Characterization of time-of-flight double-photon Compton imaging system by simulation

Double-photon emission computed tomography (DPECT) has been proposed to overcome the disadvantage of a low signal-to-background ratio for conventional Compton imaging. This method has shown significant image reconstruction capability in the 2D plane. However, its performance is unsatisfactory when the field of view is 3-dimensional (3D). To solve this problem, we propose application of the time-of-flight (TOF) technique to DPECT as an enhancement. In this research, we used a Geant4 simulation to demonstrate the effectiveness of TOF in large 3D volume image reconstruction.

Gradient biomimetic platforms for neurogenesis studies

There is a need for the development of new cellular therapies for the treatment of many diseases, with the central nervous system (CNS) currently an area of specific focus. Due to the complexity and delicacy of its biology, there is currently a limited understanding of neurogenesis and consequently a lack of reliable test platforms, resulting in several CNS based diseases having no cure. The ability to differentiate pluripotent stem cells into specific neuronal sub-types may enable scalable manufacture for clinical therapies, with a focus also on the purity and quality of the cell population. This focus is targeted towards an urgent need for the diseases that currently have no cure, e.g. Parkinson’s disease. Differentiation studies carried out using traditional 2D cell culture techniques are designed using biological signals and morphogens known to be important for neurogenesis in vivo. However, such studies are limited by their simplistic nature, including a general poor efficiency and reproducibility, high reagent costs and an inability to scale-up the process to a manufacture-wide design for clinical use. Biomimetic approaches to recapitulate a more in vivo-like environment are progressing rapidly within this field, with application of bio(chemical) gradients presented both as 2D surfaces and within a 3D volume. This review focusses on the development and application of these advanced extracellular environments particularly for the neural niche. We emphasise the progress that has been made specifically in the area of stem cell derived neuronal differentiation. Increasing developments in biomaterial approaches to manufacture stem cells will enable the improvement of differentiation protocols, enhancing the efficiency and repeatability of the process with a move towards up-scaling. Progress in this area brings these techniques closer to enabling the development of therapies for the clinic.

3D Visualization of Bamboo Node’s Vascular Bundle

The vascular bundle is an important structural unit that determines the growth and properties of bamboo. A high-resolution X-ray microtomography (μCT) was used to observe and reconstruct a three-dimensional (3D) morphometry model of the vascular bundle of the Qiongzhuea tumidinoda node due to its advantages of quick, nondestructive, and accurate testing of plant internal structure. The results showed that the morphology of vascular bundles varied significantly in the axial direction. In the cross-section, the number of axial vascular bundles reached a maximum at the lower end of the sheath scar, and the minimum of it was at the middle of the diaphragm. The frequency of axial vascular bundles decreased from the lower end of the node to the nodal ridge, and subsequently increased until the upper end of the bamboo node. The proportion of parenchyma, fibers, and conducting tissue was 65.7%, 30.5%, and 3.8%, respectively. The conducting tissues were intertwined to form a complex 3D network structure, with a connectivity of 94.77%. The conducting tissue with the largest volume accounted for 60.26% of the total volume of the conducting tissue. The 3D-distribution pattern of the conducting tissue of the node and that of the fibers were similar, but their thickness changed in the opposite pattern. This study revealed the 3D morphometry of the conducting tissue and fibers of the bamboo node, the reconstruction of the skeleton made the morphology more intuitive. Quantitative indicators such as the 3D volume, proportion, and connectivity of each type of tissue was obtained, the bamboo node was enlarged mainly caused by the particularly developed fibers. This work laid the foundation for a better understanding of the mechanical properties and water transportation of bamboo and revealed the mystery of bamboo node shedding of Q. tumidinoda.

Integrating Rock Typing Methods Including Empirical, Deterministic, Statistical, Probabilistic, Predictive Techniques and New Applications for Practical Reservoir Characterization

This paper discusses integrating common methods and applications for "Rock Typing" (also known as Petrophysical Rock Typing-PRT) including empirical, deterministic, statistical, probalistic and automatic/predictive approaches. Many industry asset teams apply one or more of these methods when creating static reservoir models, using dynamic reservoir simulations, completing petrophysical studies for saturation height models and determining reservoir volumetrics as part of reservoir characterization studies. Our intention is to provide guidance and important information on how and when to use the various methods, so people can make an informed selection. This discussion is important as many disciplines apply these PRT techniques without understanding the pros, cons and limitations of the different methods. An important tool is comparing PRT results from multiple methods. The topics and workflows that are covered focus on various PRT techniques and workflows. We will use case-studies to illustrate the key features and make important comparisons. Key results include comparing pros and cons, how to use and combine multiple PRT techniques and verify results. This paper includes these techniques and workflows;MICP, core analysis and pore throat calibration.Core-Log Integration focused on PRT analysis.Winland, Pittman, Aguilera and Hartmann et.al Gameboard methods.K-Phi ratio, Flow Zone Indicators and Rock Quality Index methods.Classic, Modified and Stratigraphic Lorenz methods.IPSOM and HRA Probabilistic methods.Case Study – Super Plot and Advanced Automatic PRT Method.Special Topics – Carbonate Methods, NMR and Single Well Vertical Line. Practical approaches based on case studies show how PRT analysis can be applied in mature fields to identify by-passed hydrocarbon zones and zones that have a high probability of producing water using open hole, cased hole and production logs. Traditional Rock Typing (PRT) analysis can be applied as a single well technique or as a multi-well method so operations teams can identify additional business opportunities (remedial workovers, infill drilling locations or exploitation targets) and compare reservoir performance with intrinsic rock properties. New applications and additional topics cover single, multiple well approaches and new emerging PRT techniques (including NMR well logs and machine learning). We recommend how to merge classic facies with PRT analysis for 3-D applications including populating a 3D volume.

Micro-CT image gallery visually presenting the effects of ocean warming and acidification on marine gastropod shells

Digitisation of specimens (e.g. zoological, botanical) can provide access to advanced morphological and anatomical information and promote new research opportunities. The micro-CT technology may support the development of "virtual museums" or "virtual laboratories" where digital 3D imaging data are shared widely and freely. There is currently a lack of universal standards concerning the publication and curation of micro-CT datasets. The aim of the current project was to create a virtual gallery with micro-CT scans of individuals of the marine gastropod Hexaplex trunculus, which were maintained under a combination of increased temperature and low pH conditions, thus simulating future climate change scenarios. The 3D volume-rendering models created were used to visualise the structure properties of the gastropods shells. Finally, the 3D analysis performed on the micro-CT scans was used to investigate potential changes in the shell properties of the gastropods. The derived micro-CT 3D images were annotated with detailed metadata and can be interactively displayed and manipulated using online tools through the micro-CT virtual laboratory, which was developed under the LifeWatchGreece Research Infrastructure for the dissemination of virtual image galleries collection supporting the principles of FAIR data.

3D Digital Imagery a Solution for the Teaching of Osteology: Example of the Thoracic cage

Osteology is a fundamental discipline, its classical teaching becomes difficult because of plethora of students and shortage of bony parts. It’s in this context that we have made, from 3D volume imaging, a modeling of the rib cage as a test using a software for post-treatment of CT images in order to propose a pedagogical tool for studying thorax’s skeletal and adding descriptions with the help of classical works. This was a prospective study involving 27 patients aged between 35 and 45 years. The scanners used were HITACHI ECLOS 16 cuts. Once the CT scan was selected, the DICOM data was transmitted to the post-processing console. The images were processed on the console "Aquarius Intuition Edition Version 4. 4. 7. 855113", for one patient we used Veiwer Osirix 10.6.8 Mac. All bones have been dynamically described thanks to the volume rendering. We thus obtained volumetric reconstructions of three-dimensional CT images of the different bone structures superimposed on those taught in classical anatomy practical work. We obtained a scenario of practical work in the form of a slide show that the teacher can use for works with or without model and even remotely. The virtual reality obtained with the 3D reconstructions of CT scans of the rib cage is a tool for self-learning of osteology for students but also a way for teachers to do practical work without having to use models, and even at a distance. KEY WORDS: 3D imaging, Teaching, Tomodensitometry, Osteology.

Predicting neurodevelopmental outcomes in fetuses with isolated mild ventriculomegaly

BackgroundFetal ventriculomegaly is the the most common intracranial abnormality detected antenatally. When ventriculomegaly is mild and the only, isolated, abnormality detected (isolated mild ventriculomegaly (IMVM)) the prognosis is generally considered to be good. We aim to determine if there are features on in utero MRI (iuMRI) that can identify fetuses with IMVM who have lower risks of abnormal neurodevelopment outcome.MethodsWe studied cases recruited into the MRI to enhance the diagnosis of fetal developmental brain abnormalities in utero (MERIDIAN) study, specifically those with: confirmed IMVM, 3D volume imaging of the fetal brain and neurodevelopmental outcomes at 3 years. We explored the influence of sex of the fetus, laterality of the ventriculomegaly and intracranial compartmental volumes in relation to neurodevelopmental outcome.FindingsForty-two fetuses met the criteria (33 male and 9 female). There was no obvious correlation between fetal sex and the risk of poor neurodevelopmental outcome. Unilateral IMVM was present in 23 fetuses and bilateral IMVM in 19 fetuses. All fetuses with unilateral IMVM had normal neurodevelopmental outcomes, while only 12/19 with bilateral IMVM had normal neurodevelopmental outcomes. There was no obvious correlation between measure of intracranial volumes and risk of abnormal developmental outcomes.InterpretationThe most important finding is the very high chance of a good neurodevelopmental outcome observed in fetuses with unilateral IMVM, which is a potentially important finding for antenatal counselling. There does not appear to be a link between the volume of the ventricular system or brain volume and the risk of poor neurodevelopmental outcome.

A Study on the Prediction of Reproductive Outcomes in Frozen Embryo Transfer Cycles by Calculating the Volume of Uterine Junctional Zone with Three-Dimensional Ultrasound

Purpose To prospectively study the influence of the volume of the uterine junctional zone (JZ) as a novel predictor of reproductive outcomes in frozen embryo transfer cycles. Methods Among the first 30 patients, intra- and interobserver repeatability was evaluated and expressed as a coefficient of repeatability. The same classification system was used to evaluate the JZ of 142 infertility patients undergoing in vitro fertilization (IVF). Ultrasonography was performed on the day before transplantation. The three-dimensional (3D) volume images were then analyzed to obtain the volume of the endometrium (EV), the average thickness of the JZ on the coronal plane, and the volume of the JZ (JZV). The JZV was then divided by the EV. These parameters were compared with the outcomes of clinical pregnancy. Results The 3D image showed that the JZ achieved a good intra- and interobserver consistency (k = 0.862, k = 0.694). The total pregnancy rate was 47%. There was a highly significant difference between pregnant and non-pregnant women with respect to age (p < 0.001), JZV (p = 0.003), and JZV/EV (p < 0.001) on the day before transplantation. Age and JZV/EV were independent factors for predicting the success of IVF transplantation (p = 0.010, p = 0.016). The area under the ROC curve of JZV/EV in predicting clinical pregnancy was 0.688, the cut-off value was 0.54, the sensitivity was 83.8%, and the specificity was 50.0%. Conclusion Age and JZV/EV are independent factors for predicting the success of frozen embryo transfer cycles in IVF. A smaller JZV/EV was more beneficial for clinical pregnancy.

Artefacts in Volume Data Generated with High Resolution Episcopic Microscopy (HREM)

High resolution episcopic microscopy (HREM) produces digital volume data by physically sectioning histologically processed specimens, while capturing images of the subsequently exposed block faces. Our study aims to systematically define the spectrum of typical artefacts inherent to HREM data and to research their effect on the interpretation of the phenotype of wildtype and mutant mouse embryos. A total of 607 (198 wildtypes, 409 mutants) HREM data sets of mouse embryos harvested at embryonic day (E) 14.5 were systematically and comprehensively examined. The specimens had been processed according to essentially identical protocols. Each data set comprised 2000 to 4000 single digital images. Voxel dimensions were 3 × 3 × 3 µm3. Using 3D volume models and virtual resections, we identified a number of characteristic artefacts and grouped them according to their most likely causality. Furthermore, we highlight those that affect the interpretation of embryo data and provide examples for artefacts mimicking tissue defects and structural pathologies. Our results aid in optimizing specimen preparation and data generation, are vital for the correct interpretation of HREM data and allow distinguishing tissue defects and pathologies from harmless artificial alterations. In particular, they enable correct diagnosis of pathologies in mouse embryos serving as models for deciphering the mechanisms of developmental disorders.

3D volume reconstruction of brain tissues using nonlinear filters, k-means clustering, and Bland-Altman analysis

This paper aims to provide a sound estimation of the true value and proportion of white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF) of the brain DTI images for a proper 3D volume reconstruction. During the pre-processing stage, two nonlinear filters are operated, i.e. bilateral and anisotropic diffusion. The segmentation of each brain tissue is performed using the k-means clustering algorithm. To minimize filters bias and for obtaining the best reproducible results, a statistical analysis has been performed. Thus, the skewness and kurtosis statistics features were computed for each segmented brain tissue and filter. The fuzzy k-means method allows for clustering analysis and the Bland-Altman analysis investigates the agreement between two filtering techniques of the same statistics feature and brain tissue. Then the 3D reconstruction method is presented using ImageJ and the image stacks for raw and processed data. We conclude that anisotropic diffusion filter offers the best results and 3D reconstruction of brain tissues is feasible.