3D Analysis Research Articles

First person – Takayuki Miyaki

ABSTRACT First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping researchers promote themselves alongside their papers. Takayuki Miyaki is first author on ‘ Ultrastructural analysis of whole glomeruli using array tomography’, published in JCS. Takayuki is an Assistant professor in the lab of Koichiro Ichimura at Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo, Japan, investigating 3D ultrastructural analysis of cells and tissues, especially podocytes and glomeruli, using volume electron microscopy.

NanoPlex: a universal strategy for fluorescence microscopy multiplexing using nanobodies with erasable signals

Fluorescence microscopy has long been a transformative technique in biological sciences. Nevertheless, most implementations are limited to a few targets, which have been revealed using primary antibodies and fluorescently conjugated secondary antibodies. Super-resolution techniques such as Exchange-PAINT and, more recently, SUM-PAINT have increased multiplexing capabilities, but they require specialized equipment, software, and knowledge. To enable multiplexing for any imaging technique in any laboratory, we developed NanoPlex, a streamlined method based on conventional antibodies revealed by engineered secondary nanobodies that allow the selective removal of fluorescence signals. We develop three complementary signal removal strategies: OptoPlex (light-induced), EnzyPlex (enzymatic), and ChemiPlex (chemical). We showcase NanoPlex reaching 21 targets for 3D confocal analyses and 5–8 targets for dSTORM and STED super-resolution imaging. NanoPlex has the potential to revolutionize multi-target fluorescent imaging methods, potentially redefining the multiplexing capabilities of antibody-based assays.

A 3D finite element analysis of biomechanical effects on teeth and bone during true intrusion of anteriors using miniscrews

The primary objective of this study was to investigate the biomechanical effects and stresses on bone, periodontal ligament (PDL), cementum and displacement along X-, Y- and Z-axis during true intrusion of incisors using mini-implants with Finite Element Analysis; the secondary objective of the study was to find out the best method for anterior intrusion in clinical practice to treat anterior deep bite malocclusions. A 3D finite element method was used to simulate true anterior intrusion with sliding mechanics using mini-implants. Two groups were modelled with mini-implants placed distal to lateral incisors for Model1, and below the anteriornasalspine (ANS) for Model2, to achieve intrusion. von Mises stress, principal stress on PDL and alveolar bone, displacements in all 3 planes were determined. Amongst the modalities compared in the present study, the stresses on bone and PDL were showing best behavior for mini-implants placed distal to lateral incisors (Model1). The teeth showed controlled tooth movement in Model1. Maximum stress was found in the cortical bone and in the PDL. Nature of the stress changed from compressive to tensile from cervical area to root apex, concentrating mainly at the apical area. Amongst the modalities compared, the best controlled tooth movements for anterior intrusion to treat anterior deep bite malocclusions, was for mini-implants placed distal to lateral incisors (Model1).

Advancing Cartilage Tissue Engineering: A Review of 3D Bioprinting Approaches and Bioink Properties.

Articular cartilage is crucial in human physiology, and its degeneration poses a significant public health challenge. While recent advancements in 3D bioprinting and tissue engineering show promise for cartilage regeneration, there remains a gap between research findings and clinical application. This review critically examines the mechanical and biological properties of hyaline cartilage, along with current 3D manufacturing methods and analysis techniques. Moreover, we provide a quantitative synthesis of bioink properties used in cartilage tissue engineering. After screening 181 initial works, 33 studies using extrusion bioprinting were analyzed and synthesized, presenting results that indicate the main materials, cells, and methods utilized for mechanical and biological evaluation. Altogether, this review motivates the standardization of mechanical analyses and biomaterial assessments of 3D bioprinted constructs to clarify their chondrogenic potential.

Spiral volumetric optoacoustic tomography of reduced oxygen saturation in the spinal cord of M83 mouse model of Parkinson's disease.

Metabolism and bioenergetics in the central nervous system play important roles in the pathophysiology of Parkinson's disease (PD). Here, we employed a multimodal imaging approach to assess oxygenation changes in the spinal cord of the transgenic M83 murine model of PD overexpressing the mutated A53T alpha-synuclein form in comparison with non-transgenic littermates. In vivo spiral volumetric optoacoustic tomography (SVOT) was performed to assess oxygen saturation (sO2) in the spinal cords of M83 mice and non-transgenic littermates. Ex vivo high-field T1-weighted (T1w) magnetic resonance imaging (MRI) at 9.4T was used to assess volumetric alterations in the spinal cord. 3D SVOT analysis and deep learning-based automatic segmentation of T1w MRI data for the mouse spinal cord were developed for quantification. Immunostaining for phosphorylated alpha-synuclein (pS129 α-syn), as well as vascular organization (CD31 and GLUT1), was performed after MRI scan. In vivo SVOT imaging revealed a lower sO2SVOT in the spinal cord of M83 mice compared to non-transgenic littermates at sub-100μm spatial resolution. Ex vivo MRI-assisted by in-house developed deep learning-based automatic segmentation (validated by manual analysis) revealed no volumetric atrophy in the spinal cord of M83 mice compared to non-transgenic littermates at 50μm spatial resolution. The vascular network was not impaired in the spinal cord of M83 mice in the presence of pS129 α-syn accumulation. We developed tools for deep-learning-based analysis for the segmentation of mouse spinal cord structural MRI data, and volumetric analysis of sO2SVOT data. We demonstrated non-invasive high-resolution imaging of reduced sO2SVOT in the absence of volumetric structural changes in the spinal cord of PD M83 mouse model.

Three-dimensional Stereoscopic Evaluation and Quantitative Gray Scale Assessment of the Nasolabial Fold and Its Application in Injection Therapy

With the growing demand for aesthetic enhancements, particularly filler injections for nasolabial folds (NLFs), there is a need for more objective and quantitative assessment methods beyond the traditional subjective scales like the Wrinkle Severity Rating Scale (WSRS). This study introduces a novel evaluation method combining 3-dimensional (3D) imaging and grayscale analysis to objectively assess NLF severity and treatment outcomes. A total of 100 healthy participants (86 females, 14 males; mean age 41.85±11.53 years) were assessed using WSRS scores and quantitative 3D measurements. The results demonstrated a significant positive correlation between WSRS scores and gray values (r=0.985, P < 0.05). Significant differences in gray values and 3D linear measurements were observed across WSRS score groups, with high intra-rater reliability confirmed by intraclass correlation coefficients. In addition, 54 patients (mean age 42.9±8.9 y) with moderate to severe NLFs received hyaluronic acid injections. One month post-treatment, WSRS scores significantly decreased (from 3.74±0.45 to 1.63±0.59, P < 0.05), and significant improvements were observed in several 3D measurements. The average gray value also decreased significantly (P < 0.05), indicating a reduction in wrinkle depth. These findings were supported by representative photos showing patient satisfaction and no severe complications. This study validates the use of 3D imaging and grayscale analysis as reliable tools for objectively assessing NLF severity and monitoring treatment efficacy, potentially improving the precision and reliability of aesthetic evaluations in clinical practice.

Advanced monitoring of damage behavior and 3D visualization of fiber distribution in assessing crack resistance mechanisms in steel fiber-reinforced concrete

This study presents a novel approach to understanding the reinforcing mechanisms of steel fiber-reinforced concrete, particularly its crack resistance and toughening effects. By integrating dynamic surface strain monitoring with advanced three-dimensional visualization techniques, new insights are provided into how steel fibers enhance concrete's structural performance. X-ray computed tomography (CT) technology enabled detailed 3D visualization and analysis of steel fibers embedded within the concrete matrix, facilitating an in-depth examination of their distribution patterns, orientation, and positioning. Additionally, the Digital Image Correlation (DIC) three-dimensional full-field strain measurement system was utilized to dynamically monitor the loading process during three-point bending tests on semicircular concrete specimens. The findings indicate that the uniform distribution of steel fibers significantly reduces stress concentration and effectively delays crack initiation and propagation. Steel fibers bridge cracks, mitigate local stress concentrations, and substitute for the tensile components of concrete after macro-crack formation, thereby inhibiting further crack propagation. Quantitative analysis of fiber distribution through 3D image reconstruction and coordinate extraction confirmed a strong correlation between fiber orientation and crack resistance. This study contributes to the field by offering a comprehensive analysis of key parameters such as fracture process strain monitoring, 3D visualization, and quantification of fiber distribution, advancing the understanding of crack propagation mechanisms and failure processes in fiber-reinforced concrete.

A novel approach to assess internal pore structure and quantify tortuosity of clogged pervious concrete through image analysis techniques

ABSTRACT The major objective of this research was to develop an innovative approach to characterise the pore structure of pervious concrete (PC) mixtures and quantify tortuosity in pre- and post-clogged conditions through 2D and 3D image analysis. Four different types of PC mixtures were prepared and subjected to computed tomography (CT) scanning to retrieve morphological information covering over 1900 images, followed by tortuosity quantification of each of 200 interconnected pore paths using vascular modelling toolkit (VMTK). The porosity of PC obtained from laboratory-based tests was 10–25% lower than image analyses. Further, along the depth of PC, a significant decrease in the number of pores in the top 60–80 mm was observed due to clogging, which revealed that maintenance be adopted only in the top 80 mm. Control and clogged PC with smaller sized aggregates and lower w/c ratio were more tortuous compared to higher w/c ratio while opposite for larger sized aggregates, ascribed to the occurrence of shorter interconnected pore paths comprising larger pore diameter, remarking that permeability will depend on both tortuosity and path diameter. CT scanning was used in predicting tortuosity and pore interconnectivity of PC through VMTK approach extensively used in medical science and seldom used in engineering.

Evaluation of the urban heat island effect based on 3D modeling and planning indicators for urban planning proposals

ABSTRACT Urban planning plays an important role in the formation of urban space and microclimate. As a middle-level planning in the Chinese urban planning system, regulatory planning has a direct impact on the shaping of 3D urban space and can maximize the operability of urban planning. However, 3D space formation is not considered in the present preparation of regulatory plans, which leads to a misunderstanding of possibly formed 3D landscapes and microclimatic effects after the plan implementation. To support 3D visualization and quantitative analysis of the urban heat island effect (UHI) for regulatory planning, this study proposes a rule-based 3D modeling method to efficiently generate 3D models. The main elements of 3D models (terrain, building, road, vegetation, and land parcel) and their content were determined after analyzing the characteristics of 3D models in the regulatory plan. The 3D modeling process was constructed and combined with an UHI evaluation model through CGA programming. An index called heat island potential (HIP) was used as the UHI evaluation index and can be quantified using the correlation equations between planning indicators and HIP. The proposed method can support the planners to generate 3D models for a planning proposal, and simultaneously analyze 3D spatial effect and UHI.

Experimental and 3D numerical analysis of embankment on soft soil improved with cement bottom ash columns

Experimental and 3D numerical analysis of embankment on soft soil improved with cement bottom ash columns

Evaluating Laser‐Based Microfabrication in Microfluidics: An Experimental and Computational Trial

The aim of this research is to validate a new prototyping method for microfluidic devices which could compete with the widely used polydimethylsiloxane soft lithography. This alternative methodology uses laser‐etched glass and pre‐cured silicone as main materials. A dual approach is chosen for validation, testing prototypes of a mixing device well known in the scientific literature. Specifically the focus is to evaluate the mixing efficiency (ME) of two fluids flowing through the device. After fine‐tuning the fabrication process, the ME is experimentally evaluated, and the results are compared with a 3D computational fluid dynamic analysis.

ITER full model in MCNP for radiation safety demonstration

The development of nuclear fusion as a safe and virtually limitless power source is receiving growing attention in the context of looming energy crisis and climate change. ITER project stands as the flagship international initiative and is advancing steadily. The construction of the Tokamak Complex is nearly finished, and the assembly of core components has begun on site. Simultaneously, the design is being finalized, and the safety case is becoming more concrete. Current approaches to radiation safety demonstration using 3D nuclear analysis with the Monte Carlo code MCNP require sophisticated artifacts to sew together simulations in separate models for the Tokamak and the rest of the facility. This results in cumbersome studies and, consequently, challengeable conclusions. To address this issue, we have built the an integral MCNP model of the ITER facility: the ITER full model. Along with improvements to the D1SUNED code, we illustrate its computational practicality and pertinence in two meaningful simulations for ITER safety case. This work represents the culmination of a two-decade-long effort of ITER modelling aiming to demonstrate adequate radiation safety. Beyond supporting the remaining design tasks, this model simplifies the corresponding 3D nuclear analysis and improves the robustness of the ITER safety case.

UWB distance estimation errors in (non-)line of sight situations within the context of 3D analysis of human movement

Abstract Integrated Ultrawideband (UWB) and Magnetic Inertial Measurement Unit (MIMU) sensors are becoming popular for indoor localization applications, as a higher accuracy can be achieved than with just MIMU sensors. These integrated sensors could extend stability and accuracy in the field of 3D analysis of human movement (3D AHM) if they can deliver position estimates with an accuracy close to 1 cm. Achieving this high accuracy of 1 cm remains challenging, with most studies reporting position estimation errors around 5 cm, often due to Non-Line of Sight (NLOS) conditions and systematic UWB sensor distance estimation errors. Studying the distance error characteristic of UWB in situations of 3D AHM is essential to deal with these errors. While research on UWB distance errors in Line of Sight (LOS) and NLOS situations exists, few studies focus on the NLOS errors caused by the human body and were not in the relevant scenarios of 3D AHM. Therefore, this article examines UWB sensor performance and distance error characteristics in LOS and NLOS situations typical for the 3D AHM. Both the LOS and NLOS situations were studied in the typical 3D AHM distance range of 0.2 m to 2 m. The NLOS situations were studied first with a human subject as NLOS causing object and then with simulated human body segments (PVC pipes filled with water) of varying diameters. In LOS situations, consistent systematic bias errors were observed, along with incidental errors at specific positions in the room. In NLOS scenarios caused by the human and simulated body segments, a consistent and reproducible overestimation of distances was found. The reproducibility of these errors based on relative node and object positions suggests that systematic mitigation methods could significantly reduce errors, enabling more accurate and reproducible 3D human movement analysis.

Investigation of Surge Phenomena in a Centrifugal Compressor by 3D-1D Coupling Approach

Abstract Critical instability, such as surge phenomena, can occur at low flow rates for a compressor system, leading to flow rate fluctuations and potential damage. To study this, traditional numerical analysis requires a comprehensive approach encompassing the compressor and its piping system. This demands extensive computational resources and time due to the complexity of capturing internal flow during surge, including separation and vortex generation. To overcome these limitations, this research proposes a computational strategy combining 3D and 1D analysis for enhanced efficiency and reduced computational demands, which employs 1D analysis for more straightforward flow regions like piping and 3D analysis for the more complex compressor section. This approach is facilitated using AMESim for 1D and STAR-CCM+ for 3D simulations, enabling seamless integration and data exchange between different dimensional analyses. The method improves computational efficiency and reasonably approximates surge phenomena compared to experimental data. The 3D and 1D coupled analysis closely aligns with experimental data, providing a viable and more effective alternative method for surge analysis in compressor systems. This methodology promises to streamline the study of compressor surge phenomena, providing a practical tool for engineers and researchers.

Three-dimensional Analysis of Skeletal Stability in Cleft Lip and Palate Patients Undergoing Bimaxillary Surgery With Le Fort I Osteotomy and Intraoral Vertical Ramus Osteotomy.

Orthognathic surgery in patients with lip and palate clefts is challenging owing to scar tissue from primary repairs and severe deformities. In this study, we evaluated the stability of Le Fort I osteotomy with intraoral vertical ramus osteotomy (IVRO) in patients with cleft lip and palate using 3-dimensional (3D) analysis. This retrospective study comprised 14 cleft lip and palate patients (3 females, 11 males; the average age at surgery: 23.8y) who underwent bimaxillary orthognathic surgery involving Lefort I osteotomy and IVRO. Cone-beam computed tomography (CBCT) images were obtained at preoperative (T0), 1-month postoperative (T1), and 1-year follow-up (T2) periods. The 3D analysis assessed the transitions and rotations of the maxilla and mandible using a virtual triangle. The maxilla showed stability in all directions at the 1-year follow-up with minimal relapse. The distal segment of the mandible exhibited clinically acceptable anterior (1.15mm relapse) movements and pitch rotation (2.88° counterclockwise relapse) during the first year postoperatively. The proximal mandibular segment underwent anterior-inferior transition (1.21 and 2.01mm, respectively) and lateral-outward rotation (4.90° and 7.51°, respectively) postsurgery, remaining unchanged 1 year postoperation. Le Fort I osteotomy with IVRO provides skeletal stability in patients with cleft lips and palates. This study demonstrated a minimal maxillary relapse and clinically acceptable movements in the distal mandibular segment during the first postoperative year. The proximal mandibular segment moved anteriorly and inferiorly, rotated laterally and outward after surgery, and remained unchanged at the 1-year follow-up.

Three-dimensional Analysis of Presurgical Nasoalveolar Molding Outcomes in Patients with Unilateral Cleft Lip and Palate: A Preliminary Study Using LED Surface Scanning Technology.

ObjectivesPresurgical infant orthopedic appliances, such as presurgical nasoalveolar molding (PNAM) devices, are used to attain optimal conditions for primary repair of the lip and nose (PRoLN) in patients with cleft lip. We aimed to analyze the three-dimensional (3D) outcomes of PNAM using an LED surface scanner. MethodsFifteen patients with unilateral cleft lip and palate (CLP) were included in this study and treated using a PNAM device. The patients’ faces were digitized pre- and post-PNAM using an Artec Space Spider scanner, and the scanned data were analyzed using 3D software (Geomagic Control X and ANSYS SpaceClaim). The columellar angle (CA), nostril curvature (NC) on the affected (NC_A) and unaffected (NC_U) sides, gap of cleft lip (GCL), alar width (AW), and nasal tip angle (NTA) were measured. ResultsCA increased significantly by 10.00° and NC_A by 0.030 mm-1 (p<0.001). GCL decreased by 4.98 mm2 on average and NC_U by 0.015 mm-1 (p=0.029 and 0.046, respectively). AW also decreased by approximately 1.22 mm pre- and post-treatment (p=0.002), and NTA, which shows a lateral profile, decreased by approximately 3.32° (p=0.002). ConclusionsThis study confirmed the orthopedic benefits of PNAMd treatment through 3D analysis using an LED surface scanner. Further studies involving a larger number of participants are warranted to study the effects of PNAM and analyze longitudinal changes in patients with CLP. Clinical SignificanceThis study shows that PNAM effectively corrects columellar deviation and nostril shape in patients with unilateral cleft lip, with 3D scanners enhancing primary lip and nose repair outcomes.

Loss of right ventricular outflow function in pulmonary hypertension

Right ventricular outflow tract (RVOT) function is not systematically quantified by three-dimensional (3D) echocardiography. We tested the hypothesis that loss of RVOT function in pulmonary hypertension (PH) is related to disease severity independently of other echocardiographic parameters. In this observational study, patients with PH, disease controls, and a matched healthy control group underwent 3D echocardiography and RVOT analysis using ReVISION software. The study included 43 patients (38 with PH, 5 disease controls) and 43 healthy controls. Median 3D RVOT ejection fraction (EF) was 30.4% in the patients and 44.2% in the healthy controls (p < 0.001). Patients with low 3D RVOT-EF (<30.4%) were more frequently categorized in higher risk groups and had a higher incidence of clinical worsening than those with high 3D RVOT-EF. Even in patients with RV-EF ≥35%, those with low 3D RVOT-EF had worse outcomes. Segmental RVOT analysis identifies high-risk patients even with normal overall RV function.

Peri-implant stress distribution in maxillary All-on-4 prosthesis fabricated on multi-unit angled abutment with cobalt chromium framework versus those with titanium framework: A 3D Finite Element Analysis

Peri-implant stress distribution in maxillary All-on-4 prosthesis fabricated on multi-unit angled abutment with cobalt chromium framework versus those with titanium framework: A 3D Finite Element Analysis

Peri-implant stress distribution in mandibular All-on-4 prostheses fabricated on multi-unit abutments with cobalt chromium framework versus those with zirconia framework: A 3D Finite Element Analysis

Peri-implant stress distribution in mandibular All-on-4 prostheses fabricated on multi-unit abutments with cobalt chromium framework versus those with zirconia framework: A 3D Finite Element Analysis

Contribution of the Cygnus Bubble to the Galactic Cosmic Ray Spectrum and Diffuse γ-Ray Emissions

Since the discovery of cosmic rays (CRs) over a century ago, their origin has remained a mystery and a key research question. Recently, the LHAASO experiment identified the first CR superacceleration source, the Cygnus bubble, which can accelerate CRs to energies exceeding 10 PeV. A pertinent question is how much the Cygnus bubble contributes to the CR spectrum observed on Earth. With the aim of answering that question, a 3D propagation analysis was conducted on CRs in this study. The Cygnus bubble was incorporated into our propagation model in order to determine its contributions to the observed spectra. First, we calculated the spectrum and spatial morphology of the Cygnus bubble to reproduce the observed LHAASO data. Subsequently, we calculated the diffuse γ-ray emissions produced by the CRs from the Cygnus bubble and the energy spectrum of the CR particles near Earth after propagation. Finally, we utilized a CR spatial-dependent propagation model to calculate the large-scale CR energy spectrum and the resulting diffuse γ-ray emissions. Our results indicate that (1) the Cygnus bubble contributes minimally to the CR spectrum observed on Earth, (2) the emissions produced by the CR particles from the Cygnus bubble dominate the diffuse γ-ray emissions in that region, and (3) the structural fluctuations of the diffuse γ-ray emissions observed by LHAASO are likely due to the local CR halo. We anticipate that LHAASO will identify more CR halo sources to validate our model.