3D Image Analysis Research Articles

Factors affecting progressive facial swelling immediately after orthognathic surgery: A retrospective cohort study

The aim of this study was to identify clinical factors associated with progressive facial swelling after orthognathic surgery. Patients diagnosed with jaw deformities and undergoing orthognathic surgery were retrospectively evaluated, and those with surgical site infection, Le Fort I osteotomy, or genioplasty only were excluded. Facial swelling volume was calculated by comparing facial volume preoperatively and three days postoperatively using 3D images and image analysis software (VECTRA H2). FXIII was measured within three days after surgery in only patients with unexplained postoperative bleeding or hematoma. The correlation between facial swelling volume and clinical factors was statistically analyzed. Facial swelling volume was examined in 78 patients. Univariate analysis showed a significant difference between facial swelling volume (mean = 41.6 cm3) and operation time (mean = 209.3 min, r = 0.283, p = 0.012), ΔHb level (mean = 1.18 g/dL, r = 0.235, p = 0.039), as well as decreased factor XIII activity (mean = 75.3%, p = 0.012). Multivariate analysis showed a significant difference between facial swelling volume and FXIII deficiency (standard error = 6.44, p = 0.031).Progressive facial swelling immediately after orthognathic surgery may be due to factor XIII deficiency.

The contribution of image processing in the evaluation of guided bone regeneration

One of the most ambitious goals of modern bone surgery is to predict the shape of the bone defect, monitor the progress of bone regeneration, and assess the quantity and quality of newly formed bone. Calcium phosphate biomaterials such as hydroxyapatite and tricalcium phosphate are commonly used as bone substitutes in maxillofacial and dental surgery. The objective of this work is to use cone-beam computed tomography (CBCT) and image processing to assess the spatial (architectural) layout, rate of bone generation and osseointegration of implanted commercial granules (PAH 40%, β-TCP 60%, size 0.5 to 1 mm) in the bone defect generated after tooth extraction. CBCT measurements were performed at 48 hours and 12 months. The analysis of 3D images and the application of appropriate morphological mathematical operations allowed us to evaluate the volume of the cavity to be filled, the volume occupied by the granules and the volume of porosity generated by the random stacking of the granules. The result shows that the bone generation rate reaches a value of 89% after one year of implantation. This study shows that by using 3D image processing techniques CBCT, the same results as classical anatomical and histological studies can be obtained.

Evaluating the feasibility of measuring planar area of Sclerophytum penghuense and Cladiella hartogi using 2D image analysis

Soft coral (Octocorallia: Alcyonacea) farming has been widely used to decrease the fishing pressure on wild populations harvested for use in the ornamental trade and studies related to natural products. With a soft and flexible body, only a few attempts have been made to quantify the growth rate, either in the field or in aquarium systems. In this study, the planar area measurement approach was applied and evaluated for its applicability to soft corals. All fragments of Sclerophytum penghuense and Cladiella hartogi were placed on individual tiles (10 × 10 cm) and randomly distributed in the mesocosm. Two treatments were applied: (1) finger touch treatment, and (2) air exposure for one minute to avoid the influence of morphological flexibility caused by the hydroskeleton before taking photographs underwater. Two independent tests were carried out including (1) applying two treatments before taking photographs for four sides (only for S. penghuense), and (2) comparing the planar area and linear measurement with its dry weight (for both species). Since the shape of C. hartogi is stable through time, the first test was not required for C. hartogi. The photographs were taken twice per day (11:00am and 8:00pm), and five pictures were taken for each side. The results showed that there was no significant difference between one and five pictures used (P > 0.05). Furthermore, taking photographs of two sides that are perpendicular to each other is recommended to provide sufficient statistical power. Meanwhile, the air treatment made the fragments less flexible during the photographing process which should be used in this standardized 2D image analysis. Our results also showed that planar area was strongly correlated (P < 0.001) with its dry weight (R2 = 0.929 for S. penghuense and R2 = 0.945 for C. hartogi). In addition, the air exposure treatment was consistently similar during both times (daytime and nighttime). Based on the results, we suggest this standardized 2D method to measure the growth of soft corals by measuring planar area changes through time.

Patient-derived lymphoma spheroids integrating immune tumor microenvironment as preclinical follicular lymphoma models for personalized medicine

BackgroundFollicular lymphoma (FL), the most common indolent non-Hodgkin’s Lymphoma, is a heterogeneous disease and a paradigm of the contribution of immune tumor microenvironment to disease onset, progression, and therapy resistance....

Impact of leptin deficiency on male tibia and vertebral body 3D bone architecture independent of changes in body weight.

Leptin an adipokine with potent effects on energy balance and body weight plays an important role in defining bone architecture in growing mammals. However, major changes in body weight can also influence morphology of trabecular and cortical bone. Therefore, we examined the impact of leptin deficiency on tibia and vertebral body 3D bone architecture independent of changes in body weight. Furthermore, advances in computational 3D image analysis suggest that average morphological values may mask regional specific differences in trabecular bone thickness. The study utilized leptin-deficient Ob/Ob mice (n = 8) weight-paired to C57BL/6 (C57) control mice (n = 8) which were split into either lean or obese groups for 24 ± 2 weeks. Whole tibias and L3 vertebrae were fixed before high resolution microcomputed tomography (μCT) scanning was performed. Leptin deficiency independent of body weight reduced tibia cortical bone volume, trabecular bone volume/tissue volume, number, and mineral density. Mean tibia trabecular thickness showed no significant differences between all groups; however, significant changes in trabecular thickness were found when analyzed by region. This study demonstrates that leptin deficiency significantly impacts tibia and vertebral body trabecular and cortical bone 3D architecture independent of changes in body weight.

Quantitative 3D characterization of chromite ore particles

The main techniques used to characterize raw materials are currently bulk or 2D. This is a consequence of the current lack of standardized and automated methods to characterize particulate materials in 3D. Here, we apply a workflow to characterize a crushed chromite ore with nine particle size classes below 1 mm using X-ray computed tomography. All data processing of all samples follows the same sequence of steps, which means that the analysis can be automated with limited user input as opposed to traditional 3D image processing methods that require user input specific to each particle size fraction. Results of chromite composition, particle size distribution and chromite liberation are obtained for individual particles and compared with the results from x-ray diffraction and 2D-based automated mineralogy. The results shows a consistent accuracy across all size classes down to 75 μm. For the larger particle sizes (>600 μm) the chromite liberation curves are more consistent than those obtained from 2D-based automated mineralogy, possibly due to the stereological bias of 2D sections. The particle size distributions is the property for which the 2D bias causes a larger divergence from 3D results across all particle sizes. In conclusion, the workflow is more automatable (thus, faster and cheaper) and less bias (thus, more accurate and standardisable) than other 3D image analysis methods. Additionally, it stands as complementary to established techniques for particle-based characterization, especially to measure particle properties that 2D-based methods may not measure representatively for larger particle sizes and when sampling is limited. Further testing of the workflow in progressively more complex materials is necessary, but its potential to transform the way mineral particulate materials are characterized is demonstrated.

CartoCell, a high-content pipeline for 3D image analysis, unveils cell morphology patterns in epithelia

Decades of research have not yet fully explained the mechanisms of epithelial self-organization and 3D packing. Single-cell analysis of large 3D epithelial libraries is crucial for understanding the assembly and function of whole tissues. Combining 3D epithelial imaging with advanced deep-learning segmentation methods is essential for enabling this high-content analysis. We introduce CartoCell, a deep-learning-based pipeline that uses small datasets to generate accurate labels for hundreds of whole 3D epithelial cysts. Our method detects the realistic morphology of epithelial cells and their contacts in the 3D structure of the tissue. CartoCell enables the quantification of geometric and packing features at the cellular level. Our single-cell cartography approach then maps the distribution of these features on 2D plots and 3D surface maps, revealing cell morphology patterns in epithelial cysts. Additionally, we show that CartoCell can be adapted to other types of epithelial tissues.

Retracted: Intelligent Garment Graphic Design System for Artificial Intelligence and 3D Image Analysis

Retracted: Intelligent Garment Graphic Design System for Artificial Intelligence and 3D Image Analysis

Unveiling the Impact of Cross-Linking Redox-Active Polymers on Their Electrochemical Behavior by 3D Imaging and Statistical Microstructure Analysis

Unveiling the Impact of Cross-Linking Redox-Active Polymers on Their Electrochemical Behavior by 3D Imaging and Statistical Microstructure Analysis

Heuristic Approach to Predict the Performance Degradation of a Solid Oxide Fuel Cell Cathode.

The present work aims to predict the degradation in the performance of a solid oxide fuel cell (SOFC) cathode owing to cation interdiffusion between the electrolyte and cathode and surface segregation. Cation migration in the (La0.60Sr0.40)0.95Co0.20Fe0.80O3-x (LSCF)-Gd0.10Ce0.90O1.95 (GDC) composite cathode is evaluated in relation to time up to 1000 h using scanning transmission electron microscopy (STEM)-energy-dispersive X-ray spectroscopy (EDXS). The resulting insulating phase formed within the GDC interlayer is quantified by means of the volume fraction using a two-dimensional (2D) image analysis technique. For the very first time, the amount of the insulating phase in the GDC interlayer is quantified, and the corresponding performance degradation of the LSCF cathode is predicted. Mathematical relationships are established for the estimation of degradation due to surface segregation of the cathode. The ohmic resistance between the cathode and the GDC interlayer/electrolyte interface and the polarization resistance of the cathode, characterized by electrochemical impedance spectroscopy (EIS), show an excellent match with the predicted results. The combined degradation analysis and modeling for the cathode lifetime prediction provide a systematic understanding of the time-dependent cation migration and segregation behavior.

PGC-1α-mediated angiogenesis prevents pulmonary hypertension in mice.

Pulmonary hypertension (PH) is a life-threatening disease characterized by a progressive narrowing of pulmonary arterioles. Although VEGF is highly expressed in lung of patients with PH and in animal PH models, the involvement of angiogenesis remains elusive. To clarify the pathophysiological function of angiogenesis in PH, we compared the angiogenic response in hypoxia (Hx) and SU5416 (a VEGFR2 inhibitor) plus Hx (SuHx) mouse PH models using 3D imaging. The 3D imaging analysis revealed an angiogenic response in the lung of the Hx-PH, but not of the severer SuHx-PH model. Selective VEGFR2 inhibition with cabozantinib plus Hx in mice also suppressed angiogenic response and exacerbated Hx-PH to the same extent as SuHx. Expression of endothelial proliferator-activated receptor γ coactivator 1α (PGC-1α) increased along with angiogenesis in lung of Hx-PH but not SuHx mice. In pulmonary endothelial cell-specific Ppargc1a-KO mice, the Hx-induced angiogenesis was suppressed, and PH was exacerbated along with increased oxidative stress, cellular senescence, and DNA damage. By contrast, treatment with baicalin, a flavonoid enhancing PGC-1α activity in endothelial cells, ameliorated Hx-PH with increased Vegfa expression and angiogenesis. Pulmonary endothelial PGC-1α-mediated angiogenesis is essential for adaptive responses to Hx and might represent a potential therapeutic target for PH.

Tissue clearing applications in memory engram research.

A memory engram is thought to be the physical substrate of the memory trace within the brain, which is generally depicted as a neuronal ensemble activated by learning to fire together during encoding and retrieval. It has been postulated that engram cell ensembles are functionally interconnected across multiple brain regions to store a single memory as an "engram complex", but visualizing this engram complex across the whole brain has for long been hindered by technical limitations. With the recent development of tissue clearing techniques, advanced light-sheet microscopy, and automated 3D image analysis, it has now become possible to generate a brain-wide map of engram cells and thereby to visualize the "engram complex". In this review, we first provide a comprehensive summary of brain-wide engram mapping studies to date. We then compile a guide on implementing the optimal tissue clearing technique for engram tagging approaches, paying particular attention to visualize engram reactivation as a critical mnemonic property, for which whole-brain multiplexed immunostaining becomes a challenging prerequisite. Finally, we highlight the potential of tissue clearing to simultaneously shed light on both the circuit connectivity and molecular underpinnings of engram cells in a single snapshot. In doing so, novel brain regions and circuits can be identified for subsequent functional manipulation, thus providing an opportunity to robustly examine the "engram complex" underlying memory storage.

Analysis and 3D Imaging of Multidimensional Complex THz Fields and 3D Diagnostics Using 3D Visualization via Light Field

We present a numerical platform for 3D imaging and general analysis of multidimensional complex THz fields. A special 3D visualization is obtained by converting electromagnetic (EM) radiation to a light field via the Wigner distribution function, which is known for discovering (revealing) hidden details. This allows for 3D diagnostics using the simple techniques of geometrical optics, which significantly facilitates the whole analysis. This simulation was applied to a complex field composed of complex beams emitted as ultra-narrow femtosecond pulses. A method was developed for the generation of phase–amplitude and spectral characteristics of complex multimode radiation in a free-electron laser (FEL) operating under various parameters. The tool was successful at diagnosing an early design of the transmission line (TL) of an innovative accelerator at the Schlesinger Family Center for Compact Accelerators, Radiation Sources, and Applications.

Multi-scale and multi-modal imaging study of mantle xenoliths and petrological implications

Abstract The accurate textural characterization of mantle xenoliths is one of the fundamental steps to understanding the main processes occurring in the upper mantle, such as sub-solidus recrystallization, magmatic crystallization, and metasomatism. Texture, composition, and mineralogy reflect the temperature, pressure, stress conditions, melting, and/or contamination events undergone before and during the entrapment in the host magma. For these reasons, characterizing the three-dimensional (3D) texture of silicate, oxide, sulfide, and glass phases has great importance in the study of mantle xenoliths. We performed a multi-scale and multi-modal 3D textural analysis based on X-ray computed microtomography (µ-CT) data of three mantle xenoliths from different geodynamic settings (i.e., mobile belt zone, pericraton, oceanic hotspot). The samples were selected to represent different, variably complex internal structures composed of grains of different phases, fractures, voids, and fluid inclusions of different sizes. We used an approach structured in increasing steps of spatial and contrast resolution, starting with in-house X-ray µ-CT imaging (spatial resolution from 30 µm down to 6.25 µm) and moving to high-resolution synchrotron X-ray µ-CT at the micrometer scale. We performed a 3D characterization of mantle xenoliths, comparing the results with the analysis of conventional 2D images (thin sections) obtained by optical microscopy and simulating the random sectioning of several thin sections to estimate the probability of correct modal classification. The 3D models allow the extraction of textural information that cannot be quantified solely from thin sections: spinel layering, distribution of silicic glass, and related vesicles. Moreover, high-density volumes identified as sulfides were detected in two xenoliths, showing no relation with the spinel layering in one case and a preferential concentration along fractures in the other. Given the variety of textures and mineral assemblages of mantle xenoliths worldwide, the results are used to suggest experimental and analytical protocols for the characterization of these materials.

Three-Dimensional Light Field Fundus Imaging: Automatic Determination of Diagnostically Relevant Optic Nerve Head Parameters.

Morphological changes to the optic nerve head (ONH) can be detected at the early stages of glaucoma. Three-dimensional imaging and analysis may aid in the diagnosis. Light field (LF) fundus cameras can generate three-dimensional (3D) images of optic disc topography from a single shot and are less susceptible to motion artifacts. Here, we introduce a processing method to determine diagnostically relevant ONH parameters automatically and present the results of a subject study performed to validate this method. The ONHs of 17 healthy subjects were examined and images were acquired with both an LF fundus camera and by optical coherence tomography (OCT). The LF data were analyzed with a novel algorithm and compared with the results of the OCT study. Depth information was reconstructed, and a model with radial basis functions was used for processing of the 3D point cloud and to provide a finite surface. The peripapillary rising and falling edges were evaluated to determine optic disc and cup contours and finally calculate the parameters. Nine of the 17 subjects exhibited prominent optic cups. The contours and ONH parameters determined by an analysis of LF 3D imaging largely agreed with the data obtained from OCT. The median disc areas, cup areas, and cup depths differed by 0.17mm², -0.04 mm², and -0.07 mm, respectively. The findings presented here suggest the possibility of using LF data to evaluate the ONH. LF data can be used to determine geometric parameters of the ONH and thus may be suitable for future use in glaucoma diagnostics.

An atlas of healthy and injured cell states and niches in the human kidney

Understanding kidney disease relies on defining the complexity of cell types and states, their associated molecular profiles and interactions within tissue neighbourhoods1. Here we applied multiple single-cell and single-nucleus assays (>400,000 nuclei or cells) and spatial imaging technologies to a broad spectrum of healthy reference kidneys (45 donors) and diseased kidneys (48 patients). This has provided a high-resolution cellular atlas of 51 main cell types, which include rare and previously undescribed cell populations. The multi-omic approach provides detailed transcriptomic profiles, regulatory factors and spatial localizations spanning the entire kidney. We also define 28 cellular states across nephron segments and interstitium that were altered in kidney injury, encompassing cycling, adaptive (successful or maladaptive repair), transitioning and degenerative states. Molecular signatures permitted the localization of these states within injury neighbourhoods using spatial transcriptomics, while large-scale 3D imaging analysis (around 1.2 million neighbourhoods) provided corresponding linkages to active immune responses. These analyses defined biological pathways that are relevant to injury time-course and niches, including signatures underlying epithelial repair that predicted maladaptive states associated with a decline in kidney function. This integrated multimodal spatial cell atlas of healthy and diseased human kidneys represents a comprehensive benchmark of cellular states, neighbourhoods, outcome-associated signatures and publicly available interactive visualizations.

Improvement of Plasterboard Properties by the Control of Polymethylhydrosiloxane Dosage, Stirring Time, and Drying Temperature Applied to the Calcium Sulfate Hemihydrate and Water Mixture.

Plasterboard is an important building material in the construction industry because it allows for quick installation of walls, partitions, and ceilings. Although a common material, knowledge about its performance related to modern polymers and fabrication conditions is still lacking. The present work analyzes how some manufacturing factors applied during the plaster board fabrication impact on some plasterboard properties, including water absorption, flexural strength, and thermal conductivity. The manufacturing variables evaluated are the dose (D) of polymethylhydrosiloxane (PMHS), the agitation time of the mixture (H), and the drying temperature of the plaster boards after setting (T). The results suggest that factors D, H, and T induce changes in the porosity and the morphological structure of the calcium sulfate dihydrate crystals formed. Performance is evaluated at two levels of each factor following a statistical method of factorial experimental design centered on a cube. Morphological changes in the crystals of the resulting boards were evaluated with scanning electron microscopy (SEM) and the IMAGEJ image analysis program. Porosity changes were evaluated with X-ray microcomputed tomography (XMT) and 3D image analysis tools. The length-to-width ratio of the crystals decreases as it goes from low PMHS dosage to high dosage, favoring a better compaction of the plasterboard under the right stirring time and drying temperature. In contrast, the porosity generated by the incorporation of PMHS increases when going from low-level to high-level conditions and affects the maximum size of the pores being generated, with a maximum value achieved at 0.6% dosage, 40 s, and 140 °C conditions. The presence of an optimal PMHS dosage value that is approximately 0.6-1.0% is evidenced. In fact, when comparing trails without and with PMHS addition, a 10% decrease in thermal conductivity is achieved at high H (60 s) and high T (150 °C) level conditions. Water absorption decreases by more than 90% when PMHS is added, mainly due to the hydrophobic action of the PMHS. Minimum water absorption levels can be obtained at high drying temperatures. Finally, the resistance to flexion is not affected by the addition of PMHS because apparently there are two opposing forces acting: on one hand is the decrease in the length-width ratio giving more compactness, and on the other hand is the generation of pores. The maximum resistance to flexion was found around a dosage of 0.6% PMHS. In conclusion, the results suggest that the addition of PMHS, the correct agitation time of the mixture, and the drying temperature reduce the water absorption and the thermal conductivity of the gypsum boards, with no significant changes in the flexural resistance.

Accuracy of digital workflow for placing orthodontic miniscrews using generic and licensed open systems. A 3d imaging analysis of non-native .stl files for guided protocols

BackgroundThis study aimed to assess the accuracy of digital workflow for guided insertion of miniscrews in the anterior palate using restorative implant dentistry software and licensed software for orthodontic applications.MethodsTwenty subjects (8 males, 12 females, mean age = 16.7 ± 2.1 years) were prospectively selected to receive guided insertion of bicortical palatal miniscrews. Virtual planning was performed using restorative implant dentistry software (Blue Sky Plan*, version 4.7) (group 1 = 10 subjects) and licensed orthodontic software (Dolphin Imaging Software, version 11.0) (group 2 = 10 subjects). A specific 3D Imaging technology was applied to permit the registration of the planned and achieved position of the miniscrews based on the superimposition of maxillary models. The angular deviation (accuracy error) between the planned and the achieved positions of the miniscrews were recorded. Independent Student’s test was used with statistical significance set at p value < 0.05.ResultsThe mean accuracy error recorded in group 1 was 7.15° ± 1.09 (right side) and 6.19 ± 0.80 (left side) while the mean error in group 2 was 6.74° ± 1.23 (right side) and 5.79 ± 0.95 (left side). No significant differences were recorded between the two groups (p > 0.05); instead, miniscrews placed on the right side were almost one degree higher than the left side (p < 0.05) in both groups.ConclusionsThe clinical accuracy error was similar when using generic and licensed orthodontic software for guided systems.

Effects of fragmentation on production at Peak mine Midlands, Zimbabwe

Over the years, the cost of production at Peak Mine Midlands, Zimbabwe, has been high due to oversized rock fragments. This led to increased mining costs far above what was planned by the mine. Initial investigations showed that valuable production hours were lost in trying to deal with the oversized rock fragments at the draw points. This study was conducted at Peak Mine Midlands, Zimbabwe, on 1210 level. The methods used to assess the effects of fragmentation on production at the mine included visual assessment, analysis of the drill and blasting costs of the production data, 2D image analysis, sieve analysis, time and motion studies, analysis of the explosive’s consumption, mining blasting trials and post-mine blast experiments. The results show that the current ring hole designs used in the sublevel open stopes at Peak Mine do not give optimal particle size distribution after the primary blasts as the sieve analyses show that 50% of the sizes of materials at the draw points are larger than 1,000 mm. While 4 secondary blasts were budgeted per shift to reduce the sizes of the boulders to sizes that will pass through the grizzly’s sieves, 7 secondary blasts were done per shift and this led to about 75% increase in the cost of explosives consumed by the mine. The results also show that 35.96 minutes of production time were lost on each secondary blast conducted. Four trial blasts conducted on different ring hole patterns show that ring #1 which has a burden of 1.2 m instead of 1.8 m in the other ring holes led to a significant reduction in drilling and blasting costs from USD $33.79 in trial #4 (the control case) to $28.80 in trial #1. The sieve analyses also show that the optimal fragment sizes from primary blasts are in the range of X = +200 mm and X = +300 mm. So, the designed ring hole patterns in the sublevel open stopes should produce particles with sizes in the range of  150 mm and  +350 mm from the primary blasts.

Characterization of deteriorated railway ballast morphological changes using 3D scanning and supervised machine learning data analytics

This study presents a method that utilizes 3D digital image processing and advanced data analytics to differentiate between fresh and used railway ballast materials. Railway ballast degrades over time, necessitating replacement with fresh material. However, fresh ballast may be scarce in some areas, and replacement costs have risen significantly. Recycling large aggregates from deteriorated ballast offers a solution to reduce track maintenance costs and greenhouse gas emissions, gaining popularity in track maintenance activities. Current ballast recycling practices, however, do not account for the morphological changes in the aggregates and their impact on the ballast’s mechanical behavior. A machine learning algorithm is trained to differentiate fresh and used ballast automatically. The study examines the morphological parameters of fresh and used ballast materials using 3D scanning and image analysis techniques. A machine learning algorithm was trained to automatically distinguish between fresh and used ballast. The results reveal that sphericity and convexity were crucial parameters for differentiating fresh and used ballast, with identified threshold values of 0.89 for convexity and 0.8 for sphericity. The insights from this study may assist the decision for ballast recycling, reducing the demand for fresh ballast while maintaining track performance.