contrast at 800 nm of the tethered capsule suggest the potential of the technology as an enabling tool for surveillance of early esophageal diseases on awake patients without the need for sedation.      

Quantification of Lawsonia intracellularis in porcine faeces by real‐time PCR

Aim: To develop and to validate a method for the quantification of Lawsonia intracellularis in porcine faeces by real‐time PCR. Methods and Results: A real‐time PCR including a calibrator based on plasmid DNA for quantification by means of ΔΔCt method was evaluated. The parameters specificity, detection limit, quantification limit, linearity, range, repeatability, precision and recovery were validated. The detection limit of the agent was 1 copy per reaction, and quantification was reliable between 10¹ and 10⁷ copies per μl reaction volume. The linearity calculated by logistic regression revealed a slope of ?3·329 reflecting an efficiency of 99·7% for the assay. Moreover, it was shown that storage of samples and repetition of tests including DNA isolation by same or other investigators did not influence the outcome. Conclusion: The quantification method described herein revealed consistent results for the quantitation of L. intracellularis in porcine faeces samples. Significance and Impact of the Study: In contrast to common PCR in combination with gel electrophoresis, this validated quantification method based on real‐time PCR enhances a reliable quantification and is even more sensitive.     

Four‐dimensional imaging of murine subpleural alveoli using high‐speed optical coherence tomography

The investigation of lung dynamics on alveolar scale is crucial for the understanding and treatment of lung diseases, such as acute lung injury and ventilator induced lung injury, and to promote the development of protective ventilation strategies. One approach to this is the establishment of numerical simulations of lung tissue mechanics where detailed knowledge about three‐dimensional alveolar structure changes during the ventilation cycle is required. We suggest four‐dimensional optical coherence tomography (OCT) imaging as a promising modality for visualizing the structural dynamics of single alveoli in subpleural lung tissue with high temporal resolution using a mouse model. A high‐speed OCT setup based on Fourier domain mode locked laser technology facilitated the acquisition of alveolar structures without noticeable motion artifacts at a rate of 17 three‐dimensional stacks per ventilation cycle. The four‐dimensional information, acquired in one single ventilation cycle, allowed calculating the volume‐pressure curve and the alveolar compliance for single alveoli. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Development and evaluation of real‐time PCR assays for bloodmeal identification in Culicoides midges

Culicoides (Diptera: Ceratopogonidae) midges are the biological vectors of a number of arboviruses of veterinary importance. However, knowledge relating to the basic biology of some species, including their host‐feeding preferences, is limited. Identification of host‐feeding preferences in haematophagous insects can help to elucidate the transmission dynamics of the arboviruses they may transmit. In this study, a series of semi‐quantitative real‐time polymerase chain reaction (qPCR) assays to identify the vertebrate host sources of bloodmeals of Culicoides midges was developed. Two pan‐reactive species group and seven species‐specific qPCR assays were developed and evaluated. The assays are quick to perform and less expensive than nucleic acid sequencing of bloodmeals. Using these assays, it was possible to rapidly test nearly 700 blood‐fed midges of various species from several geographic locations in Australia.     

Quantification of diabetic macular ischemia using novel three‐dimensional optical coherence tomography angiography metrics

We applied three‐dimensional (3D) analysis to optical coherence tomography angiography (OCTA) to measure macular ischemia in eyes affected by non‐proliferative diabetic retinopathy (DR). A previously validated algorithm was applied to OCTA data in order to obtain 3D visualization of the retinal vasculature. Successively, a global thresholding algorithm was applied and two novel quantitative metrics were introduced: 3D vascular volume and 3D perfusion density. Two‐dimensional (2D) OCTA metrics were also obtained with different binarization thresholds for comparison. Of the 30 patients included, 15 were diagnosed with DR and 15 were controls. The 3D vascular volume and 3D perfusion density were reduced in DR eyes (P < .0001). The 2D variables also significantly differ between groups. The 3D perfusion density had the highest area under the receiver operating characteristic curve (0.964) among tested variables. Assessing quantitative perfusion using 3D analysis is reliable and promising, and with an elevated diagnostic efficacy in identifying DR eyes.     

Full‐field swept‐source optical coherence tomography and neural tissue classification for deep brain imaging

Optical coherence tomography can differentiate brain regions with intrinsic contrast and at a micron scale resolution. Such a device can be particularly useful as a real‐time neurosurgical guidance tool. We present, to our knowledge, the first full‐field swept‐source optical coherence tomography system operating near a wavelength of 1310 nm. The proof‐of‐concept system was integrated with an endoscopic probe tip, which is compatible with deep brain stimulation keyhole neurosurgery. Neuroimaging experiments were performed on ex vivo brain tissues and in vivo in rat brains. Using classification algorithms involving texture features and optical attenuation, images were successfully classified into three brain tissue types.     

Comparison of retinal nerve fiber layer thickness measurements by spectral‐domain optical coherence tomography systems using a phantom eye model

To quantify differences in nerve fiber layer thickness measurements by various spectral‐domain optical coherence tomography (SD‐OCT) systems, we developed a phantom eye model. We tested twelve SD‐OCT systems of four manufacturers. All systems combined overestimated the 49 µm thick phantom RNFL thickness on average by 18 µm. Within brands, thickness measurements differed statistically significant for one Topcon, one RTVue and one Cirrus. Between brands, thickness determined with RTVue and Topcon differed statistically significant from Cirrus and Spectralis. The maximum difference between mean thicknesses is 3.6 µm within brands and 7.7 µm between brands. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Evaluation of real‐time PCR methods for quantification of Acanthamoeba in anthropogenic water and biofilms

Aims: To assess two real‐time PCR methods (the Riviere and Qvarnstrom assays) for environmental Acanthamoeba. Methods and Results: DNA extracted from Acanthamoeba castellanii taken from water and biofilms of cooling towers was analysed by the Riviere and Qvarnstrom assays. To quantify environmental Acanthamoeba, the calibration curves (DNA quantity vs cell number) were constructed with samples spiked with A. castellanii. The calibration curves for both quantitative PCR assays showed low variation (coefficient of variation of C_t≤ 5·7%) and high linearity (R² ≥ 0·99) over six orders of magnitudes with detection limit of three cells per water sample. DNA quantity determined by Qvarnstrom assay was equivalent between trophozoites and cysts (P = 0·49), whereas a significant difference was observed with Riviere assay (P < 0·0001). Riviere assay failed to detect Acanthamoeba in 21% (15/71) of the environmental samples which were positively detected by Qvarnstrom assay, while one sample (1·4%) was shown positive by Riviere assay but negative by Qvarnstrom assay. Moreover, Acanthamoeba counts by Qvarnstrom assay were greater than those by Riviere assay (P < 0·0001). Conclusions: Qvarnstrom assay performs better than Riviere assay for detection and quantification of Acanthamoeba in anthropogenic water and biofilms. Significance and Impact of the Study: Qvarnstrom assay may significantly contribute to a better knowledge about the distribution and abundance of Acanthamoeba in environments.     

A compact high‐speed full‐field optical coherence microscope for high‐resolution in vivo skin imaging

A compact high‐speed full‐field optical coherence microscope has been developed for high‐resolution in vivo imaging of biological tissues. The interferometer, in the Linnik configuration, has a size of 11 × 11 × 5 cm³ and a weight of 210 g. Full‐field illumination with low‐coherence light is achieved with a high‐brightness broadband light‐emitting diode. High‐speed full‐field detection is achieved by using part of the image sensor of a high‐dynamic range CMOS camera. En face tomographic images are acquired at a rate of 50 Hz, with an integration time of 0.9 ms. The image spatial resolution is 0.9 μm × 1.2 μm (axial × transverse), over a field of view of 245 × 245 μm². Images of human skin, revealing in‐depth cellular‐level structures, were obtained in vivo and in real‐time without the need for stabilization of the subject. The system can image larger fields, up to 1 × 1 mm², but at a reduced depth.