Three-dimensional Spatial Mapping Research Articles

Bioorthogonal chemical labeling of endogenous neurotransmitter receptors in living mouse brains

Neurotransmitter receptors are essential components of synapses for communication between neurons in the brain. Because the spatiotemporal expression profiles and dynamics of neurotransmitter receptors involved in many functions are delicately governed in the brain, in vivo research tools with high spatiotemporal resolution for receptors in intact brains are highly desirable. Covalent labeling by chemical reaction (chemical labeling) of proteins without genetic manipulation is now a powerful method for analyzing receptors in vitro. However, selective target receptor labeling in the brain has not yet been achieved. This study shows that ligand-directed alkoxyacylimidazole (LDAI) chemistry can be used to selectively tether synthetic probes to target endogenous receptors in living mouse brains. The reactive LDAI reagents with negative charges were found to diffuse well over the whole brain and could selectively label target endogenous receptors, including AMPAR, NMDAR, mGlu1, and GABAAR. This simple and robust labeling protocol was then used for various applications: three-dimensional spatial mapping of endogenous receptors in the brains of healthy and disease-model mice; multi-color receptor imaging; and pulse-chase analysis of the receptor dynamics in postnatal mouse brains. Here, results demonstrated that bioorthogonal receptor modification in living animal brains may provide innovative molecular tools that contribute to the in-depth understanding of complicated brain functions.

Classification and spectrum optimization method of grease based on infrared spectrum

AbstractThe infrared (IR) absorption spectral data of 63 kinds of lubricating greases containing six different types of thickeners were obtained using the IR spectroscopy. The Kohonen neural network algorithm was used to identify the type of the lubricating grease. The results show that this machine learning method can effectively eliminate the interference fringes in the IR spectrum, and complete the feature selection and dimensionality reduction of the high-dimensional spectral data. The 63 kinds of greases exhibit spatial clustering under certain IR spectrum recognition spectral bands, which are linked to characteristic peaks of lubricating greases and improve the recognition accuracy of these greases. The model achieved recognition accuracy of 100.00%, 96.08%, 94.87%, 100.00%, and 87.50% for polyurea grease, calcium sulfonate composite grease, aluminum (Al)-based grease, bentonite grease, and lithium-based grease, respectively. Based on the different IR absorption spectrum bands produced by each kind of lubricating grease, the three-dimensional spatial distribution map of the lubricating grease drawn also verifies the accuracy of classification while recognizing the accuracy. This paper demonstrates fast recognition speed and high accuracy, proving that the Kohonen neural network algorithm has an efficient recognition ability for identifying the types of the lubricating grease.

Three-dimensional spatial mapping of the human hematopoietic microenvironment in healthy and diseased bone marrow.

The bone marrow hematopoietic microenvironment (HME) plays a pivotal role in regulating normal and diseased hematopoiesis. However, the spatial organization of the human HME has not been thoroughly investigated yet. Therefore, we developed a three-dimensional (3D) immunofluorescence model to analyze changes in the cellular architecture in control and diseased bone marrows (BMs). BM biopsies from patients with myeloproliferative neoplasms (MPNs) were stained sequentially for CD31, CD34, CD45, and CD271 with repetitive bleaching steps to realize five color images with DAPI as a nuclear stain. Hematopoietically normal age-matched BM biopsies served as controls. Twelve subsequent slides per sample were stacked to create three-dimensional bone marrow reconstructions with the imaging program Arivis Visions 4D. Iso-surfaces for niche cells and structures were created and exported as mesh objects for spatial distribution analysis in the 3D creation suite Blender. We recapitulated the bone marrow architecture using this approach and produced comprehensive 3D models of endosteal and perivascular BM niches. MPN bone marrows displayed apparent differences compared to the controls, especially concerning CD271 staining density, megakaryocyte (MK) morphology, and distribution. Furthermore, measurements of the spatial relationships of MKs and hematopoietic stem and progenitor cells with vessels and bone structures in their corresponding niche environments revealed the most pronounced differences in the vascular nice in polycythemia vera. Taken together, using a repetitive staining and bleaching approach allowed us to establish a 5-color analysis of human BM biopsies, which is difficult to achieve with conventional staining approaches. Based on this, we generated 3D BM models which recapitulated key pathological features and, importantly, allowed us to define the spatial relationships between different bone marrow cell types. We, therefore, believe that our method can provide new and valuable insights into bone marrow cellular interaction research.

Spatial clustering analysis of scarlet fever incidence in China from 2016 to 2020

To investigate the incidence trend and spatial clustering characteristics of scarlet fever in China from 2016 to 2020 to provide evidence for development of regional disease prevention and control strategies. The incidence data of scarlet fever in 31 provinces and municipalities in mainland China from 2016 to 2020 were obtained from the Chinese Health Statistics Yearbook and the Public Health Science Data Center led by the Chinese Center for Disease Control and Prevention.The three-dimensional spatial trend map of scarlet fever incidence in China was drawn using ArcGIS to determine the regional trend of scarlet fever incidence.GeoDa spatial autocorrelation analysis was used to explore the spatial aggregation of scarlet fever in China in recent years. From 2016 to 2020, a total of 310 816 cases of scarlet fever were reported in 31 provinces, municipalities directly under the central government and autonomous regions, with an average annual incidence of 4.48/100 000.The reported incidence decreased from 4.32/100 000 in 2016 to 1.18/100 000 in 2020(Z=103.47, P < 0.001).The incidence of scarlet fever in China showed an obvious regional clustering from 2016 to 2019(Moran's I>0, P < 0.05), but was randomly distributed in 2020(Moran's I>0, P=0.16).The incidence of scarlet fever showed a U-shaped distribution in eastern and western regions of China, and increased gradually from the southern to northern regions.Inner Mongolia Autonomous Region and Hebei and Gansu provinces had the High-high (H-H) clusters of scarlet fever in China. Scarlet fever still has a high incidence in China with an obvious spatial clustering.For the northern regions of China with H-H clusters of scarlet fever, the allocation of health resources and public health education dynamics should be strengthened, and local scarlet fever prevention and control policies should be made to contain the hotspots of scarlet fever.

CT-Loc: Cross-domain visual localization with a channel-wise transformer

We tackle the cross-domain visual localization problem of estimating camera position and orientation from real images without three-dimensional (3D) spatial mapping or modeling. Recent studies have shown suboptimal performance in this task owing to the photometric and geometric differences between synthetic and real images. In this study, we present a deep learning approach that uses a channel-wise transformer localization (CT-Loc) framework. Inspired by the human behavior of looking for structural landmarks to estimate one’s location, CT-Loc encodes the most salient features of task-relevant objects in target scenes. To evaluate the efficacy of the proposed method in a real-world application, we built a complex and large-scale dataset of the interior of the mechanical room during operations and conducted extensive performance comparisons with the publicly available state-of-the-art University of Melbourne Corridor and Virtual KITTI 2 datasets. Compared with the otherwise best-performing BIM-PoseNet indoor camera localization model, our method significantly reduces position and orientation errors through the application of attention weights and saliency maps while also learning only the visual structural patterns (e.g., floors and doors) that are most relevant to localization tasks. Our model successfully ignores uninformative objects. This approach yields higher-level robust camera-pose regression localization results without requiring prebuilt maps. The code is available at https://github.com/kdaeho27/CT-Loc.

Three-dimensional nanoscale analysis of light-dependent organelle changes in Arabidopsis mesophyll cells.

Different organelles function coordinately in numerous intracellular processes. Photorespiration incidental to photosynthetic carbon fixation is organized across three subcellular compartments: chloroplasts, peroxisomes, and mitochondria. Under light conditions, these three organelles often form a ternary organellar complex in close proximity, suggesting a connection with metabolism during photorespiration. However, due to the heterogeneity of intercellular organelle localization and morphology, organelles' responses to changes in the external environment remain poorly understood. Here, we used array tomography by field emission scanning electron microscopy to image organelles inside the whole plant cell at nanometer resolution, generating a three-dimensional (3D) spatial map of the light-dependent positioning of chloroplasts, peroxisomes, nuclei, and vacuoles. Our results show, in light-treated cells, the volume of peroxisomes increased, and mitochondria were simplified. In addition, the population of free organelles decreased, and the ternary complex centered on chloroplasts increased. Moreover, our results emphasized the expansion of the proximity area rather than the increase in the number of proximity sites interorganelles. All of these phenomena were quantified for the first time on the basis of nanoscale spatial maps. In summary, we provide the first 3D reconstruction of Arabidopsis mesophyll cells, together with nanoscale quantified organelle morphology and their positioning via proximity areas, and then evidence of their light-dependent changes.

Design of a Panoramic Virtual Dynamic Display System for Digital Museums Based on Visual Interaction Technology

To address the spatial and temporal limitations of historical museums, a panoramic virtual dynamic display system for digital museums is designed using visual interactive technology. The VM file is generated by using the Digital Museum Design module to obtain a list of available objects, and the VM file is analysed by the Digital Museum View module to stretch and change the two-dimensional flat map into a three-dimensional spatial map for viewers to browse. The system software designs the technical construction process of the digital museum, uses a linearisation algorithm to calculate the number of clicks, visualises the font according to the number of clicks reflecting the weights, and builds a tag cloud component to provide interactive services to facilitate efficient understanding of the museum information by the viewer.

Two-Stage Incremental Three-Dimensional Spatial Mapping Approach Using a Single-Layer Lidar

Two-Stage Incremental Three-Dimensional Spatial Mapping Approach Using a Single-Layer Lidar

Estimation of anisotropic elastic moduli from high energy X-Ray data and finite element simulations

A suite of finite element simulations was executed to find optimal values for high-temperature single crystal elastic moduli of low solvus high refractory (LSHR) nickel super alloy from high energy x-ray diffraction microscopy (HEDM) measurements. In the experiment, a polycrystalline specimen was scanned in an unloaded state to determine a three-dimensional spatial map of lattice orientations in the gauge volume. The specimen was then heated and loaded while performing in situ X-ray measurements to determine grain-averaged elastic strain tensors at several macroscopic loads. The finite element simulations, utilizing three meshes of increasing resolution, mimicked the experimental loading. Initial simulations were conducted to find a box containing the optimal moduli, from which a finer grid of trial moduli was created. A suite of simulations was then executed using these meshes and moduli. For each simulation, an error was determined by comparing the simulated strain field to the measured one, with the resulting data set providing rich information about this fitting process. Anisotropy of the optimal moduli was studied relative to the level of mesh refinement, and a tendency for the anisotropy to decrease as the mesh refinement increases was found. Optimal values of anisotropic moduli and isotropic moduli were determined using the presented optimization methodology; the anisotropic moduli gave appreciably better results. Furthermore, we examined the sensitivity of the error to changes in the moduli; the takeaway was that size of the modulus had a primary effect on the sensitivity, with larger moduli being harder to fit.

Three-dimensional noise and spatial mapping system with aerial blimp robot

Three-dimensional noise and spatial mapping system with aerial blimp robot

Complementary use of pulsed and continuous wave emission modes to stabilize melt pool geometry in laser powder bed fusion

The most common defects in laser powder bed fusion (LPBF) namely porosity, geometrical errors, roughness and thermal deformations are principally linked with the energy input to the process. In common practice, a single set of process parameters is used to produce a whole component independently from the dimensions of the actual scan path within a given layer. However, melt pool stability is highly dependent on the scanned geometry. A possible strategy to maintain a constant melt pool is the mixed use of pulsed wave (PW) and continuous wave (CW) emission regimes. Accordingly, this work investigates the complementary use of continuous and modulated emission at fixed energy density on large and thin sections respectively. The proposed approach is tested on AISI 316L stainless steel and melt pool observations are conducted employing a coaxial monitoring system built for purpose. Temporally resolved measurements of intensity and geometrical properties of the melt pool were extracted as well as a three-dimensional spatial mapping of the molten pool area. The results demonstrate that moving from CW to a PW regime at the transition zones to thinner sections is effective in maintaining a constant melt pool size thus avoiding heat build-up and part extrusion from the powder bed.

Demonstration of longitudinally polarized optical needles.

Longitudinally polarized optical needles are beams that exhibit ultra-long depth of field, subwavelength transverse confinement, and polarization oriented along the longitudinal direction. Although several techniques have been proposed to generate such needles, their scarce experimental observations have been indirect and incomplete. Here, we demonstrate the creation and full three-dimensional verification of a longitudinally polarized optical needle. This needle is produced by generating a radially polarized Bessel-Gauss beam at the focus of a high numerical aperture microscope objective. Using three-dimensional spatial mapping of second-harmonic generation from a single vertically aligned GaAs nanowire, we directly verify such a longitudinally polarized optical needle's properties, which are formed at the focus. The needle exhibits a dominant polarization, which is oriented along the longitudinal direction, an ultra-long depth of field (30 λ), and high spatial homogeneity. These are in agreement with corresponding focal field calculations that use vector diffraction theory. Our findings open new opportunities for manipulation and utilization of longitudinally polarized optical needles.

A three-dimensional spatial mapping approach to quantify fine-scale heterogeneity among leaves within canopies.

Premise of the study:The three-dimensional structure of tree canopies creates environmental heterogeneity, which can differentially influence the chemistry, morphology, physiology, and/or phenology of leaves. Previous studies that subdivide canopy leaves into broad categories (i.e., “upper/lower”) fail to capture the differences in microenvironments experienced by leaves throughout the three-dimensional space of a canopy.Methods:We use a three-dimensional spatial mapping approach based on spherical polar coordinates to examine the fine-scale spatial distributions of photosynthetically active radiation (PAR) and the concentration of ultraviolet (UV)-absorbing compounds (A300) among leaves within the canopies of black mangroves (Avicennia germinans).Results:Linear regressions revealed that interior leaves received less PAR and produced fewer UV-absorbing compounds than leaves on the exterior of the canopy. By allocating more UV-absorbing compounds to the leaves on the exterior of the canopy, black mangroves may be maximizing UV-protection while minimizing biosynthesis of UV-absorbing compounds.Discussion:Three-dimensional spatial mapping provides an inexpensive and portable method to detect fine-scale differences in environmental and biological traits within canopies. We used it to understand the relationship between PAR and A300, but the same approach can also be used to identify traits associated with the spatial distribution of herbivores, pollinators, and pathogens.

TH-CD-303-11: Simultaneous Reference-Image and Deformation-Field Reconstruction for 4DCBCT with Periodic and Non-Periodic Breathing Based On 5D Respiratory Motion Model

Purpose: 4DCBCT reconstructs a temporal sequence of CBCT images, and often involves the binning of projection data to each temporal phase. Thus it suffers from binning errors during non-periodic breathing. The 5D model parameterizes respiratory motion by breathing amplitude and rate (e.g. tidal volume and airflow) independent of breathing irregularity. We propose to develop a new 4DCBCT reconstruction method based on the 5D model. Methods: The proposed CBCT technique requires that the breathing amplitude and rate are measured during CBCT. The proposed 5D-model-based method reconstructs a reference breathing phase, and time-independent deformation fields corresponding to the motion due to amplitude and rate. Therefore, the new method reconstructs 7 three-dimensional spatial maps, with reduced numbers of unknowns compared with the standard 4DCBCT method when 10 or more breathing phases are reconstructed. In addition, the 5D method explicitly manages non-periodic breathing.The 5D method is formulated as a simultaneous reference-image and deformation-field reconstruction problem, with total-variation (TV) regularization for both images and motions. Then the 4DCBCT reconstruction is carried out by alternately solving image reconstruction and image registration, in which the split Bregman method is used to reconstruct the reference image, and the Chambolle's duality-based algorithm is used to reconstruct the differential deformation fields. Moreover, the proximal terms are applied to ensure the convergence of the developed optimization algorithm for this nonconvex problem. Results: The proposed 5D method was validated in simulation based on measurements of a lung patient, in comparison with the state-of-art spatiotemporal-TV-based 4DCBCT iterative method. And the results show that the 5D method had significantly improved image quality and quantitative error, for both periodic and non-periodic breathing studies. Conclusion: We have developed a new 4DCBCT method based on 5D respiratory motion model, with improved image reconstruction during both periodic and non-periodic breathing studies. Jiulong Liu and Hao Gao were partially supported by the NSFC (#11405105), the 973 Program (#2015CB856000) and the Shanghai Pujiang Talent Program (#14PJ1404500).

The Spatial Dependency of Shoulder Muscle Demands for Seated Lateral Hand Force Exertions

As the modern workplace is dominated by submaximal repetitive tasks, knowledge of the effect of task location is important to ensure workers are unexposed to potentially injurious demands imposed by repetitive work in awkward or sustained postures. The purpose of this investigation was to develop a three-dimensional spatial map of the muscle activity for the right upper extremity during laterally directed submaximal force exertions. Electromyographic (EMG) activity was recorded from fourteen muscles surrounding the shoulder complex as the participants exerted 40N of force in two directions (leftward, rightward) at 70 defined locations. Hand position in both push directions strongly influenced total and certain individual muscle demands as identified by repeated measures analysis of variance (P < .001). During rightward exertions individual muscle activation varied from 1 to 21% MVE and during leftward exertions it varied from 1 to 27% MVE with hand location. Continuous prediction equations for muscular demands based on three-dimensional spatial parameters were created with explained variance ranging from 25 to 73%. The study provides novel information for evaluating existing and proactive workplace designs, and may help identify preferred geometric placements of lateral exertions in occupational settings to lower muscular demands, potentially mitigating fatigue and associated musculoskeletal risks.

Mass spectrometry imaging for drugs and metabolites

Mass spectrometric imaging (MSI) is a powerful analytical technique that provides two- and three-dimensional spatial maps of multiple compounds in a single experiment. This technique has been routinely applied to protein, peptide, and lipid molecules with much less research reporting small molecule distributions, especially pharmaceutical drugs. This review's main focus is to provide readers with an up-to-date description of the substrates and compounds that have been analyzed for drug and metabolite composition using MSI technology. Additionally, ionization techniques, sample preparation, and instrumentation developments are discussed.

The catheterization laboratory and interventional vascular suite of the future: Anticipating innovations in design and function

The catheterization laboratory and interventional vascular suite of the future: Anticipating innovations in design and function

Three-dimensional molecular line transfer: a simulated star-forming region

We present the first non-LTE, co-moving frame molecular line calculations of a star-forming cluster simulated using smoothed particle hydrodynamics (SPH), from which we derive high-resolution synthetic observations. We have resampled a particle representation onto an adaptive mesh and self-consistently solved the equations of statistical equilibrium in the co-moving frame, using TORUS, a three-dimensional adaptive mesh refined (AMR) radiative transfer (RT) code. We verified the applicability of the code to the conditions of the SPH simulation by testing its output against other codes. We find that the level populations obtained for optically thick and thin scenarios closely match the ensemble average of the other codes. We have used the code to obtain non-LTE level populations of multiple molecular species throughout the cluster and have created three-dimensional velocity-resolved spatial maps of the emergent intensity. Line profiles of cores traced by N2H+ (1-0) are compared to probes of low density gas, 13CO (1-0) and C18O (1-0), surrounding the cores along the line of sight. The relative differences of the line-centre velocities are shown to be small compared to the velocity dispersion, matching recent observations. We conclude that one cannot reject competitive accretion as a viable theory of star formation based on observed velocity profiles.

Noncontact optical imaging in mice with full angular coverage and automatic surface extraction

During the past decade, optical imaging combined with tomographic approaches has proved its potential in offering quantitative three-dimensional spatial maps of chromophore or fluorophore concentration in vivo. Due to its direct application in biology and biomedicine, diffuse optical tomography (DOT) and its fluorescence counterpart, fluorescence molecular tomography (FMT), have benefited from an increase in devoted research and new experimental and theoretical developments, giving rise to a new imaging modality. The most recent advances in FMT and DOT are based on the capability of collecting large data sets by using CCDs as detectors, and on the ability to include multiple projections through recently developed noncontact approaches. For these to be implemented, we have developed an imaging setup that enables three-dimensional imaging of arbitrary shapes in fluorescence or absorption mode that is appropriate for small animal imaging. This is achieved by implementing a noncontact approach both for sources and detectors and coregistering surface geometry measurements using the same CCD camera. A thresholded shadowgrammetry approach is applied to the geometry measurements to retrieve the surface mesh. We present the evaluation of the system and method in recovering three-dimensional surfaces from phantom data and live mice. The approach is used to map the measured in vivo fluorescence data onto the tissue surface by making use of the free-space propagation equations, as well as to reconstruct fluorescence concentrations inside highly scattering tissuelike phantom samples. Finally, the potential use of this setup for in vivo small animal imaging and its impact on biomedical research is discussed.

Diffuse optical tomography and spectroscopy of breast cancer and fetal brain

Diffuse optical techniques utilize light in the near infrared spectral range to measure tissue physiology noninvasively. Based on these measurements, either average bulk optical properties or three-dimensional spatial maps of tissue properties such as total hemoglobin concentration, blood oxygen saturation and scattering can be obtained using model-based reconstruction algorithms. In this thesis, diffuse optical techniques were applied for in vivo breast cancer imaging and transabdominal fetal brain oxygenation monitoring. For clinical in vivo breast cancer imaging, diffuse optical tomography technique and related instrumentation were developed. The clinical diffuse optical tomography instrument utilized near infrared light sources of multiple wavelengths, and multiple source-detector positions in a parallel plate geometry. Transmission continuous-wave measurements by a lens-coupled CCD camera and remission frequency-domain measurements by fiber-coupled detector channels were performed simultaneously. Human subject measurements were carried out in the prone position. The breast was softly compressed and the space adjacent to the breast was filled with a matching fluid with similar optical properties to that of the breast. A nonlinear conjugate gradient inverse algorithm with a priori spectral constraints was utilized to reconstruct three-dimensional endogeneous optical and physiological breast properties. Bulk physiological properties were quantified for 52 healthy subjects in the parallel-plate transmission geometry. Three-dimensional images of the breast were reconstructed for 21 subjects with breast carcinomas. Tumor contrast with respect to normal tissue was found in total hemoglobin concentration and scattering coefficient. An optical index combining total hemoglobin concentration and scattering coefficient shows the tumor contrast to be 2–3 times larger compared to the healthy tissue. Tumor contrast and tumor volume changes during neoadjuvant chemotherapy were tracked for one subject and compared to the dynamic contrast-enhanced magnetic resonance imaging (MRI). Our measurement revealed tumor shrinkage during the course of chemotherapy, in reasonable agreement with magnetic resonance images of the same subject. Finally, the feasibility of measuring blood flow of breast tumors using optical methods was demonstrated for seven subjects. In a qualitatively different set of experiments, the feasibility of transabdominal fetal brain oxygenation monitoring was demonstrated on pregnant ewes with induced transient fetal hypoxia. Preliminary noninvasive clinical measurements before and after human Cesarean sections were discussed, identifying future directions. Overall, this research has translated diffuse optical tomography techniques into a clinical research environment.