Phase correlation applied to the 3D registration of CT and CBCT image volumes

PurposeIn this study, a 3D phase correlation algorithm was investigated to test feasibility for use in determining the anatomical changes that occur throughout a patient's radiotherapy treatment. The algorithm determines the transformations between two image volumes through analysis in the Fourier domain and has not previously been used in radiotherapy for 3D registration of CT and CBCT volumes.MethodsVarious known transformations were applied to a patient's prostate CT image volume to create 12 different test cases. The mean absolute error and standard deviation were determined by evaluating the difference between the known contours and those calculated from the registration process on a point-by-point basis. Similar evaluations were performed on images with increasing levels of noise added. The improvement in structure overlap offered by the algorithm in registering clinical CBCT to CT images was evaluated using the Dice Similarity Coefficient (DSC).ResultsA mean error of 2.35 (σ = 1.54) mm was calculated for the 12 deformations applied. When increasing levels of noise were introduced to the images, the mean errors were observed to rise up to a maximum increase of 1.77 mm. For CBCT to CT registration, maximum improvements in the DSC of 0.09 and 0.46 were observed for the bladder and rectum, respectively.ConclusionsThe Fourier-based 3D phase correlation registration algorithm investigated displayed promising results in CT to CT and CT to CBCT registration, offers potential in terms of efficiency and robustness to noise, and is suitable for use in radiotherapy for monitoring patient anatomy throughout treatment.     

A Method for the Evaluation of Image Quality According to the Recognition Effectiveness of Objects in the Optical Remote Sensing Image Using Machine Learning Algorithm

Objective and effective image quality assessment (IQA) is directly related to the application of optical remote sensing images (ORSI). In this study, a new IQA method of standardizing the target object recognition rate (ORR) is presented to reflect quality. First, several quality degradation treatments with high-resolution ORSIs are implemented to model the ORSIs obtained in different imaging conditions; then, a machine learning algorithm is adopted for recognition experiments on a chosen target object to obtain ORRs; finally, a comparison with commonly used IQA indicators was performed to reveal their applicability and limitations. The results showed that the ORR of the original ORSI was calculated to be up to 81.95%, whereas the ORR ratios of the quality-degraded images to the original images were 65.52%, 64.58%, 71.21%, and 73.11%. The results show that these data can more accurately reflect the advantages and disadvantages of different images in object identification and information extraction when compared with conventional digital image assessment indexes. By recognizing the difference in image quality from the application effect perspective, using a machine learning algorithm to extract regional gray scale features of typical objects in the image for analysis, and quantitatively assessing quality of ORSI according to the difference, this method provides a new approach for objective ORSI assessment.     

Prognostic Value of Tumor-Associated Macrophages According to Histologic Locations and Hormone Receptor Status in Breast Cancer

Tumor-associated macrophages (TAMs) are involved in tumor progression by promoting epithelial-mesenchymal transition (EMT), tumor cell invasion, migration and angiogenesis. However, in breast cancer, the clinical relevance of the TAM infiltration according to distinct histologic locations (intratumoral vs. stromal) and hormone receptor status is unclear. We investigated the significance of the levels of TAM infiltration in distinct histologic locations in invasive breast cancer. We also examined the relationship of the TAM levels with the clinicopathologic features of tumors, expression of EMT markers, and clinical outcomes. Finally, we analyzed the prognostic value of TAM levels according to hormone receptor status. High levels of infiltration of intratumoral, stromal and total TAMs were associated with high histologic grade, p53 overexpression, high Ki-67 proliferation index and negative hormone receptor status. Infiltration of TAMs was also correlated with overexpression of vimentin, smooth muscle actin and alteration of β-catenin. Overall, a high level of infiltration of intratumoral TAMs was associated with poor disease-free survival, and was found to be an independent prognostic factor. In subgroup analyses by hormone receptor status, a high level of infiltration of intratumoral TAM was an independent prognostic factor in the hormone receptor-positive subgroup, but not in the hormone-receptor negative subgroup. Our findings suggest that intratumoral TAMs play an important role in tumor progression in breast cancer, especially in the hormone receptor-positive group, and the level of TAM infiltration may be used as a prognostic factor and even a therapeutic target in breast cancer.     

Accuracy in Quantitative 3D Image Analysis

Quantitative 3D imaging is becoming an increasingly popular and powerful approach to investigate plant growth and development. With the increased use of 3D image analysis, standards to ensure the accuracy and reproducibility of these data are required. This commentary highlights how image acquisition and postprocessing can introduce artifacts into 3D image data and proposes steps to increase both the accuracy and reproducibility of these analyses. It is intended to aid researchers entering the field of 3D image processing of plant cells and tissues and to help general readers in understanding and evaluating such data.Advances in digital imaging have led to the generation of an increasing number of 3D data sets (Truernit et al., 2008; Fernandez et al., 2010; Kierzkowski et al., 2012; Roeder et al., 2012). Whole-mount and time-lapse imaging enable all cells in an organ to be analyzed in 3D over time, providing a comprehensive analysis of plant growth and development (Roeder et al., 2011).The generation of these 3D image data sets has led to the development of novel computational approaches to facilitate their analysis (Cunha et al., 2010; Kierzkowski et al., 2012; Bassel et al., 2014; Yoshida et al., 2014). With the development of these new methods comes a need for quality control and standard measures to ensure the accurate analysis of data sets. An overall objective of this approach is the accurate capture and quantification of the 3D geometry of biological objects. The inaccurate abstraction of shape data and introduction of artifacts during image acquisition and postprocessing must be kept to a minimum.Following imaging, typically using confocal microscopy, 3D objects can be identified through the process of segmentation (Roeder et al., 2012). This can be achieved using automatic seeding through a watershed approach or by inflating “balloons” with defined seeds in individual cells (Federici et al., 2012). Vertices and meshes that describe cell surfaces may then be generated using an algorithm such as marching cubes (Lorensen and Cline, 1987). Vertices at defined spacings can be placed on the surface of unique segments, and the surfaces describing these geometric shapes are represented by the triangles connecting adjacent vertices constituting a polygonal mesh.The mesh describing segment surfaces is ultimately what defines the shape of an object in question. Rough and irregular features are often represented by meshes owing to the imperfect nature of data collection from biological samples (Desbrun et al., 1999; Taubin, 2000). In the context of plant cells whose surfaces are naturally smooth, the segmentations and meshes describing them are in practice noisy and contain undesirable geometric irregularities. The lower the quality of the original image being segmented, the greater the irregularities in the mesh that describe the shape.In order to improve the quality of irregularly triangulated polygonal meshes, smoothing operations can be performed. In this way, the roughness of the surface can be reduced, improving the texture and representation of a segmented object.A straightforward and easy to implement operation to remove noise in 3D meshes is Laplacian smoothing (Field, 1988). This process repositions vertices to an average position (barycentre) along a mesh surface to create a smoothed effect. However, Laplacian smoothing has the side effect of slightly shrinking the object in question (Taubin, 2000). While this shrinkage effect is well documented among computer scientists who develop algorithms to modify polygonal meshes, it is perhaps less well understood and discussed by the end user biological community.Smoothing of meshes has the positive effect of making surfaces smoother and removing noise, while enhancing the visual aesthetic of segmented objects providing the appearance that their geometry has been captured accurately (Figures 1A and 1B). In cases where objects have been poorly segmented, the need to remove the jagged appearance of meshes is greater, and additional smoothing steps are often used. This repeated Laplacian smoothing leads to additional smoothing-induced shrinkage and greater abstraction of the object being analyzed. Given that the mesh itself is intended to represent the 3D geometry of an object in question, changing its overall size by smoothing represents a perturbation and manipulation of data that inaccurately reflects the quantitative capture of geometry. The need to remove rough edges in meshes due to noise needs to be balanced with the accuracy that the mesh represents an object in question.Open in a separate windowFigure 1.Effect of Laplacian Smoothing on the Cellular Structure of a 3D Segmented Arabidopsis Radicle.(A) Surface rendering of a mesh following generation using marching cubes with a cube size of 2 μm and no smoothing. Bar = 10 μm.(B) Same as (A) following one Laplacian smoothing pass. (C) Same as (A) following six smoothing passes. (D) Same as (A) following nine smoothing passes. (E) An original confocal stack showing cell walls in green and the multicolored segmented stack before generating the mesh using marching cubes. (F) Smoothing of the mesh in (A) using the Taubin λ/μ algorithm with λ = 0.5, μ = −0.53, and nine smoothing steps. An example of an unsmoothed mesh representing the cells of 3D segmented plant organ can in seen in Figure 1A. The rough edges and irregularities of this primary unsmoothed mesh, coming from a suboptimal noisy confocal image stack, do not accurately represent the surface of these plant cells. The mesh in Figure 1B, which has been smoothed once, appears to be a more accurate representation of cell shape than the unsmoothed mesh in Figure 1A and has not been shrunk dramatically.In the context of plant organ cellular segmentations, additional Laplacian smoothing steps create even smoother cells, but also exaggerated gaps between adjacent cells due to cell shrinkage (Figures 1C and 1D). These spaces do not reflect reality as adjacent cells are physically appressed against their cell walls, which are rarely more than several microns thick. This example demonstrates the abstraction of cell shape that can occur following multiple Laplacian smoothing steps, and the gaps between cells are a hallmark of data that have been postprocessed to the point of inaccuracy.Other factors can affect the response of 3D segmented cells to Laplacian smoothing. These include mesh triangle size, with larger triangles being more susceptible to shrinkage (Desbrun et al., 1999), and cell size, with smaller cells being more susceptible to smoothing-based shrinking than larger cells (Figure 1D).If the purpose of 3D segmentation is strictly qualitative, smoothing-based shrinkage may not present a problem. However, if quantitative analyses are applied to shrunken meshes, this will result in inaccurate data.     

Metabolic Discrimination of Catharanthus roseus Calli According to Their Relative Locations Using 1H-NMR and Principal Component Analysis

Creating a plant-cell suspension culture involves first transferring the callus into liquid media, but there are no objective criteria for selecting the location of the callus to be transferred. In this study, inner and outer cells of Catharanthus roseus with various elicitors in solid-state cultures were differentiated by ¹H NMR (nuclear magnetic resonance) spectrometry and principal component analysis (PCA). It was found that the samples of various elicitors and relative locations could be separated in PCA-derived score plots. Especially, there was a clear separation between nontreated samples and those cotreated with silver nitrate and methyl jasmonate. Loading-plot analysis was therefore applied to data obtained from nontreated samples and those cotreated with silver nitrate and methyl jasmonate to determine the separation of major metabolites on score plots. The levels of valine, lactic acid, threonine, alanine, arginine, acetic acid, malic acid, succinic acid, citric acid, asparagine, choline, lactose, fumaric acid, phenylalanine, tryptophan, and formic acid were higher in the inner callus than in the outer callus, whereas 2-oxoglutaric acid, oxalacetic acid, sucrose, and glucose dominated in the outer callus. The results obtained in this study suggest that inner and outer calli can be differentiated by ¹H-NMR-based metabolomic analysis.     

Infant Cardiac CT Angiography with 64-Slice and 256-Slice CT: Comparison of Radiation Dose and Image Quality Using a Pediatric Phantom

Background

The aims of this study were to investigate the image quality and radiation exposure of pediatric protocols for cardiac CT angiography (CTA) in infants under one year of age.

Methodology/Principal Findings

Cardiac CTA examinations were performed using an anthropomorphic phantom representing a 1-year-old child scanned with non-electrocardiogram-gated (NG), retrospectively electrocardiogram-gated helical (RGH) and prospectively electrocardiogram-gated axial (PGA) techniques in 64-slice and 256-slice CT scanners. The thermoluminescent dosimeters (TLD) were used for direct organ dose measurement, while dose-length product and effective mAs were also used to estimate the patient dose. For image quality, noise and signal-to-noise-ratio (SNR) were assessed based on regions-of-interest drawn on the reconstructed CT images, and were compared with the proposed cardiac image quantum index (CIQI). Estimated dose results were in accordant to the measured doses. The NG scan showed the best image quality in terms of noise and SNR. The PGA scan had better image quality than the RGH scan with 83.70% dose reduction. Noise and SNR were also corresponded to the proposed CIQI.

Conclusions/Significance

The PGA scan protocol was a good choice in balancing radiation exposure and image quality for infant cardiac CTA. We also suggested that the effective mAs and the CIQI were suitable in assessing the tradeoffs between radiation dose and image quality for cardiac CTA in infants. These results are useful for future implementation of dose reduction strategies in pediatric cardiac CTA protocols.     

Air Quality Monitoring of the Post-Operative Recovery Room and Locations Surrounding Operating Theaters in a Medical Center in Taiwan

To prevent surgical site infection (SSI), the airborne microbial concentration in operating theaters must be reduced. The air quality in operating theaters and nearby areas is also important to healthcare workers. Therefore, this study assessed air quality in the post-operative recovery room, locations surrounding the operating theater area, and operating theaters in a medical center. Temperature, relative humidity (RH), and carbon dioxide (CO₂), suspended particulate matter (PM), and bacterial concentrations were monitored weekly over one year. Measurement results reveal clear differences in air quality in different operating theater areas. The post-operative recovery room had significantly higher CO₂ and bacterial concentrations than other locations. Bacillus spp., Micrococcus spp., and Staphylococcus spp. bacteria often existed in the operating theater area. Furthermore, Acinetobacter spp. was the main pathogen in the post-operative recovery room (18%) and traumatic surgery room (8%). The mixed effect models reveal a strong correlation between number of people in a space and high CO₂ concentration after adjusting for sampling locations. In conclusion, air quality in the post-operative recovery room and operating theaters warrants attention, and merits long-term surveillance to protect both surgical patients and healthcare workers.     

Construction of a Preclinical Multimodality Phantom Using Tissue-mimicking Materials for Quality Assurance in Tumor Size Measurement

World Health Organization (WHO) and the Response Evaluation Criteria in Solid Tumors (RECIST) working groups advocated standardized criteria for radiologic assessment of solid tumors in response to anti-tumor drug therapy in the 1980s and 1990s, respectively. WHO criteria measure solid tumors in two-dimensions, whereas RECIST measurements use only one-dimension which is considered to be more reproducible ^{1, 2, 3,4,5}. These criteria have been widely used as the only imaging biomarker approved by the United States Food and Drug Administration (FDA) ⁶. In order to measure tumor response to anti-tumor drugs on images with accuracy, therefore, a robust quality assurance (QA) procedures and corresponding QA phantom are needed.To address this need, the authors constructed a preclinical multimodality (for ultrasound (US), computed tomography (CT) and magnetic resonance imaging (MRI)) phantom using tissue-mimicking (TM) materials based on the limited number of target lesions required by RECIST by revising a Gammex US commercial phantom ⁷. The Appendix in Lee et al. demonstrates the procedures of phantom fabrication ⁷. In this article, all protocols are introduced in a step-by-step fashion beginning with procedures for preparing the silicone molds for casting tumor-simulating test objects in the phantom, followed by preparation of TM materials for multimodality imaging, and finally construction of the preclinical multimodality QA phantom. The primary purpose of this paper is to provide the protocols to allow anyone interested in independently constructing a phantom for their own projects. QA procedures for tumor size measurement, and RECIST, WHO and volume measurement results of test objects made at multiple institutions using this QA phantom are shown in detail in Lee et al. ⁸.     

Characterization of the Light Environment in Canopies Using 3D Digitising and Image Processing

A method to measure light interception by vegetation canopiesis presented which uses a 3D digitiser and image processingsoftware. The 3D digitiser allows for simultaneous acquisitionof the spatial co-ordinates of leaf locations and orientations.Software for image synthesis is used to make virtual photographsof the real canopy. Information on light interception is derivedfrom the virtual images by using simple features of image analysissoftware. The method is applied to cotton, grapevine and youngmango plants. Calculations are made of light interception atthe canopy level, light partitioning between plant organs, verticalprofiles of light interception, fisheye photographs and leafirradiance distribution.Copyright 1998 Annals of Botany Company 3D digitising, image analysis, light interception,Gossypium hirsutumL.Vitis viniferaL.,Mangifera indicaL., cotton, grapevine, mango, canopy.     

Plasma 25-hydroxyvitamin D3 response to a pharmacological dose of vitamin D3 or 25-hydroxyvitamin D3 during chronic ethanol administration in the rat

Plasma 25-(OH)D3 concentrations following an intra-portal injection of 100 micrograms Kg-1 of D3 or 100 micrograms Kg-1 of 25-(OH)D3 was studied in D depleted rats fed ethanol diet and pair-fed controls. When challenged with D3, the rats under ethanol feeding were unable to increase their plasma 25(OH)D3 concentrations above those observed in controls. Plasma 25(OH)D3 concentrations following 25(OH)D3 administration were however lowered by the ethanol treatment 3 and 96 hr after 25(OH)D3 administration (p less than 0.05). These results suggest that animals chronically exposed to ethanol have an unaltered plasma 25(OH)D3 response following a pharmacological dose of D3 while the drug treatment contributes to an accelerated plasma 25(OH)D3 disappearance following 25(OH)D3.The former observations also suggest that D3 does not seem to be a high affinity substrate for the ethanol-induced cytochrome P-450.     

脑血管三维DSA影像的质量控制

目的:探讨脑血管三维DSA的质量控制措施,提高影像质量.方法:对67例影像质量较差的三维DSA图像,通过与旋转DSA图像的比对分析,确定影响脑血管三维DSA图像质量的因素.结果:脑血管三维DSA图像质量与头颅运动、三维模式的选择、延迟方式与时间、对比剂注入的速率与总量、连接管和导管内对比剂充盈状态、影像的后处理、扫描定位的准确性和设备定期调试较准有关.结论:要获得良好的三维DSA影像,需遵循质量控制措施多方面综合考虑.     

From 3D to 2D: a review of the molecular imprinting of proteins

Molecular imprinting is a generic technology that allows for the introduction of sites of specific molecular affinity into otherwise homogeneous polymeric matrices. Commonly this technique has been shown to be effective when targeting small molecules of molecular weight <1500, while extending the technique to larger molecules such as proteins has proven difficult. A number of key inherent problems in protein imprinting have been identified, including permanent entrapment, poor mass transfer, denaturation, and heterogeneity in binding pocket affinity, which have been addressed using a variety of approaches. This review focuses on protein imprinting in its various forms, ranging from conventional bulk techniques to novel thin film and monolayer surface imprinting approaches.     

Selenium dioxide oxidation of vitamin D3 acetate to a dimer of 1-oxotransvitamin D3 acetate

The treatment of vitamin D3 acetate with selenium dioxide and t-butyl hydroperoxide leads to a mixture from which a Diels-Alder dimer of 1-oxotransvitamin D3 acetate was isolated.     

Locations of a Human Satellite DNA in Human Chromosomes

USING techniques for DNA/RNA or DNA/DNA hybridization in situ, Pardue and Gall¹ and Jones² made several significant discoveries on the chromosomal locations of the mouse satellite DNA: (1) this fraction of DNA is found in all chromosomes except the Y, (2) the cytological location of the satellite DNA is limited to the centromeric region of each chromosome and is probably absent in other regions and (3) the centromeric regions of all mouse chromosomes are hetero-chromatic.     

Substrate Topography Induces a Crossover from 2D to 3D Behavior in Fibroblast Migration

In a three-dimensional environment, cells migrate through complex topographical features. Using microstructured substrates, we investigate the role of substrate topography in cell adhesion and migration. To do so, fibroblasts are plated on chemically identical substrates composed of microfabricated pillars. When the dimensions of the pillars (i.e., the diameter, length, and spacing) are varied, migrating cells encounter alternating flat and rough surfaces that depend on the spacing between the pillars. Consequently, we show that substrate topography affects cell shape and migration by modifying cell-to-substrate interactions. Cells on micropillar substrates exhibit more elongated and branched shapes with fewer actin stress fibers compared with cells on flat surfaces. By analyzing the migration paths in various environments, we observe different mechanisms of cell migration, including a persistent type of migration, that depend on the organization of the topographical features. These responses can be attributed to a spatial reorganization of the actin cytoskeleton due to physical constraints and a preferential formation of focal adhesions on the micropillars, with an increased lifetime compared to that observed on flat surfaces. By changing myosin II activity, we show that actomyosin contractility is essential in the cellular response to micron-scale topographic signals. Finally, the analysis of cell movements at the frontier between flat and micropillar substrates shows that cell transmigration through the micropillar substrates depends on the spacing between the pillars.     

Application of 2D and 3D NMR experiments to the conformational study of a diantennary oligosaccharide

Summary By the application of homonuclear 3D NOE-HOHAHA and heteronuclear 3D HMQC-NOE experiments in studies of complex oligosaccharides. NOEs can be investigated which are hidden in conventional 2D NOE spectra. In the 3D NOE-HOHAHA spectrum ₃ cross sections were considered to be the most suitable for assignment of NOEs. Alternatively, these cross sections could be measured separately in selective 2D HOHAHA-NOE spectroscopy. The advantages and limitations of the 2D alternative are compared with those of the 3D NOE-HOHAHA approach. In 3D HMQC-NOE spectroscopy the larger chemical shift displacement of the carbon spectrum with respect to the proton spectrum can be used to unmask NOEs hidden in the bulk region. If the extra proton dimension is not needed, 2D HMQC-NOE is a good alternative.The suitability of 2D and 3D NOE-HOHAHA and HMQC-NOE experiments for the estimation of proton-proton distances is demonstrated by comparing the results of these experiments on a diantennary asparagine-linked oligosaccharide with those of a conventional 2D NOE experiment. NOEs identified in the 2D and 3D NOE-HOHAHA as well as HMQC-NOE experiments, so far not identified or not quantified in 2D NOE experiments, are discussed in relation to each glycosidic linkage. The flexibility of the Man(1-3)Man linkage is demonstrated, confirming the existence of an ensemble of conformations for this linkage.