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Three-dimensional electron microscopy images of brain tissue and their dense segmentations are now petascale and growing. These volumes require the mass production of dense segmentation-derived neuron skeletons, multi-resolution meshes, image hierarchies (for both modalities) for visualization and analysis, and tools to manage the large amount of data. However, open tools for large-scale meshing, skeletonization, and data management have been missing. Igneous is a Python-based distributed computing framework that enables economical meshing, skeletonization, image hierarchy creation, and data management using cloud or cluster computing that has been proven to scale horizontally. We sketch Igneous's computing framework, show how to use it, and characterize its performance and data storage.

ABSTRACT Purpose To evaluate the retinal blood vascular network of the retinographies of patients with different grades of diabetic retinopathy. Methods Ninety Retinographies (MESSIDOR database) were used, with different grades of diabetic retinopathy divided into 4 groups: no retinopathy (n=23), grade one (n=20), grade two (n=20) and grade three (n=27) diabetic retinopathy. The grades of diabetic retinopathy were classified according to the number of microaneurysms, number of hemorrhages and the presence of neovascularization. The images were skeletonized and quantified by fractal methods: dimension of box-counting (Dbc) and information (Dinf). Results The means of Dbc values of groups were around 1.25, without statistically significant difference in the dimension values between groups for whole retina. There was also no statistical difference in Dinf values between groups, whose means ranged between 1.294 ± 0.013 (group of grade 1) and 1.3 ± 0.017 (group of grade 3). The retinographies were divided into regions of equal areas. The fractal values of some retinal regions showed statistical differences, but these differences were not enough to show the sensitivity of fractal methods in identifying diabetic retinopathy. Conclusion The fractal methods were not able to identify the different grades of diabetic retinopathy in retinographies.

Retinal vessel segmentation, skeletonization, and the generation of vessel segments are considered significant steps in any automated system for measuring the vessel biomarkers of several disease diagnoses. Most of the current tortuosity quantification methods rely on precise vascular segmentation and skeletonization of the retinal vessels. Additionally, the existence of a reference dataset for accurate vessel segment images is an essential need for implementing deep learning solutions and an automated system for measuring the vessel biomarkers of several disease diagnoses, especially for optimized quantification of vessel tortuosity or accurate measurement of AV-nicking. This study aimed to present an improved method for skeletonizing and extracting the retinal vessel segments from the 504 images in the AV classification dataset. The study utilized the Six Sigma process capability index, sigma level, and yield to measure the vessels’ tortuosity calculation improvement before and after optimizing the extracted vessels. As a result, the study showed that the sigma level for the vessel segment optimization improved from 2.7 to 4.39, the confirming yield improved from 88 percent to 99.77 percent, and the optimized vessel segments of the AV classification dataset retinal images are available in monochrome and colored formats.

This paper presents a high-speed skeletonization algorithm for detecting the skeletons of linear objects from their binary images. The primary objective of our research is to achieve rapid extraction of the skeletons from binary images while maintaining accuracy for high-speed cameras. The proposed algorithm uses edge supervision and a branch detector to efficiently search inside the object, avoiding unnecessary computation on irrelevant pixels outside the object. Additionally, our algorithm addresses the challenge of self-intersections in linear objects with a branch detection module, which detects existing intersections and initializes new searches on emerging branches when necessary. Experiments on various binary images, such as numbers, ropes, and iron wires, demonstrated the reliability, accuracy, and efficiency of our approach. We compared the performance of our method with existing skeletonization techniques, showing its superiority in terms of speed, especially for larger image sizes.

Over the past decade, deep learning frameworks such as convolutional neural networks (CNNs) have made major research inroads in upstream oil and gas, with applications in seismic processing/imaging, velocity model building, petrophysics, geological seismic interpretation, all the way to development, production and supply chain logistics. CNN fault prediction centers around the idea of image edge detection and, for improved prediction results, three data-driven steps are recommended. First, pre-condition the seismic data to increase signal-to-noise ratio as much as possible: iterative dip-steered median filtering and principal component filtering are adopted to further improve signal-to-noise ratio and sharpness for edge detection. Second, a fault probability volume obtained through deep learning (DL) -based fault detection using a U-Net architecture, taking synthetic seismic models as samples that can improve DL-based fault prediction in lieu of readily available labeled fault sets that may be prohibitively time-consuming to generate. Finally, edge enhancement is performed on the inference results to improve precision and fault continuity. A comparative analysis between related edge enhancement technologies is also presented. Results for three different faulting modes (normal, reverse and strike-slip) over three real seismic field data sets from China demonstrate the robustness of the proposed workflow. [ABSTRACT FROM AUTHOR]

A fast algorithm for solving large multi-scale scattering problems by the volume–surface integral equation (VSIE) is proposed. The sub-matrices of the near-field interactions (NFIs) in terms of the multi-level fast multipole algorithm (MLFMA) are compressed by the skeletonization after the theoretical and numerical investigations on their low-rankness are carried out. A block-diagonal preconditioner (BDP) based on the recursive skeletonization (RS) is developed to improve the conditioning of the impedance matrix of the VSIE. The rules to select hyperparameters in the proposed method are given. Numerical experiments conducted on scattering problems show the performance of the proposed algorithm. [ABSTRACT FROM AUTHOR]

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Tree skeletons play an important role in tree structure analysis and 3D model reconstruction. However, it is a challenge to extract a skeleton from a tree point cloud with complex branches. In this paper, an automatic and fast tree skeleton extraction method (FTSEM) based on voxel thinning is proposed. In this method, a wood–leaf classification algorithm was introduced to filter leaf points for the reduction of the leaf interference on tree skeleton generation, tree voxel thinning was adopted to extract a raw tree skeleton quickly, and a breakpoint connection algorithm was used to improve the skeleton connectivity and completeness. Experiments were carried out in Haidian Park, Beijing, in which 24 trees were scanned and processed to obtain tree skeletons. The graph search algorithm (GSA) was used to extract tree skeletons based on the same datasets. Compared with the GSA method, the FTSEM method obtained more complete tree skeletons. The time cost of the FTSEM method was evaluated using the runtime and time per million points (TPMP). The runtime of FTSEM was from 1.0 s to 13.0 s, and the runtime of GSA was from 6.4 s to 309.3 s. The average value of TPMP was 1.8 s for FTSEM and 22.3 s for GSA, respectively. The experimental results demonstrate that the proposed method is feasible, robust, and fast with good potential for tree skeleton extraction. [ABSTRACT FROM AUTHOR]

Abstract Background In the context of biomarker discovery and molecular characterization of diseases, laser capture microdissection is a highly effective approach to extract disease-specific regions from complex, heterogeneous tissue samples. For the extraction to be successful, these regions have to satisfy certain constraints in size and shape and thus have to be decomposed into feasible fragments. Results We model this problem of constrained shape decomposition as the computation of optimal feasible decompositions of simple polygons. We use a skeleton-based approach and present an algorithmic framework that allows the implementation of various feasibility criteria as well as optimization goals. Motivated by our application, we consider different constraints and examine the resulting fragmentations. We evaluate our algorithm on lung tissue samples in comparison to a heuristic decomposition approach. Our method achieved a success rate of over 95% in the microdissection and tissue yield was increased by 10–30%. Conclusion We present a novel approach for constrained shape decomposition by demonstrating its advantages for the application in the microdissection of tissue samples. In comparison to the previous decomposition approach, the proposed method considerably increases the amount of successfully dissected tissue.

Morphological analysis of protein channels is a key step for a thorough understanding of their biological function and mechanism. In this respect, molecular dynamics (MD) is a very powerful tool, enabling the description of relevant biological events at the atomic level, which might elude experimental observations, and pointing to the molecular determinants thereof. In this work, we present a computational geometry-based approach for the characterization of the shape and dynamics of biological ion channels or pores to be used in combination with MD trajectories. This technique relies on the earliest works of Edelsbrunner and on the NanoShaper software, which makes use of the alpha shape theory to build the solvent-excluded surface of a molecular system in an aqueous solution. In this framework, a channel can be simply defined as a cavity with two entrances on the opposite sides of a molecule. Morphological characterization, which includes identification of the main axis, the corresponding local radius, and the detailed description of the global shape of the cavity, is integrated with a physico-chemical description of the surface facing the pore lumen. Remarkably, the possible existence or temporary appearance of fenestrations from the channel interior towards the outer lipid matrix is also accounted for. As a test case, we applied the present approach to the analysis of an engineered protein channel, the mechanosensitive channel of large conductance.

Background: Xylosyltransferases-I and II (XT-I and XT-II) catalyze the initial and rate limiting step of the proteoglycan (PG) biosynthesis and therefore have an import impact on the homeostasis of the extracellular matrix (ECM). The reason for the occurrence of two XT-isoforms in all higher organisms remains unknown and targeted genome-editing strategies could shed light on this issue. Methods: XT-I deficient neonatal normal human dermal fibroblasts were generated by using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated proteins (Cas) 9 system. We analyzed if a reduced XT-I activity leads to abnormalities regarding ECM-composition, myofibroblast differentiation, cellular senescence and skeletal and cartilage tissue homeostasis. Results: We successfully introduced compound heterozygous deletions within exon 9 of the XYLT1 gene. Beside XYLT1, we detected altered gene-expression levels of further, inter alia ECM-related, genes. Our data further reveal a dramatically reduced XT-I protein activity. Abnormal myofibroblast-differentiation was demonstrated by elevated alpha-smooth muscle actin expression on both, mRNA- and protein level. In addition, wound-healing capability was slightly delayed. Furthermore, we observed an increased cellular-senescence of knockout cells and an altered expression of target genes knowing to be involved in skeletonization. Conclusion: Our data show the tremendous relevance of the XT-I isoform concerning myofibroblast-differentiation and ECM-homeostasis as well as the pathophysiology of skeletal disorders. [ABSTRACT FROM AUTHOR]

Hepatic vessel skeletonization serves as an important means of hepatic vascular analysis and vessel segmentation. This paper presents a survey of techniques and algorithms for hepatic vessel skeletonization in medical images. We summarized the latest developments and classical approaches in this field. These methods are classified into five categories according to their methodological characteristics. The overview and brief assessment of each category are provided in the corresponding chapters, respectively. We provide a comprehensive summary among the cited publications, image modalities and datasets from various aspects, which hope to reveal the pros and cons of every method, summarize its achievements and discuss the challenges and future trends. [ABSTRACT FROM AUTHOR]

Data visualization is a technique used to see the unseen information, that will help humanity to discover important things. There are many methods to represent the datasets, but data visualization is the best because it can preserve the information. Skeleton is used to analyse the visualization, thus data visualization gives efficient results. Comparison among well-known methods is the goal of this paper. The conclusion of this paper showed all the comparative results will be important for any further study. This study will use data visualization to discover novel dataset representations, which is the main goal of data visualization and can be useful in presenting necessary data. [ABSTRACT FROM AUTHOR]

Benefiting from the rapid development of electron microscopy imaging and deep learning technologies, an increasing number of brain image datasets with segmentation and synapse detection are published. Most of the automated segmentation methods label voxels rather than producing neuron skeletons directly. A further skeletonization step is necessary for quantitative morphological analysis. Currently, several tools are published for skeletonization as well as morphological and synaptic connectivity analysis using different computer languages and environments. Recently the Julia programming language, notable for elegant syntax and high performance, has gained rapid adoption in the scientific computing community. Here, we present a Julia package, called RealNeuralNetworks.jl, for efficient sparse skeletonization, morphological analysis, and synaptic connectivity analysis. Based on a large-scale Zebrafish segmentation dataset, we illustrate the software features by performing distributed skeletonization in Google Cloud, clustering the neurons using the NBLAST algorithm, combining morphological similarity and synaptic connectivity to study their relationship. We demonstrate that RealNeuralNetworks.jl is suitable for use in terabyte-scale electron microscopy image segmentation datasets. [ABSTRACT FROM AUTHOR]

Benefiting from the rapid development of electron microscopy imaging and deep learning technologies, an increasing number of brain image datasets with segmentation and synapse detection are published. Most of the automated segmentation methods label voxels rather than producing neuron skeletons directly. A further skeletonization step is necessary for quantitative morphological analysis. Currently, several tools are published for skeletonization as well as morphological and synaptic connectivity analysis using different computer languages and environments. Recently the Julia programming language, notable for elegant syntax and high performance, has gained rapid adoption in the scientific computing community. Here, we present a Julia package, called RealNeuralNetworks.jl, for efficient sparse skeletonization, morphological analysis, and synaptic connectivity analysis. Based on a large-scale Zebrafish segmentation dataset, we illustrate the software features by performing distributed skeletonization in Google Cloud, clustering the neurons using the NBLAST algorithm, combining morphological similarity and synaptic connectivity to study their relationship. We demonstrate that RealNeuralNetworks.jl is suitable for use in terabyte-scale electron microscopy image segmentation datasets.

ObjectiveTo compare performance assessment of two methods of measuring radial peripapillary capillary (RPC) vessel density (VD) after skeletonization using MATLAB and Image J in glaucoma clinical setting.MethodsSeventy-three eyes of 73 glaucoma patients from Beijing Tongren Hospital were included in this prospective study. Original images of RPC were obtained using optical coherence tomography angiography. Two approaches were executed before measuring. Method 1 (M1) required image sharpening, removal of big vessels, and skeletonization. Method 2 (M2) required skeletonization and removal of major vessels. Each method was executed twice. Repeatability and correlations with glaucomatous parameters were assessed. Factors associated with retinal nerve fiber layer thickness (RNFLT) and visual field mean deviation (MD) were analyzed.ResultsAverage VD was 13.86 ± 2.73 and 7.50 ± 2.50% measured by M1 and M2. Percentage of total elimination of the major vessels was 36.99 and 100% by M1 and M2, respectively. The intrasession and intersession reproducibility was higher by M2 (ICC = 0.979, ICC = 0.990) than by M1 (ICC = 0.930, ICC = 0.934). VD measured by M2 showed stronger correlations with glaucomatous parameters than by M1. By stepwise multiple linear regression, thinner RNFLT was associated with smaller VD measured by M2 (B = 4.643, P < 0.001). Worse MD was associated with smaller VD measured by M1 (B = 1.079, P = 0.015).ConclusionThe VD measured by M2 showed better reproducibility and higher correlation with glaucomatous structural parameters. Image sharpning helps display of hazy vasculature in glaucoma, which may reflect visual function better. Researchers should carefully choose image processing methods according to their research object.

A Skeleton that is extracted by a skeletonization algorithm from a binary image is useful for object description, matching, recognition and compression. The parallel thinning algorithm, one of the skeletonization algorithms is well known to have computational effciency. The main contribution of this paper is that we proposed a novel fully parallel thinning algorithm based on a comprehensive investigation of the well-known Zhang-Suen (ZS)-series algorithms and the one-pass thinning algorithm (OPTA)-series algorithms, which not only has good performance in terms of (8,4) connectivity preservation and single-pixel thickness, but also has the following qualities: it is more robust to the boundary noise than the OPTA-series algorithms and it is faster than the ZS-series algorithms in terms of thinning speed, as confirmed by the experiments presented in this paper. [ABSTRACT FROM AUTHOR]

Skeleton creation is an important phase in the character animation pipeline. However, handcrafting skeleton takes extensive labor time and domain knowledge. Automatic skeletonization provides a solution. However, most of the current approaches are far from real-time and lack the flexibility to control the skeleton complexity. In this paper, we present an efficient skeletonization method, which can be seamlessly integrated into the sketch-based modeling process in real-time. The method contains three steps: (i) local sub-skeleton extraction; (i i) sub-skeleton connection; and (i i i) global skeleton refinement. Firstly, the local skeleton is extracted from processed polygon stroke and forms a subpart along with the sub-mesh. Then, local sub-skeletons are connected according to the intersecting relationships and modeling sequence of subparts. Lastly, a global refinement method is proposed to gives users coarse-to-fine control on the connected skeleton. We demonstrate the effectiveness of our method on a variety of examples created from both novices and professionals. [Display omitted] • A real-time skeletonization algorithm for immediately constructing an animatable skeleton from user sketch. • A flexible solution for skeleton complexity control. • An easy-to-use system for creating animatable models featured by sketch-based shape modeling and automatic rigging. [ABSTRACT FROM AUTHOR]

Purpose: To evaluate the retinal blood vascular network of the retinographies of patients with different grades of diabetic retinopathy. Methods: Ninety Retinographies (MESSIDOR database) were used, with different grades of diabetic retinopathy divided into 4 groups: no retinopathy (n=23), grade one (n=20), grade two (n=20) and grade three (n=27) diabetic retinopathy. The grades of diabetic retinopathy were classified according to the number of microaneurysms, number of hemorrhages and the presence of neovascularization. The images were skeletonized and quantified by fractal methods: dimension of box-counting (Dbc) and information (Dinf). Results: The means of Dbc values of groups were around 1.25, without statistically significant difference in the dimension values between groups for whole retina. There was also no statistical difference in Dinf values between groups, whose means ranged between 1.294 ± 0.013 (group of grade 1) and 1.3 ± 0.017 (group of grade 3). The retinographies were divided into regions of equal areas. The fractal values of some retinal regions showed statistical differences, but these differences were not enough to show the sensitivity of fractal methods in identifying diabetic retinopathy. Conclusion: The fractal methods were not able to identify the different grades of diabetic retinopathy in retinographies. [ABSTRACT FROM AUTHOR]

Internal thoracic arteries (ITAs) are the gold standard conduits for coronary revascularization because of their long-term patency and anti-atherosclerotic properties. Harvesting and preparation of ITAs for revascularization is a technically demanding procedure with multiple challenges. Over the last few decades, various methods and techniques for ITAs harvesting have been introduced by different surgeons and applied in clinical practice with different results. Harvesting of ITAs in pedicled or skeletonized fashion, with electrocautery or harmonic scalpel, with open or intact pleura, with clipping the end or keeping it perfused; papaverine delivery with intraluminal injection, perivascular injection, injecting into endothoracic fascia, and papaverine topical spray are the different techniques introduced by the number of researchers. At the same time, access to the ITAs for harvesting has also been studied. Access and harvesting through median sternotomy, mini anterolateral thoracotomy, thoracoscopic, and robotic-assisted harvesting of ITAs are the different techniques used in clinical practice. However, the single standard method for harvesting and preparation of ITAs has yet to be determined. In this review article, we aimed to discuss and analyze all these techniques of harvesting and preparing ITAs with the help of literature to find the best way for ITAs harvesting and preparation for myocardial revascularization. [ABSTRACT FROM AUTHOR]

A digital twin describes the virtual representation of a real process. This twin is constantly updated with real data and can thus control and adapt the real model. Designing suitable digital twins for path planning of autonomous robots or drones is often challenging due to the large number of different dynamic environments and multi-task and agent systems. However, common path algorithms are often limited to two tasks and to finding shortest paths. In real applications, not only a short path but also the width of the passage with a path as centered as possible are crucial, since robotic systems are not ideal and require recalibration frequently. In this work, so-called homotopic shrinking is used to generate the digital twin, which can be used to extract all possible path proposals including their passage widths for 2D and 3D environments and multiple tasks and robots. The erosion of the environment is controlled by constraints such that the task stations, the robot or drone positions, and the topology of the environment are considered. Such a deterministic path algorithm can flexibly respond to changing environmental conditions and consider multiple tasks simultaneously for path generation. A distinctive feature of these paths is the central orientation to the non-passable areas, which can have significant benefits for worker and patient safety. The method is tested on 2D and 3D maps with different tasks, obstacles, and multiple robots. For example, the robust generation of the digital twin for a maze and also the dynamic adaptation in case of sudden changes in the environment is covered. This variety of use cases and the comparison with alternative methods result in significant advantages, such as high robustness, consideration of multiple targets, and high safety distances to obstacles and areas that cannot be traversed. Finally, it was shown that the environment for the digital twin can be reduced to reasonable paths by constrained shrinking, both for real 2D maps and for complex virtual 2D and 3D maps.

We present a method that skeletonizes the first arriving seismic refractions by machine learning and inverts them for the subsurface velocity model. In this study, first arrivals can be compressed in a low-rank sense with their skeletal features extracted by a well-trained autoencoder. Empirical experiments suggest that the autoencoder’s $1\times 1$ or $2\times 1$ latent vectors vary continuously with respect to the input seismic data. It is, therefore, reasonable to introduce a misfit functional measuring the discrepancies between the predicted and the observed data in a low-dimensional latent space. The benefit of this approach is that an elaborated autoencoding neural network not only refines intrinsic information hidden in the refractions but also improves the quality of inversion for a reliable background velocity model. Numerical tests on both synthetic and field data demonstrate the effectiveness of this method, especially in recovering the low-to-intermediate wavenumber parts of the subsurface velocity distribution. Comparisons are made with the other three relevant methods, the wave-equation travel-time (WT) inversion, the envelope inversion, and the full waveform inversion (FWI). As expected, the cycle skipping problem is alleviated due to the reduction of dimensions of data space. This method outperforms the envelope inversion in resolution, and it is no worse than WT. Moreover, there is no need for careful manual travel-time picking with this methodology. In general, this inversion framework provides an extendable strategy to compress any input data for reconstructing high-dimensional physical parameters. [ABSTRACT FROM AUTHOR]

An algorithm for analyzing the characteristics of the pigment network of skin neoplasms is proposed. It is based on the assessment of the deviation coefficient of the average lengths of the pigment network segments in the local areas of the neoplasm from the average value of the lengths of the pigment network segments throughout the area of the neoplasm. The use of the algorithm makes it possible to distinguish the typical pigment network from an atypical one. An atypical pigment network is a core feature in identifying early melanoma. The algorithm can be used in automated systems to support medical decision-making in the diagnosis of skin neoplasms. [ABSTRACT FROM AUTHOR]

The paper analyses Peirce’s hypoiconicity through the lens of Husserlian intentionality. Peirce’s triple structure of hypoiconicity as resemblance relation, diagrammatical reasoning and metaphoric displacement is shown to require intentional acts in its production and interpretation. Regarding hypoiconicity as a semiotic schematization of Vorstellung, the paper places it in the context of Husserl’s conception of intentionality in which iconicity appears as a stepping-stone towards the skeletonization of resemblance in diagrammatical abstraction and as schematic displacement in metaphor. As such, hypoiconic intentionality is argued to play a role also in Peirce’s community conception of language. The paper’s core claim is that intentionality provides an avenue for revealing hypoiconicity as a major, critical concept of semiotics, functioning as paradigm case for investigating the convergence of semiotics and phenomenology.

Hypertensive retinopathy severity classification is proportionally related to tortuosity severity grading. No tortuosity severity scale enables a computer-aided system to classify the tortuosity severity of a retinal image. This work aimed to introduce a machine learning model that can identify the severity of a retinal image automatically and hence contribute to developing a hypertensive retinopathy or diabetic retinopathy automated grading system. First, the tortuosity is quantified using fourteen tortuosity measurement formulas for the retinal images of the AV-Classification dataset to create the tortuosity feature set. Secondly, a manual labeling is performed and reviewed by two ophthalmologists to construct a tortuosity severity ground truth grading for each image in the AV classification dataset. Finally, the feature set is used to train and validate the machine learning models (J48 decision tree, ensemble rotation forest, and distributed random forest). The best performance learned model is used as the tortuosity severity classifier to identify the tortuosity severity (normal, mild, moderate, and severe) for any given retinal image. The distributed random forest model has reported the highest accuracy (99.4%) compared to the J48 Decision tree model and the rotation forest model with minimal least root mean square error (0.0000192) and the least mean average error (0.0000182). The proposed tortuosity severity grading matched the ophthalmologist’s judgment. Moreover, detecting the tortuosity severity of the retinal vessels’, optimizing vessel segmentation, the vessel segment extraction, and the created feature set have increased the accuracy of the automatic tortuosity severity detection model.

Branch identification is key to the robotic pruning system for apple trees. High identification accuracy and the positioning of junction points between branch and trunk are important prerequisites for pruning with a robotic arm. Recently, with the development of deep learning, Transformer has been gradually applied to the field of computer vision and achieved good results. However, the effect of branch identification based on Transformer has not been verified so far. Taking Swin-T and Resnet50 as a backbone, this study detected and segmented the trunk, primary branch and support of apple trees on the basis of Mask R-CNN and Cascade Mask R-CNN. The results show that, when Intersection over Union (IoU) is 0.5, the bbox mAP and segm mAP of Cascade Mask R-CNN Swin-T are the highest, which are 0.943 and 0.940; as for the each category identification, Cascade Mask R-CNN Swin-T shows no significant difference with the other three algorithms in trunk and primary branch; when the identified object is a support, the bbox AP and segm AP of Cascade Mask R-CNN Swin-T is significantly higher than that of other algorithms, which are 0.879 and 0.893. Next, Cascade Mask R-CNN SW-T is combined with Zhang & Suen to obtain the junction point. Compared with the direct application of Zhang & Suen algorithm, the skeleton obtained by this method is advantaged by trunk diameter information, and its shape and junction points position are closer to the actual apple trees. This model and method can be applied to follow-up research and offer a new solution to the robotic pruning system for apple trees.

Objectives: The advent of micro‐computed tomography (μCT) made cancellous bone more accessible than ever before. Nevertheless, the characterization of cancellous bone is made difficult by its inherent complexity and the difficulties in defining homology across datasets. Here we propose novel virtual methodological approaches to overcome those issues and complement existing methods. Materials and methods: We present a protocol for the isolation of the whole cancellous region within a μCT scanned bone. This method overcomes the subsampling issues and allows studying cancellous bone as a single unit. We test the protocol on a set of primate bones. In addition, we describe a set of morphological indices calculated on the topological skeleton of the cancellous bone: node density, node connectivity, trabecular angle, trabecular tortuosity, and fractal dimension. The usage of the indices is shown on a small comparative sample of primate femoral heads. Results: The isolation protocol proves reliable in isolating cancellous structures from several different bones, regardless of their shape. The indices seem to detect some functional differences, although further testing on comparative samples is needed to clarify their potential for the study of cancellous architecture. Conclusions: The approaches presented overcome some of the difficulties of trabecular bone studies. The methods presented here represent an alternative or supporting method to the existing tools available to address the biomechanics of cancellous bone. [ABSTRACT FROM AUTHOR]

Background: In the context of biomarker discovery and molecular characterization of diseases, laser capture microdissection is a highly effective approach to extract disease-specific regions from complex, heterogeneous tissue samples. For the extraction to be successful, these regions have to satisfy certain constraints in size and shape and thus have to be decomposed into feasible fragments. Results: We model this problem of constrained shape decomposition as the computation of optimal feasible decompositions of simple polygons. We use a skeleton-based approach and present an algorithmic framework that allows the implementation of various feasibility criteria as well as optimization goals. Motivated by our application, we consider different constraints and examine the resulting fragmentations. We evaluate our algorithm on lung tissue samples in comparison to a heuristic decomposition approach. Our method achieved a success rate of over 95% in the microdissection and tissue yield was increased by 10–30%. Conclusion: We present a novel approach for constrained shape decomposition by demonstrating its advantages for the application in the microdissection of tissue samples. In comparison to the previous decomposition approach, the proposed method considerably increases the amount of successfully dissected tissue. [ABSTRACT FROM AUTHOR]

Chemotherapy for non-central nervous system cancers is associated with abnormalities in brain structure and function. Diffusion tensor imaging (DTI) allows for studying in vivo microstructural changes in brain white matter. Tract-based spatial statistics (TBSS) is a widely used processing pipeline in which DTI data are typically normalized to a generic DTI template and then 'skeletonized' to compensate for misregistration effects. However, this approach greatly reduces the overall white matter volume that is subjected to statistical analysis, leading to information loss. Here, we present a re-analysis of longitudinal data previously analyzed with standard TBSS (Menning et al., BIB 2018, 324–334). For our current approach, we constructed a pipeline with an optimized registration method in Advanced Normalization Tools (ANTs) where DTI data are registered to a study-specific, high-resolution T1 template and the skeletonization step is omitted. In a head to head comparison, we show that with our novel approach breast cancer survivors who had received chemotherapy plus or minus endocrine therapy (BC + SYST, n = 26) showed a global decline in overall FA that was not present in breast cancer survivors who did not receive systemic therapy (BC-SYST, n = 23) or women without a cancer diagnosis (no cancer controls, NC, n = 30). With the standard TBSS approach we did not find any group differences. Moreover, voxel-based analysis for our novel pipeline showed a widespread decline in FA in the BC + SYST compared to the NC group. Interestingly, the BC-SYST group also showed a decline in FA compared to the NC group, although in much less voxels. These results were not found with the standard TBSS approach. We demonstrate that a modified processing pipeline makes DTI data more sensitive to detecting changes in white matter integrity in non-CNS cancer patients after treatment, particularly chemotherapy. [ABSTRACT FROM AUTHOR]

Establishing meaningful relationships between cellular structure and function requires accurate morphological reconstructions. In particular, there is an unmet need for high quality surface reconstructions to model subcellular and synaptic interactions among neurons and glia at nanometer resolution. We address this need with VolRoverN, a software package that produces accurate, efficient, and automated 3D surface reconstructions from stacked 2D contour tracings. While many techniques and tools have been developed in the past for 3D visualization of cellular structure, the reconstructions from VolRoverN meet specific quality criteria that are important for dynamical simulations. These criteria include manifoldness, water-tightness, lack of self- and object-object-intersections, and geometric accuracy. These enhanced surface reconstructions are readily extensible to any cell type and are used here on spiny dendrites with complex morphology and axons from mature rat hippocampal area CA1. Both spatially realistic surface reconstructions and reduced skeletonizations are produced and formatted by VolRoverN for easy input into analysis software packages for neurophysiological simulations at multiple spatial and temporal scales ranging from ion electro-diffusion to electrical cable models.

Tree skeletons play an important role in tree structure analysis and 3D model reconstruction. However, it is a challenge to extract a skeleton from a tree point cloud with complex branches. In this paper, an automatic and fast tree skeleton extraction method (FTSEM) based on voxel thinning is proposed. In this method, a wood–leaf classification algorithm was introduced to filter leaf points for the reduction of the leaf interference on tree skeleton generation, tree voxel thinning was adopted to extract a raw tree skeleton quickly, and a breakpoint connection algorithm was used to improve the skeleton connectivity and completeness. Experiments were carried out in Haidian Park, Beijing, in which 24 trees were scanned and processed to obtain tree skeletons. The graph search algorithm (GSA) was used to extract tree skeletons based on the same datasets. Compared with the GSA method, the FTSEM method obtained more complete tree skeletons. The time cost of the FTSEM method was evaluated using the runtime and time per million points (TPMP). The runtime of FTSEM was from 1.0 s to 13.0 s, and the runtime of GSA was from 6.4 s to 309.3 s. The average value of TPMP was 1.8 s for FTSEM and 22.3 s for GSA, respectively. The experimental results demonstrate that the proposed method is feasible, robust, and fast with good potential for tree skeleton extraction.

Hepatic vessel skeletonization serves as an important means of hepatic vascular analysis and vessel segmentation. This paper presents a survey of techniques and algorithms for hepatic vessel skeletonization in medical images. We summarized the latest developments and classical approaches in this field. These methods are classified into five categories according to their methodological characteristics. The overview and brief assessment of each category are provided in the corresponding chapters, respectively. We provide a comprehensive summary among the cited publications, image modalities and datasets from various aspects, which hope to reveal the pros and cons of every method, summarize its achievements and discuss the challenges and future trends.

In this research, we study the problem of font image skeletonization using an end-to-end deep adversarial network, in contrast with the state-of-the-art methods that use mathematical algorithms. Several studies have been concerned with skeletonization, but a few have utilized deep learning. Further, no study has considered generative models based on deep neural networks for font character skeletonization, which are more delicate than natural objects. In this work, we take a step closer to producing realistic synthesized skeletons of font characters. We consider using an end-to-end deep adversarial network, SkelGAN, for font-image skeletonization, in contrast with the state-of-the-art methods that use mathematical algorithms. The proposed skeleton generator is proved superior to all well-known mathematical skeletonization methods in terms of character structure, including delicate strokes, serifs, and even special styles. Experimental results also demonstrate the dominance of our method against the state-of-the-art supervised image-to-image translation method in font character skeletonization task. [ABSTRACT FROM AUTHOR]