3D Landscape Research Articles

Correlations between Urban Morphological Indicators and PM2.5 Pollution at Street-Level: Implications on Urban Spatial Optimization

During rapid urbanization, microclimate environment deterioration through events such as haze pollution and heat waves has continuously occurred in cities, which greatly affects the living environment, production activities, and health of urban residents. Therefore, it is particularly necessary to explore methods for controlling and optimizing the urban microclimate environment. In this paper, based on the mechanism of the effect of urban spatial structure at street-level on the distribution of atmospheric particulate matter, an indicator system that can be employed to comprehensively describe and quantify urban morphological structure at street-level was constructed from eight aspects: the spatial morphology of street-valleys, intensity of land use and development, geometric structure of buildings, inhomogeneity of buildings, roughness of the underlying surface, distribution of ecological landscapes, 3D architectural landscape morphology, and ventilation potential. Furthermore, using satellite remote sensing images and vector thematic maps of Shanghai, indicator factors were quantified by applying GIS technique. The intrinsic mechanism of the influence of the urban morphology on the diffusion and transport of atmospheric particulate matter was comprehensively analyzed by combining statistical methods and data mining algorithm, and eight key dominant factors were identified that can be considered to improve the urban ventilation conditions and help control urban air pollution, namely, the land use intensity, urban canopy resistance, vegetation cover, spatial congestion rate, comprehensive porosity, height-to-gross floor area ratio, building density, and average building volume ratio. As such, according to the quantitative analysis results for various combinations of the dominant factors, a spatial optimization strategy at street-level that can help improve the urban air quality was proposed in terms of identifying the pathways through which urban spatial elements affect the distribution of particulate matter, i.e., controlling the source–flow diversion–flow convergence process.

Construction of a sensor-based urban three-dimensional landscape network visualization model

In the process of urbanization, the design and planning of urban landscapes have become increasingly important. Aiming at the shortcomings of traditional urban planning models such as poor visual presentation and low error rate in landscape creation, this article utilized remote sensing technology to collect vegetation and building landscape data and used geographic information systems (GIS) to process and analyze the collected landscape data. With the help of analyzed data, a visualization model of urban three-dimensional (3D) landscape network was constructed using sensors and modeling techniques. Sensors were used to achieve visualization display and management of urban landscape network, enabling better development of urban 3D landscape visualization models. The user satisfaction rate of the sensor based 3D landscape visualization model was over 92.4% and the average error rate of landscape creation after 20 experiments was 3.9835%. Building a 3D urban landscape visualization model based on sensors could effectively improve user satisfaction with the model’s visualization, provide better visualization services to users and help designers better create landscapes, improving the accuracy of landscape creation.

RETRACTED ARTICLE: Application of dynamic simulation technology based on image detail enhancement algorithm in urban 3D landscape

RETRACTED ARTICLE: Application of dynamic simulation technology based on image detail enhancement algorithm in urban 3D landscape

Gene-to-gene coordinated regulation of transcription and alternative splicing by 3D chromatin remodeling upon NF-κB activation.

The NF-κB protein p65/RelA plays a pivotal role in coordinating gene expression in response to diverse stimuli, including viral infections. At the chromatin level, p65/RelA regulates gene transcription and alternative splicing through promoter enrichment and genomic exon occupancy, respectively. The intricate ways in which p65/RelA simultaneously governs these functions across various genes remain to be fully elucidated. In this study, we employed the HTLV-1 Tax oncoprotein, a potent activator of NF-κB, to investigate its influence on the three-dimensional organization of the genome, a key factor in gene regulation. We discovered that Tax restructures the 3D genomic landscape, bringing together genes based on their regulation and splicing patterns. Notably, we found that the Tax-induced gene-gene contact between the two master genes NFKBIA and RELA is associated with their respective changes in gene expression and alternative splicing. Through dCas9-mediated approaches, we demonstrated that NFKBIA-RELA interaction is required for alternative splicing regulation and is caused by an intragenic enrichment of p65/RelA on RELA. Our findings shed light on new regulatory mechanisms upon HTLV-1 Tax and underscore the integral role of p65/RelA in coordinated regulation of NF-κB-responsive genes at both transcriptional and splicing levels in the context of the 3D genome.

BL-Hi-C reveals the 3D genome structure of Brassica crops with high sensitivity.

High-throughput Chromatin Conformation Capture (Hi-C) technologies can be used to investigate the three-dimensional genomic structure of plants. However, the practical utility of these technologies is impeded by significant background noise, hindering their capability in detecting fine 3D genomic structures. In this study, we optimized the Bridge Linker Hi-C technology (BL-Hi-C) to comprehensively investigate the 3D chromatin landscape of Brassica rapa and Brassica oleracea. The Bouquet configuration of both B. rapa and B. oleracea was elucidated through the construction of a 3D genome simulation. The optimized BL-Hi-C exhibited lower background noise compared to conventional Hi-C methods. Taking this advantage, we used BL-Hi-C to identify FLC gene loops in Arabidopsis, B. rapa, and B. oleracea. We observed that gene loops of FLC2 exhibited conservation across Arabidopsis, B. rapa, and B. oleracea. While gene loops of syntenic FLCs exhibited conservation across B. rapa and B. oleracea, variations in gene loops were evident among multiple paralogs FLCs within the same species. Collectively, our findings highlight the high sensitivity of optimized BL-Hi-C as a powerful tool for investigating the fine 3D genomic organization.

Creation of 3D landscape in AutoCAD Civil 3D according to data from MapInfo

The article presents the technology of constructing a 3D model of landscape in AutoCAD Civil 3D based on data from Mapinfo. The source material is a raster cadastral map. The resulting 3D model of landscape and visualization options are presented in this work.

3D Landscape Entity Modeling Based on Geometric Elements and Computer Aided Design

3D Landscape Entity Modeling Based on Geometric Elements and Computer Aided Design

SceneDreamer: Unbounded 3D Scene Generation from 2D Image Collections.

In this work, we present, an unconditional generative model for unbounded 3D scenes, which synthesizes large-scale 3D landscapes from random noise. Our framework is learned from in-the-wild 2D image collections only, without any 3D annotations. At the core of is a principled learning paradigm comprising 1) an efficient yet expressive 3D scene representation, 2) a generative scene parameterization, and 3) an effective renderer that can leverage the knowledge from 2D images. Our approach begins with an efficient bird's-eye-view (BEV) representation generated from simplex noise, which includes a height field for surface elevation and a semantic field for detailed scene semantics. This BEV scene representation enables 1) representing a 3D scene with quadratic complexity, 2) disentangled geometry and semantics, and 3) efficient training. Moreover, we propose a novel generative neural hash grid to parameterize the latent space based on 3D positions and scene semantics, aiming to encode generalizable features across various scenes. Lastly, a neural volumetric renderer, learned from 2D image collections through adversarial training, is employed to produce photorealistic images. Extensive experiments demonstrate the effectiveness of and superiority over state-of-the-art methods in generating vivid yet diverse unbounded 3D worlds. Project Page is available at https://scene-dreamer.github.io/. Code is available at https://github.com/FrozenBurning/SceneDreamer.

#264 : 3D Time-Lapse Refractive-Index Imaging of Intact Mouse Embryos for Non-Invasive Evaluation of the Embryonic Development

Background and Aims: Time-lapse technology is an emerging assisted reproductive technology (ART) that enables simultaneous culture and monitoring of embryos in vitro during their development. It provides extra information on key events during embryo development, which can assist embryologists in selecting embryos alongside traditional morphology evaluations. Various imaging technologies have been utilised to visualise and evaluate embryos such as brightfield microscopy, darkfield microscopy, and Hoffman modulation contrast microscopy. Although these imaging technologies allow for non-invasive imaging of human embryos in a clinical setting, 3D imaging of a whole embryo with subcellular resolution remains a challenge. Method: We demonstrate 3D time-lapse label-free imaging of live mouse embryos using the 3D refractive index (RI) imaging technique. The proposed method is a quantitative phase imaging technique that measures multiple-intensity images of transmitted light through the embryos via axial scanning to reconstruct the 3D RI map of the embryos. Results: Using the proposed method, live mouse embryos were monitored at different developmental stages, ranging from 2-cell embryos to expanded blastocysts. The measured 3D RI maps of the developing embryos reveal 3D landscape of subcellular features inside the embryos (Fig. 1). In the quantitative assessment of embryonic development, various morphokinematic parameters were extracted from the measured 3D RI maps of the embryos. Conclusion: Based on the results, we envision that our method has broad applications where non-invasive and quantitative assessment of embryonic development is required.

The 3D Chromatin Landscape of B-Cell Precursor Childhood Acute Lymphoblastic Leukemia

Whilst the molecular pathogenesis of childhood B-cell precursor (BCP) acute lymphoblastic leukemia (ALL) has been studied extensively, its 3D chromatin landscape remains poorly explored. Genome-wide chromosome conformation capture methods have provided the tools to investigate the different units of chromatin organization, such as transcriptionally active (A) and inactive (B) compartments, topologically associating domains (TADs), and fine-scale chromatin loops and enhancer-promoter interactions. The aim of this study is to elucidate the chromatin architecture and topological gene regulation in childhood BCP ALL. To date, 29 primary patient samples were included, comprising the high hyperdiploid (HeH) (n=11), ETV6:: RUNX1-positive (n=8), BCR:: ABL1-positive (n=2), TCF3:: PBX1-positive (n=2), DUX4-rearranged (n=2), intrachromosomal amplification of chromosome 21 (iAMP21) (n=1), KMT2A-rearranged (n=1), near-haploid (n=1) and near-triploid (n=1) genetic subtypes. Leukemic blast cells obtained at diagnosis were analyzed using Micro-C, a high-resolution variation of Hi-C (average number of total reads = 1.4 billion, highest resolution = 5 kb) combined with pair-end sequencing. Chromatin contact heatmaps were generated for each case using Juicer and Cooler. A/B compartments were identified using FanC at 500 kb resolution and visualized in the software IGV, while TAD calling was performed by Juicer, Domaincaller and Insulation Score. Differential chromatin interaction loop calling was made using Pareidolia and Mustache, and structural variant (SV) calling was carried out by EagleC. Preliminary principal component analysis of the 29 cases, based on the first two eigenvectors of the contact matrix (500 kb resolution), showed that HeH, ETV6:: RUNX1-positive, TCF3:: PBX1-positive and DUX4-rearranged cases each clustered based on their chromatin 3D organization. Furthermore, the A/B compartments of 11 HeH and 8 ETV6:: RUNX1-positive cases were analyzed at 500 kb resolution and compartment shifts among the two subtypes were annotated. A total of 390 shifts were detected, where activating shifts (from B to A compartment) happened more often in HeH (263 shifts) than in ETV6:: RUNX1-positive cases (127 shifts). Analysis of TAD boundary strength at 25 kb resolution revealed that HeH cases displayed significantly weaker boundaries compared to ETV6:: RUNX1-positive cases. TAD boundary strength showed no bias towards the frequently gained or non-gained chromosomes in HeH ALL. By merging individual heatmaps of all HeH and ETV6:: RUNX1-positive cases using Cooler, we created subtype-specific profiles and compared the intensity of chromatin interactions between the two genetic subtypes. Chromatin interaction intensity analysis was then combined with previously published RNA-sequencing data to identify transcriptional dysregulation events that could be associated with chromatin interaction changes. Preliminary results show that there was a chromatin loop missing close to the well-known leukemia-related gene IKZF1 in HeH compared to ETV6:: RUNX1-positive cases; this gene also showed lower expression in the RNA-sequencing data. FLT3 was associated with weakened chromatin interactions and down-regulated in ETV6:: RUNX1-positive cases compared to HeH, in agreement with its known high expression in HeH. Finally, we performed screening of SVs using EagleC and Micro-C heatmaps in HeH and ETV6:: RUNX1-positive samples. Out of the 19 included cases, previous whole-genome sequencing (WGS) data were available for 16. We detected 75 SVs, of which 50 were intrachromosomal rearrangements and 25 were translocations. Micro-C heatmaps allowed visual detection of SVs smaller than 1 Mb and permitted identification of the type of SVs. WGS detected 61% of the SVs found in the HeH samples with Micro-C and 51% of those in the ETV6:: RUNX1-positive cases. In summary, we present the first high-resolution genome-wide map of chromatin 3D organization in pediatric ALL. Our results indicate that different subtypes of childhood BCP ALL have distinct 3D chromatin landscapes and that abnormal chromatin architectures affect the regulation of leukemia-related genes.

3D urban landscape rendering and optimization algorithm for smart city

3D urban landscape visualization is a key technology in digital city construction. Based on the research and analysis of the three-dimensional space of the urban landscape space, the three-dimensional space can not only allow users to intuitively perceive the development of the city. It also enables decision makers, planners, and users to more intuitively, objectively, and rationally recognize and understand the current urban development and planning design. Defining the data content of the 3D city landscape image model is the basis for creating the 3D city image model. It not only guides producers to select data, but also serves as the basis for sharing data between different applications. With the continuous development of society, the number of people living in rural areas migrating to cities to make a living has increased rapidly, leading to the growing problem of “urban congestion” in many areas. In order to effectively solve these problems, “smart cities” came into being. It quickly triggered a boom in global urban development. Based on a survey of the state-of-the-art in the field of 3D modeling and engineering design visualization, this paper analyzes 3D rendering acceleration algorithms used to speed up rendering and improve the quality of 3D design. By utilizing BSP technology, transparent objects can be drawn in any order in any scene, which solves the problem of incorrectly occluding transparent objects during rendering. This paper also applies collision detection technology, which enhances the user’s immersive feeling when roaming the landscape. In the 3D reconstruction process, it can complete the column and wall recognition for the test image with complex composition. Its recognition rate for various urban features has reached more than 80%.

Three-dimensional chromatin landscapes in hepatocellular carcinoma associated with hepatitis B virus.

Three-dimensional (3D) chromatin architecture frequently altered in cancer. However, its changes during the pathogenesis of hepatocellular carcinoma (HCC) remained elusive. Hi-C and RNA-seq were applied to study the 3D chromatin landscapes and gene expression of HCC and ANHT. Hi-C Pro was used to generate genome-wide raw interaction matrices, which were normalized via iterative correction (ICE). Moreover, the chromosomes were divided into different compartments according to the first principal component (E1). Furthermore, topologically associated domains (TADs) were visualized via WashU Epigenome Browser. Furthermore, differential expression analysis of ANHT and HCC was performed using the DESeq2 R package. Additionally, dysregulated genes associated with 3D genome architecture altered were confirmed using TCGA, qRT-PCR, immunohistochemistry (IHC), etc. RESULTS: First, the intrachromosomal interactions of chr1, chr2, chr5, and chr11 were significantly different, and the interchromosomal interactions of chr4-chr10, chr13-chr21, chr15-chr22, and chr16-chr19 are remarkably different between ANHT and HCC, which resulted in the up-regulation of TP53I3 and ZNF738 and the down-regulation of APOC3 and APOA5 in HCC. Second, 49 compartment regions on 18 chromosomes have significantly switched (A-B or B-A) during HCC tumorigenesis, contributing to up-regulation of RAP2A. Finally, a tumor-specific TAD boundary located on chr5: 6271000-6478000 and enhancer hijacking were identified in HCC tissues, potentially associated with the elevated expression of MED10, whose expression were associated with poor prognosis of HCC patients. This study demonstrates the crucial role of chromosomal structure variation in HCC oncogenesis and potential novel biomarkers of HCC, laying a foundation for cancer precision medicine development.

The implementation of a virtual field trip to aid geological interpretation within an undergraduate volcanology course

Geological skills such as interpreting outcrops are often taught during fieldwork. However, recent advancements in digital technologies and the demand for more inclusive and accessible learning has provided an opportunity to teach these skills in virtual field trips (VFT). The Iceland VFT was developed to teach students about volcanic features and processes in Iceland and help students develop geological skills within a third-year, classroom-based, physical volcanology course. To determine the effectiveness of the VFT at aiding the development of student interpretation skills, we calculated the learning gains from an applied sketching exercise administered pre- and post- VFT, where students were asked to sketch a photograph of a lava flow outcrop and interpret flow shape and features from a range of different perspectives. The largest learning gains were for lava flow interpretation in map-view (0.40) followed by lava flow interpretation in side-view (0.31). Student responses to a post-VFT evaluation exercise indicate that the instructional/360 videos and the 3D landscape and rock models allowed students to spatially explore volcanic features within the landscape which aided their ability to interpret what the lava flow outcrop within the applied sketching exercise might look like in multiple perspectives. We conclude that the VFT supported students’ geological interpretation of lava flows and recommend that virtual fieldtrips with interactive spatially challenging exercises can be used to improve students’ conceptual understanding of content delivered in lectures and laboratories as well as preparation or reinforcement of fieldwork.

Urban spontaneous plant richness in response to the 2D/3D building and green space patterns in a highly urbanized area

The impact of landscape patterns on urban plant diversity has received significant attention; however, previous studies have primarily focused on two-dimensional (2D) patterns. Limited investigations have been conducted to explore the effects of three-dimensional (3D) landscape patterns on urban plant diversity. Spontaneous plants are ideal objects for studying the response of plant diversity to urban environments due to their independence from intentional human inputs. Buildings, as a crucial symbol of urbanization, exhibit strong 3D characteristics in urban landscapes. Green spaces, the most important source of plant propagules in cities, are closely related to spontaneous plant diversity in urban areas. Therefore, we examined how 2D/3D building and green space patterns influence urban spontaneous plant species richness and compared the responses between different categories (native and non-native). We surveyed spontaneous plants in the built-up areas of Shenzhen, a highly urbanized region situated along China’s southern coast. Our survey recorded 278 species belonging to 208 genera and 77 families. Results from boosted regression tree models (BRT) indicated significant correlations between spontaneous plant species richness and various metrics, including building coverage ratio (BCR), mean building height (MAH), green space coverage ratio (GCR), edge density of green spaces (ED_G), spatial congestion degree (SCD), and floor area ratio (FAR). These metrics exhibited complex nonlinear correlations with the species richness of spontaneous plants. Furthermore, native and non-native species richness responded differently to building and green space patterns; while native species richness was equally affected by green space and building patterns, non-native species richness was more strongly impacted by building patterns than green space ones. Our study quantified the nonlinear relationships between urban spontaneous plant species richness and 2D/3D green space and building patterns, demonstrating that optimizing green space and building patterns can be a practical approach for managing and promoting spontaneous plant diversity in highly urbanized areas.

Digital terrain interactive editing technology for landscape planning and design based on deep learning

Abstract In the era of big data information digitization, digital terrain editing technology is an important research content in the virtual geographic environment, 3D landscape simulation system, which has significant value in digital planning and design practice of cities and villages, regional road networks, and landscape gardens. This paper focuses on deep learning-based digital terrain interactive editing technology for landscape planning and design. Firstly, it introduces the concept and principle of digital terrain interactive editing technology, constructs the model and terrain interactive editing algorithm, and then analyzes three systems’ digital geography interactive data from two aspects of accuracy and convergence. The results show that A system planning digital landscape garden landscape accuracy, planning accuracy, and convergence are small, and the planning accuracy reaches a minimum of 88% and a maximum of 95%. The intersection reaches a minimum of 75% and a maximum of 87%. Compared with the other two systems are high, so it can be seen that the digital interactive terrain editing for landscape planning of this design has high planning accuracy and convergence. Digital interactive editing technology is developing rapidly in China’s landscape architecture discipline research and professional practice applications. It has shown excellent development potential and application value in the landscape planning and design industry. This study improves the accuracy and efficiency of digital interactive editing technology and has great historical significance for the development and progress of the Chinese architectural design industry.

Retracted: Wavelet Transform-Based 3D Landscape Design and Optimization for Digital Cities

Retracted: Wavelet Transform-Based 3D Landscape Design and Optimization for Digital Cities

Targeted volume correlative light and electron microscopy of an environmental marine microorganism.

Photosynthetic microalgae are responsible for an important fraction of CO2 fixation and O2 production on Earth. Three-dimensional (3D) ultrastructural characterization of these organisms in their natural environment can contribute to a deeper understanding of their cell biology. However, the low throughput of volume electron microscopy (vEM) methods along with the complexity and heterogeneity of environmental samples pose great technical challenges. In the present study, we used a workflow based on a specific electron microscopy sample preparation method compatible with both light and vEM imaging in order to target one cell among a complex natural community. This method revealed the 3D subcellular landscape of a photosynthetic dinoflagellate, which we identified as Ensiculifera tyrrhenica, with quantitative characterization of multiple organelles. We show that this cell contains a single convoluted chloroplast and show the arrangement of the flagellar apparatus with its associated photosensitive elements. Moreover, we observed partial chromatin unfolding, potentially associated with transcription activity in these organisms, in which chromosomes are permanently condensed. Together with providing insights in dinoflagellate biology, this proof-of-principle study illustrates an efficient tool for the targeted ultrastructural analysis of environmental microorganisms in heterogeneous mixes.

3D genome structural variations play important roles in regulating seed oil content of Brassica napus

Dissecting the complex regulatory mechanism of seed oil content (SOC) is one of the main research goals in Brassica napus. Increasing evidence suggests that genome architecture is linked to multiple biological functions. However, the effect of genome architecture on SOC regulation remains unclear. Here, we used high-throughput chromatin conformation capture to characterize differences in the three-dimensional (3D) landscape of genome architecture of seeds from two B. napus lines, N53-2 (with high SOC) and Ken-C8 (with low SOC). Bioinformatics analysis demonstrated that differentially accessible regions and differentially expressed genes between N53-2 and Ken-C8 were preferentially enriched in regions with quantitative trait loci (QTLs)/associated genomic regions (AGRs) for SOC. A multi-omics analysis demonstrated that expression of SOC-related genes was tightly correlated with genome structural variations in QTLs/AGRs of B. napus. The candidate gene BnaA09g48250D, which showed structural variation in a QTL/AGR on chrA09, was identified by fine-mapping of a KN double-haploid population derived from hybridization of N53-2 and Ken-C8. Overexpression and knockout of BnaA09g48250D led to significant increases and decreases in SOC, respectively, in the transgenic lines. Taken together, our results reveal the 3D genome architecture of B. napus seeds and the roles of genome structural variations in SOC regulation, enriching our understanding of the molecular mechanisms of SOC regulation from the perspective of spatial chromatin structure.

Research on Landscape Architecture Modeling Simulation System Based on Computer Virtual Reality Technology

This paper develops a three-dimensional garden landscape design simulation system based on virtual reality technology. The landscape design data collection module uses files to read and write landscape design data. Use the resource library to store the basic materials required for 3D landscape design. The system realizes the functions of 3D solid modeling, 3D real-time virtual presentation of design scenes, rendering and animation production, and construction drawing. After the landscape architecture simulation system generates construction drawings, it uses the coordinate matrix method of three-dimensional graphics processing technology to render the three-dimensional texture of the model. The system realizes three-dimensional landscape design through the statistical budget and engineering data of the data statistics module. The system simulation results show that the system can effectively realize the garden landscape design of the community, and the visual effect of obtaining the garden landscape scene is better.

Scale-dependent and season-dependent impacts of 2D/3D building morphology on land surface temperature

Urbanization has caused significant changes in urban morphology in three-dimensional (3D) space. Although previous studies found a close association between 2D/3D urban morphology and land surface temperature (LST), the conclusions are various and the reasons lie in three fundamental components of urban morphology: physical form, resolution and time. Beijing's old city includes massive vernacular and modern architecture, which provides an ideal laboratory for the studies. In a new approach, 3D landscape metrics were applied to analyze built forms from the aspect of composition and configuration, and to explain their contributions to LSTs together with tree height data across scales and seasons. Tree height contributed most during summer. Compared to composition, configuration metrics were less efficient for cross-scale LST changes. The relative importance of building features is scale-dependent. At small scales (under 105 m), 3D composition features contributed more to LST, while 2D composition features were dominant at larger scales (over 180 m). At intermediate scales, 2D and 3D composition metrics together affect the LSTs. The scale and seasonal dependencies indicated in this study are derived from the application of our concept to a particular city. More experiments to other cities should be carried out for an in-depth understanding of the associations.