Pseudo‐real‐time retinal layer segmentation for high‐resolution adaptive optics optical coherence tomography

We present a pseudo‐real‐time retinal layer segmentation for high‐resolution Sensorless Adaptive Optics‐Optical Coherence Tomography (SAO‐OCT). Our pseudo‐real‐time segmentation method is based on Dijkstra's algorithm that uses the intensity of pixels and the vertical gradient of the image to find the minimum cost in a geometric graph formulation within a limited search region. It segments six retinal layer boundaries in an iterative process according to their order of prominence. The segmentation time is strongly correlated to the number of retinal layers to be segmented. Our program permits en face images to be extracted during data acquisition to guide the depth specific focus control and depth dependent aberration correction for high‐resolution SAO‐OCT systems. The average processing times for our entire pipeline for segmenting six layers in a retinal B‐scan of 496 × 400 and 240 × 400 pixels are around 25.60 and 13.76 ms, respectively. When reducing the number of layers segmented to only two layers, the time required for a 240 × 400 pixel image is 8.26 ms.     

Assessing the accuracy of high-resolution X-ray computed tomography of primate trabecular bone by comparisons with histological sections

Different lines of evidence suggest that trabecular bone architecture contains a functional signal related to an organism's locomotor behavior. An understanding of the interspecific and intraspecific variation in extant nonhuman primate trabecular structure is needed to evaluate its usefulness as a tool to reconstruct the locomotor habits of extinct primates. High-resolution X-ray computed tomography (HRXCT) is a new imaging approach with a resolution in the tens of microns that allows nondestructive access to the internal structure of bony elements. Previous studies indicate that such resolution is necessary to accurately quantify structural parameters of trabecular bone. The primary goal of this study was to test the accuracy of HRXCT by comparing stereological measurements from HRXCT images and histological thin sections of cancellous bone taken from the proximal femur and humerus of baboons. To this end, 11 bone samples were scanned on an HRXCT scanner and then thin-sectioned to reveal the scanned plane. HRXCT images were thresholded using a modified half-maximum height protocol. The stereological measurements included bone volume fraction (BV/TV), trabecular number (Tb.N), bone surface to volume ratio (BS/BV), trabecular thickness (Tb.Th), and trabecular spacing (Tb.Sp). The measurement errors on the HRXCT images were 10.90% for BV/TV, 6.06% for Tb.N, 14.19% for BS/BV, 14.33% for Tb.Th, and 7.09% for Tb.Sp, but none of these measurements were significantly different from the histological standards (alpha = 0.05). A second goal of this study was to examine the influence of thresholding, a necessary step in any morphometric study using computed tomography, on the accuracy of the quantitative morphometry. Threshold values derived from a modified half-maximum height protocol showed that parameters derived from the region of interest (area in which stereological measurements were later taken) produced better reconstructions of the actual bone structure than threshold values derived from more inclusive areas of bone. We conclude that HRXCT can accurately reconstruct the complex architecture of trabecular bone, and that thresholding is a nontrivial step in trabecular bone studies, with even slight changes in the protocol greatly affecting the morphometric data. HRXCT represents a valuable analytical tool that should be of interest to a great many researchers in physical anthropology because it allows nondestructive access to internal morphology, thereby preserving valuable and limited skeletal collections.     

Inside Front Cover: Near‐infrared bone densitometry: A feasibility study on distal radius measurement (J. Biophotonics 7/2018)

This study provides a simple method to detect human distal radius bone density based on near infrared (NIR) imaging. The information of bone mineral density can be measured by transluminational optical bone densitometric system. Compared to dual‐energy x‐ray absorptiometry (DXA) results in clinical trial, NIR images show a strong correlation to DXA. Further details can be found in the article by Chun Chung, Yu‐Pin Chen, Tsai‐Hsueh Leu, and Chia‐Wei Sun ( e201700342 ).

     

Near‐infrared bone densitometry: A feasibility study on distal radius measurement

Osteoporosis, defined as decreased bone mineral density (BMD), poses patients in dangers for fracture risk and has become a major public health problem worldwide because of is associated morbidity, mortality and costs. Without doubt, early detection and timely intervention are important to successfully manage osteoporosis and its associated complications. The dual‐energy x‐ray absorptiometry (DXA) is the most popular and standard method to measure BMD. However, limitations including radiation exposure and availability restrict its application for osteoporosis screening among general population. In this study, we developed a simple method to detect human distal radius bone density based on near infrared (NIR) image system. Among 10 volunteers (including 5 young and 5 elderly participants) receiving bone density measurement using our NIR image system at the ultradistal part of bilateral distal radius, we demonstrated a strong correlation between the optical attenuation and BMD measured with DXA, which may facilitate predicting bone density status. We hope our potential NIR image system may open a new avenue for development of osteoporosis screening facilities and help in prevention of osteoporosis related fracture and its associated complications in the near future. Pearson's correlations between BMD values from the DXA and light intensity of NIR system.      

Digital holographic microtomography for high‐resolution refractive index mapping of live cells

Quantification of three‐dimensional (3D) refractive index (RI) with sub‐cellular resolution is achieved by digital holographic microtomography (DHμT) using quantitative phase images measured at multiple illumination angles. The DHμT system achieves sensitive and fast phase measurements based on iterative phase extraction algorithm and asynchronous phase shifting interferometry without any phase monitoring or active control mechanism. A reconstruction algorithm, optical diffraction tomography with projection on convex sets and total variation minimization, is implemented to substantially reduce the number of angular scattered fields needed for reconstruction without sacrificing the accuracy and quality of the reconstructed 3D RI distribution. Tomogram of a living CA9‐22 cell is presented to demonstrate the performance of the method. Further, a statistical analysis of the average RI of the nucleoli, the nucleus excluding the nucleoli and the cytoplasm of twenty CA9‐22 cells is performed. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

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.      

Distinguishing Anuran species by high‐resolution melting analysis of the COI barcode (COI‐HRM)

Taxonomic identification can be difficult when two or more species appear morphologically similar. DNA barcoding based on the sequence of the mitochondrial cytochrome c oxidase 1 gene (COI) is now widely used in identifying animal species. High‐resolution melting analysis (HRM) provides an alternative method for detecting sequence variations among amplicons without having to perform DNA sequencing. The purpose of this study was to determine whether HRM of the COI barcode can be used to distinguish animal species. Using anurans as a model, we found distinct COI melting profiles among three congeners of both Lithobates spp. and Hyla spp. Sequence variations within species shifted the melting temperature of one or more melting domains slightly but do not affect the distinctness of the melting profiles for each species. An NMDS ordination plot comparing melting peak profiles among eight Anuran species showed overlapping profiles for Lithobates sphenocephala and Gastrophryne carolinensis. The COI amplicon for both species contained two melting domains with melting temperatures that were similar between the two species. The two species belong to two different families, highlighting the fact that COI melting profiles do not reveal phylogenetic relationships but simply reflect DNA sequence differences among stretches of DNA within amplicons. This study suggests that high‐resolution melting analysis of COI barcodes (COI‐HRM) may be useful as a simple and rapid method to distinguish animal species that appear morphologically similar.     

Sphingosine‐1‐phosphate (S1P) receptors: Promising drug targets for treating bone‐related diseases

Sphingosine‐1‐phosphate (S1P) is a natural bioactive lipid molecule and a common first or second messenger in the cardiovascular and immune systems. By binding with its receptors, S1P can serve as mediator of signalling during cell migration, differentiation, proliferation and apoptosis. Although the predominant role of S1P in bone regeneration has been noted in many studies, this role is not as well‐known as its roles in the cardiovascular and immune systems. In this review, we summarize previous research on the role of S1P receptors (S1PRs) in osteoblasts and osteoclasts. In addition, S1P is regarded as a bridge between bone resorption and formation, which brings hope to patients with bone‐related diseases. Finally, we discuss S1P and its receptors as therapeutic targets for treating osteoporosis, inflammatory osteolysis and bone metastasis based on the biological effects of S1P in osteoclastic/osteoblastic cells, immune cells and tumour cells.     

LFQuant: A label‐free fast quantitative analysis tool for high‐resolution LC‐MS/MS proteomics data

Database searching based methods for label‐free quantification aim to reconstruct the peptide extracted ion chromatogram based on the identification information, which can limit the search space and thus make the data processing much faster. The random effect of the MS/MS sampling can be remedied by cross‐assignment among different runs. Here, we present a new label‐free fast quantitative analysis tool, LFQuant, for high‐resolution LC‐MS/MS proteomics data based on database searching. It is designed to accept raw data in two common formats (mzXML and Thermo RAW), and database search results from mainstream tools (MASCOT, SEQUEST, and X!Tandem), as input data. LFQuant can handle large‐scale label‐free data with fractionation such as SDS‐PAGE and 2D LC. It is easy to use and provides handy user interfaces for data loading, parameter setting, quantitative analysis, and quantitative data visualization. LFQuant was compared with two common quantification software packages, MaxQuant and IDEAL‐Q, on the replication data set and the UPS1 standard data set. The results show that LFQuant performs better than them in terms of both precision and accuracy, and consumes significantly less processing time. LFQuant is freely available under the GNU General Public License v3.0 at http://sourceforge.net/projects/lfquant/ .     

Functional exploratory data analysis for high‐resolution measurements of urban particulate matter

In this work we propose the use of functional data analysis (FDA) to deal with a very large dataset of atmospheric aerosol size distribution resolved in both space and time. Data come from a mobile measurement platform in the town of Perugia (Central Italy). An OPC (Optical Particle Counter) is integrated on a cabin of the Minimetrò, an urban transportation system, that moves along a monorail on a line transect of the town. The OPC takes a sample of air every six seconds and counts the number of particles of urban aerosols with a diameter between 0.28 m and 10 m and classifies such particles into 21 size bins according to their diameter. Here, we adopt a 2D functional data representation for each of the 21 spatiotemporal series. In fact, space is unidimensional since it is measured as the distance on the monorail from the base station of the Minimetrò. FDA allows for a reduction of the dimensionality of each dataset and accounts for the high space‐time resolution of the data. Functional cluster analysis is then performed to search for similarities among the 21 size channels in terms of their spatiotemporal pattern. Results provide a good classification of the 21 size bins into a relatively small number of groups (between three and four) according to the season of the year. Groups including coarser particles have more similar patterns, while those including finer particles show a more different behavior according to the period of the year. Such features are consistent with the physics of atmospheric aerosol and the highlighted patterns provide a very useful ground for prospective model‐based studies.     

A high‐throughput BAC end analysis protocol (BAC‐anchor) for profiling genome assembly and physical mapping

Traditional approaches for sequencing insertion ends of bacterial artificial chromosome (BAC) libraries are laborious and expensive, which are currently some of the bottlenecks limiting a better understanding of the genomic features of auto‐ or allopolyploid species. Here, we developed a highly efficient and low‐cost BAC end analysis protocol, named BAC‐anchor, to identify paired‐end reads containing large internal gaps. Our approach mainly focused on the identification of high‐throughput sequencing reads carrying restriction enzyme cutting sites and searching for large internal gaps based on the mapping locations of both ends of the reads. We sequenced and analysed eight libraries containing over 3 200 000 BAC end clones derived from the BAC library of the tetraploid potato cultivar C88 digested with two restriction enzymes, Cla I and Mlu I. About 25% of the BAC end reads carrying cutting sites generated a 60–100 kb internal gap in the potato DM reference genome, which was consistent with the mapping results of Sanger sequencing of the BAC end clones and indicated large differences between autotetraploid and haploid genotypes in potato. A total of 5341 Cla I‐ and 165 Mlu I‐derived unique reads were distributed on different chromosomes of the DM reference genome and could be used to establish a physical map of target regions and assemble the C88 genome. The reads that matched different chromosomes are especially significant for the further assembly of complex polyploid genomes. Our study provides an example of analysing high‐coverage BAC end libraries with low sequencing cost and is a resource for further genome sequencing studies.     

A new reconstruction of Sts 14 pelvis (Australopithecus africanus) from computed tomography and three-dimensional modeling techniques

The purpose of this study is to propose a new reconstruction of the australopithecine Sts 14 pelvis from original fossils. Digital models created from CT images allow us to perform mirroring operations, select valid regions after digital interposition, and reassemble parts. The key-element of the reconstruction is the sacroiliac joint, restored from right and left articular surfaces, which places of the pubic symphysis close to the sagittal plane. The complete pelvis is obtained by 3D model mirroring of hip-bone and sacrum. The present reconstruction of the Sts 14 pelvis is consistent with Schmid's (1983) [Folia Primatol. 40, 283-306, 1983] and Häusler and Schmid's A.L. 288-1 [J. Hum. Evol. 29, 363-383, 1995] pelvic reconstructions by illustrating a relatively platypelloid shape of the pelvic cavity and laterally inclined iliac blades. The pelvic morphology suggests that australopithecines had a less posteriorly tilted sacrum in erect posture than modern humans. As compared with Lovejoy's [Am. J. Phys. Anthropol. Suppl. 50, 460, 1979] A.L. 288-1 pelvic reconstruction, the less transversely flattened shape of the Sts 14 pelvic cavity led to obstetrical mechanics characterized as in humans by ante-ischiatic birth and a curved trajectory. We deduce a human-like movement of rotation and flexion of the fetal skull in the Sts 14 pelvic cavity.     

Use of computed tomography as a non‐invasive method for diagnosing cephenemyiosis in roe deer (Capreolus capreolus)

This study was conducted to assess the reliability of computed tomography (CT) for diagnosing bot fly infestations by Cephenemyia stimulator (Clark) (Diptera: Oestridae) in roe deer (Capreolus capreolus L.) (Artiodactyla: Cervidae). For this purpose, the heads of 30 animals were analysed, firstly by CT and then by necropsy, which was used as the reference standard method. The prevalence values obtained by both methods were identical; the prevalence of infestation was 40.0% overall, and was higher in males (45.5%) than in females (25.0%). These results highlight the usefulness of CT as an alternative or non‐invasive method for diagnosing cephenemyiosis in live‐captured roe deer and in hunting trophies or museum collections that cannot be destroyed or damaged.     

Synthesis and characterization of ethosomal contrast agents containing iodine for computed tomography (CT) imaging applications

As a first step in the development of novel liver-specific contrast agents using ethosomes for computed tomography (CT) imaging applications, we entrapped iodine within ethosomes, which are phospholipid vesicular carriers containing relatively high alcohol concentrations, synthesized using several types of alcohol, such as methanol, ethanol, and propanol. The iodine containing ethosomes that were prepared using methanol showed the smallest vesicle size (392?nm) and the highest CT density (1107 HU). The incorporation of cholesterol into the ethosomal contrast agents improved the stability of the ethosomes but made the vesicle size large. The ethosomal contrast agents were taken up well by macrophage cells and showed no cellular toxicity. The results demonstrated that ethosomes containing iodine, as prepared in this study, have potential as contrast agents for applications in CT imaging.     

X‐ray microtomography (micro‐CT): a reference technology for high‐resolution quantification of xylem embolism in trees

As current methods for measuring xylem embolism in trees are indirect and prone to artefacts, there is an ongoing controversy over the capacity of trees to resist or recover from embolism. The debate will not end until we get direct visualization of the vessel content. Here, we propose desktop X‐ray microtomography (micro‐CT) as a reference direct technique to quantify xylem embolism and thus validate more widespread measurements based upon either hydraulic or acoustic methods. We used desktop micro‐CT to measure embolism levels in dehydrated or centrifuged shoots of laurel – a long‐vesseled species thought to display daily cycles of embolism formation and refilling. Our direct observations demonstrate that this Mediterranean species is highly resistant to embolism and is not vulnerable to drought‐induced embolism in a normal range of xylem tensions. We therefore recommend that embolism studies in long‐vesseled species should be validated by direct methods such as micro‐CT to clear up any misunderstandings on their physiology.     

Scale diversity in bigeye tuna (Thunnus obesus): Fat‐filled trabecular scales made of cellular bone

Tunas of the genus Thunnus possess many morphological and physiological adaptations for their high‐performance epipelagic ecology. Although Thunnus anatomy has been studied, there are no quantitative studies on the structure of their scales. We investigated the scales of bigeye tuna (Thunnus obesus) from ten regions of the body using micro computed tomography (µCT)‐scanning and histology to quantitatively and qualitatively compare regional scale morphology. We found a diversity of scale sizes and shapes across the body of bigeye tuna and discriminant function analysis on variables derived from µCT‐data showed that scales across the body differ quantitatively in shape and size. We also report the discovery of a novel scale type in corselet, tail, and cheek regions. These modified scales are ossified shells supported by internal trabeculae, filled with fat, and possessing an internal blood supply. Histological analysis showed that the outer lamellar layers of these thickened scales are composed of cellular bone, unexpected for a perciform fish in which bone is typically acellular. In the fairing region of the anterior body, these fat‐filled scales are stacked in layers up to five scales deep, forming a thickened bony casing. Cheek scales also possess a fat‐filled internal trabecular structure, while most posterior body scales are more plate‐like and similar to typical teleost scales. While the function of these novel fat‐filled scales is unknown, we explore several possible hypotheses for their function.