Biomimetic phantom with anatomical accuracy for evaluating brain volumetric measurements with magnetic resonance imaging

Purpose: Brain image volumetric measurements (BVM) methods have been used to quantify brain tissue volumes using magnetic resonance imaging (MRI) when investigating abnormalities. Although BVM methods are widely used, they need to be evaluated to quantify their reliability. Currently, the gold-standard reference to evaluate a BVM is usually manual labeling measurement. Manual volume labeling is a time-consuming and expensive task, but the confidence level ascribed to this method is not absolute. We describe and evaluate a biomimetic brain phantom as an alternative for the manual validation of BVM. Methods: We printed a three-dimensional (3D) brain mold using an MRI of a three-year-old boy diagnosed with Sturge-Weber syndrome. Then we prepared three different mixtures of styrene-ethylene/butylene-styrene gel and paraffin to mimic white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF). The mold was filled by these three mixtures with known volumes. We scanned the brain phantom using two MRI scanners, 1.5 and 3.0 Tesla. Our suggestion is a new challenging model to evaluate the BVM which includes the measured volumes of the phantom compartments and its MRI. We investigated the performance of an automatic BVM, i.e., the expectation–maximization (EM) method, to estimate its accuracy in BVM. Results: The automatic BVM results using the EM method showed a relative error (regarding the phantom volume) of 0.08, 0.03, and 0.13 (±0.03 uncertainty) percentages of the GM, CSF, and WM volume, respectively, which was in good agreement with the results reported using manual segmentation. Conclusions: The phantom can be a potential quantifier for a wide range of segmentation methods

Volumetric reconstruction and determination of minimum crosssectional area of the pharynx in patients with cleft lip and palate: comparison between two different softwares

Objective: The aim of this study was to assess the accuracy of volumetric reconstruction of the pharynx by comparing the volume and minimum crosssectional area (mCSA) determined with open-source applications (ITK-Snap, www.itksnap.org ; SlicerCMF) and commercial software (Dolphin3D, 11.8, Dolphin Imaging & Management Solutions, Chatsworth, CA, USA) previously validated in the literature. Material and Methods: The sample comprised of 35 cone-beam computed tomography (CBCT) scans of patients with unilateral cleft lip and palate, with mean age of 29±15. Three-dimensional volumetric models of the pharynx were reconstructed using semi-automatic segmentation using the applications ITK-Snap (G1) and Dolphin3D (G2). Volumes and minimum cross-sectional areas were determined. Inter- and intra-observer error were calculated using ICC test. Comparison between applications was calculated using the Wilcoxon test. Results: Volumes and minimum crosssectional area were statistically similar between applications. ITK-Snap showed higher pharynx volumes, but lower mCSA. Visual assessment showed that 62.86% matched the region of mCSA in Dolphin3D and SPHARM-PDM. Conclusion:Measurements of volume and mCSA are statistically similar between applications. Therefore, open-source applications may be a viable option to assess upper airway dimensions using CBCT exams

Three dimensional quantification of soil hydraulic properties using X-ray Computed Tomography and image based modelling

We demonstrate the application of a high-resolution X-ray Computed Tomography (CT) method to quantify water distribution in soil pores under successive reductive drying. We focus on the wet end of the water release characteristic (WRC) (0 to -75 kPa) to investigate changes in soil water distribution in contrasting soil textures (sand and clay) and structures (sieved and field structured), to determine the impact of soil structure on hydraulic behaviour. The 3D structure of each soil was obtained from the CT images (at a 10 µm resolution). Stokes equations for flow were solved computationally for each measured structure to estimate hydraulic conductivity. The simulated values obtained compared extremely well with the measured saturated hydraulic conductivity values. By considering different sample sizes we were able to identify that the smallest possible representative sample size which is required to determine a globally valid hydraulic conductivity

High-Frame-Rate Volumetric Porcine Renal Vasculature Imaging

Objective:The aim of this study was to assess the feasibility and imaging options of contrast-enhanced volumetric ultrasound kidney vasculature imaging in a porcine model using a prototype sparse spiral array. Methods: Transcutaneous freehand in vivo imaging of two healthy porcine kidneys was performed according to three protocols with different microbubble concentrations and transmission sequences. Combining high-frame-rate transmission sequences with our previously described spatial coherence beamformer, we determined the ability to produce detailed volumetric images of the vasculature. We also determined power, color and spectral Doppler, as well as super-resolved microvasculature in a volume. The results were compared against a clinical 2-D ultrasound machine. Results: Three-dimensional visualization of the kidney vasculature structure and blood flow was possible with our method. Good structural agreement was found between the visualized vasculature structure and the 2-D reference. Microvasculature patterns in the kidney cortex were visible with super-resolution processing. Blood flow velocity estimations were within a physiological range and pattern, also in agreement with the 2-D reference results. Conclusion:Volumetric imaging of the kidney vasculature was possible using a prototype sparse spiral array. Reliable structural and temporal information could be extracted from these imaging results.</p

Outcomes of Unilateral Alveolar Clefts Grafted Using Recombinant Human Bone Morphogenetic Protein-2: A Retrospective Volumetric Analysis Using CBCT

Purpose of this study is to evaluate the success rates of secondary alveolar grafts using recombinant human bone morphogenetic protein with CBCT and to evaluate the effects of several variables on these outcomes. After our inclusion/exclusion criteria, records of 24 patients receiving secondary alveolar grafts at the University of Nebraska Medical Center were evaluated. Pre-graft and 6-month post-graft cleft volumes were measured using ITK-SNAP 3.8.0 software to determine a percent residual defect following surgery. Of the 24 patients, one was excluded as the graft surgery was deemed a failure. The patients’ gender, age, side of cleft, cleft side canine root lengths, angulations, and distance from the occlusal plane were also measured. The mean volumetric values for the pre-graft and post-graft clefts were 1049.30mm3 and 413.75mm3, respectively with a mean residual defect value of 0.32 (SD = 0.22). The difference in percent residual defect following the graft was not statistically significant for any of the variables measured, except for gender (F=10.63; DF=1,21; p=0.0037). This study showed females undergoing secondary grafts of unilateral alveolar clefts have a lower percent residual defect six months following surgery. However, the results of this study may not represent clinical outcomes and larger sample sizes may be helpful to conclude statistically significant differences between our variables

Area and Length Minimizing Flows for Shape Segmentation

©1997 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or distribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder.Presented at the 1997 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, June 17-19, 1997, San Juan, Puerto Rico.DOI: 10.1109/CVPR.1997.609390Several active contour models have been proposed to unify the curve evolution framework with classical energy minimization techniques for segmentation, such as snakes. The essential idea is to evolve a curve (in 20) or a surface (in 30) under constraints from image forces so that it clings to features of interest in an intensity image. Recently the evolution equation has. been derived from first principles as the gradient flow that minimizes a modified length functional, tailored io features such as edges. However, because the flow may be slow to converge in practice, a constant (hyperbolic) term is added to keep the curve/surface moving in the desired direction. In this paper, we provide a justification for this term based on the gradient flow derived from a weighted area functional, with image dependent weighting factor. When combined with the earlier modified length gradient flow we obtain a pde which offers a number of advantages, as illustrated by several examples of shape segmentation on medical images. In many cases the weighted area flow may be used on its own, with significant computational savings

LV Volume Quantification via Spatiotemporal Analysis of Real-Time 3-D Echocardiography

This paper presents a method of four-dimensional (4-D) (3-D+Time) space-frequency analysis for directional denoising and enhancement of real-time three-dimensional (RT3D) ultrasound and quantitative measures in diagnostic cardiac ultrasound. Expansion of echocardiographic volumes is performed with complex exponential wavelet-like basis functions called brushlets. These functions offer good localization in time and frequency and decompose a signal into distinct patterns of oriented harmonics, which are invariant to intensity and contrast range. Deformable-model segmentation is carried out on denoised data after thresholding of transform coefficients. This process attenuates speckle noise while preserving cardiac structure location. The superiority of 4-D over 3-D analysis for decorrelating additive white noise and multiplicative speckle noise on a 4-D phantom volume expanding in time is demonstrated. Quantitative validation, computed for contours and volumes, is performed on in vitro balloon phantoms. Clinical applications of this spatiotemporal analysis tool are reported for six patient cases providing measures of left ventricular volumes and ejection fraction

Terabyte-scale supervised 3D training and benchmarking dataset of the mouse kidney

The performance of machine learning algorithms, when used for segmenting 3D biomedical images, does not reach the level expected based on results achieved with 2D photos. This may be explained by the comparative lack of high-volume, high-quality training datasets, which require state-of-the-art imaging facilities, domain experts for annotation and large computational and personal resources. The HR-Kidney dataset presented in this work bridges this gap by providing 1.7 TB of artefact-corrected synchrotron radiation-based X-ray phase-contrast microtomography images of whole mouse kidneys and validated segmentations of 33 729 glomeruli, which corresponds to a one to two orders of magnitude increase over currently available biomedical datasets. The image sets also contain the underlying raw data, threshold- and morphology-based semi-automatic segmentations of renal vasculature and uriniferous tubules, as well as true 3D manual annotations. We therewith provide a broad basis for the scientific community to build upon and expand in the fields of image processing, data augmentation and machine learning, in particular unsupervised and semi-supervised learning investigations, as well as transfer learning and generative adversarial networks