Synthesis of geometrically realistic and watertight neuronal ultrastructure manifolds for in silico modeling.

Understanding the intracellular dynamics of brain cells entails performing three-dimensional molecular simulations incorporating ultrastructural models that can capture cellular membrane geometries at nanometer scales. While there is an abundance of neuronal morphologies available online, e.g. from NeuroMorpho.Org, converting those fairly abstract point-and-diameter representations into geometrically realistic and simulation-ready, i.e. watertight, manifolds is challenging. Many neuronal mesh reconstruction methods have been proposed; however, their resulting meshes are either biologically unplausible or non-watertight. We present an effective and unconditionally robust method capable of generating geometrically realistic and watertight surface manifolds of spiny cortical neurons from their morphological descriptions. The robustness of our method is assessed based on a mixed dataset of cortical neurons with a wide variety of morphological classes. The implementation is seamlessly extended and applied to synthetic astrocytic morphologies that are also plausibly biological in detail. Resulting meshes are ultimately used to create volumetric meshes with tetrahedral domains to perform scalable in silico reaction-diffusion simulations for revealing cellular structure-function relationships. Availability and implementation: Our method is implemented in NeuroMorphoVis, a neuroscience-specific open source Blender add-on, making it freely accessible for neuroscience researchers.

Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience.

Ultraliser is a neuroscience-specific software framework capable of creating accurate and biologically realistic 3D models of complex neuroscientific structures at intracellular (e.g. mitochondria and endoplasmic reticula), cellular (e.g. neurons and glia) and even multicellular scales of resolution (e.g. cerebral vasculature and minicolumns). Resulting models are exported as triangulated surface meshes and annotated volumes for multiple applications in in silico neuroscience, allowing scalable supercomputer simulations that can unravel intricate cellular structure-function relationships. Ultraliser implements a high-performance and unconditionally robust voxelization engine adapted to create optimized watertight surface meshes and annotated voxel grids from arbitrary non-watertight triangular soups, digitized morphological skeletons or binary volumetric masks. The framework represents a major leap forward in simulation-based neuroscience, making it possible to employ high-resolution 3D structural models for quantification of surface areas and volumes, which are of the utmost importance for cellular and system simulations. The power of Ultraliser is demonstrated with several use cases in which hundreds of models are created for potential application in diverse types of simulations. Ultraliser is publicly released under the GNU GPL3 license on GitHub (BlueBrain/Ultraliser). SIGNIFICANCE: There is crystal clear evidence on the impact of cell shape on its signaling mechanisms. Structural models can therefore be insightful to realize the function; the more realistic the structure can be, the further we get insights into the function. Creating realistic structural models from existing ones is challenging, particularly when needed for detailed subcellular simulations. We present Ultraliser, a neuroscience-dedicated framework capable of building these structural models with realistic and detailed cellular geometries that can be used for simulations.

Mapping Understory Vegetation Density in Mediterranean Forests: Insights from Airborne and Terrestrial Laser Scanning Integration.

The understory is an essential ecological and structural component of forest ecosystems. The lack of efficient, accurate, and objective methods for evaluating and quantifying the spatial spread of understory characteristics over large areas is a challenge for forest planning and management, with specific regard to biodiversity and habitat governance. In this study, we used terrestrial and airborne laser scanning (TLS and ALS) data to characterize understory in a European beech and black pine forest in Italy. First, we linked understory structural features derived from traditional field measurements with TLS metrics, then, we related such metrics to the ones derived from ALS. Results indicate that (i) the upper understory density (5-10 m above ground) is significantly associated with two ALS metrics, specifically the mean height of points belonging to the lower third of the ALS point cloud within the voxel (HM1/3) and the corresponding standard deviation (SD1/3), while (ii) for the lower understory layer (2-5 m above ground), the most related metric is HM1/3 alone. As an example application, we have produced a map of forest understory for each layer, extending over the entire study region covered by ALS data, based on the developed spatial prediction models. With this study, we also demonstrated the power of hand-held mobile-TLS as a fast and high-resolution tool for measuring forest structural attributes and obtaining relevant ecological data.

Three-Dimensional Point Cloud Segmentation Algorithm Based on Depth Camera for Large Size Model Point Cloud Unsupervised Class Segmentation.

This paper proposes a 3D point cloud segmentation algorithm based on a depth camera for large-scale model point cloud unsupervised class segmentation. The algorithm utilizes depth information obtained from a depth camera and a voxelization technique to reduce the size of the point cloud, and then uses clustering methods to segment the voxels based on their density and distance to the camera. Experimental results show that the proposed algorithm achieves high segmentation accuracy and fast segmentation speed on various large-scale model point clouds. Compared with recent similar works, the algorithm demonstrates superior performance in terms of accuracy metrics, with an average Intersection over Union (IoU) of 90.2% on our own benchmark dataset.

Development of a novel program for conversion from tetrahedral-mesh-based phantoms to DICOM dataset for radiation treatment planning: TET2DICOM.

PURPOSE: Tetrahedral mesh (TM)-based computational human phantoms have recently been developed for evaluation of exposure dose with the merit of precisely representing human anatomy and the changing posture freely. However, conversion of recently developed TM phantoms to the Digital Imaging and Communications in Medicine (DICOM) file format, which can be utilized in the clinic, has not been attempted. The aim of this study was to develop a technique, called TET2DICOM, to convert the TM phantoms to DICOM datasets for accurate treatment planning. MATERIALS AND METHODS: The TM phantoms were sampled in voxel form to generate the DICOM computed tomography images. The DICOM-radiotherapy structure was defined based on the contour data. To evaluate TET2DICOM, the shape distortion of the TM phantoms during the conversion process was assessed, and the converted DICOM dataset was implemented in a commercial treatment planning system (TPS). RESULTS: The volume difference between the TM phantoms and the converted DICOM dataset was evaluated as less than about 0.1% in each organ. Subsequently, the converted DICOM dataset was successfully implemented in MIM (MIM Software Inc., Cleveland, USA, version 6.5.6) and RayStation (RaySearch Laboratories, Stockholm, Sweden, version 5.0). Additionally, the various possibilities of clinical application of the program were confirmed using a deformed TM phantom in various postures. CONCLUSION: In conclusion, the TM phantom, currently the most advanced computational phantom, can be implemented in a commercial TPS and this technique can enable various TM-based applications, such as evaluation of secondary cancer risk in radiotherapy.

3D Object Detection Based on Attention and Multi-Scale Feature Fusion.

Three-dimensional object detection in the point cloud can provide more accurate object data for autonomous driving. In this paper, we propose a method named MA-MFFC that uses an attention mechanism and a multi-scale feature fusion network with ConvNeXt module to improve the accuracy of object detection. The multi-attention (MA) module contains point-channel attention and voxel attention, which are used in voxelization and 3D backbone. By considering the point-wise and channel-wise, the attention mechanism enhances the information of key points in voxels, suppresses background point clouds in voxelization, and improves the robustness of the network. The voxel attention module is used in the 3D backbone to obtain more robust and discriminative voxel features. The MFFC module contains the multi-scale feature fusion network and the ConvNeXt module; the multi-scale feature fusion network can extract rich feature information and improve the detection accuracy, and the convolutional layer is replaced with the ConvNeXt module to enhance the feature extraction capability of the network. The experimental results show that the average accuracy is 64.60% for pedestrians and 80.92% for cyclists on the KITTI dataset, which is 1.33% and 2.1% higher, respectively, compared with the baseline network, enabling more accurate detection and localization of more difficult objects.

A computational pipeline towards large-scale and multiscale modeling of traumatic axonal injury.

Contemporary biomechanical modeling of traumatic brain injury (TBI) focuses on either the global brain as an organ or a representative tiny section of a single axon. In addition, while it is common for a global brain model to employ real-world impacts as input, axonal injury models have largely been limited to inputs of either tension or compression with assumed peak strain and strain rate. These major gaps between global and microscale modeling preclude a systematic and mechanistic investigation of how tissue strain from impact leads to downstream axonal damage throughout the white matter. In this study, a unique subject-specific multimodality dataset from a male ice-hockey player sustaining a diagnosed concussion is used to establish an efficient and scalable computational pipeline. It is then employed to derive voxelized brain deformation, maximum principal strains and white matter fiber strains, and finally, to produce diverse fiber strain profiles of various shapes in temporal history necessary for the development and application of a deep learning axonal injury model in the future. The pipeline employs a structured, voxelized representation of brain deformation with adjustable spatial resolution independent of model mesh resolution. The method can be easily extended to other head impacts or individuals. The framework established in this work is critical for enabling large-scale (i.e., across the entire white matter region, head impacts, and individuals) and multiscale (i.e., from organ to cell length scales) modeling for the investigation of traumatic axonal injury (TAI) triggering mechanisms. Ultimately, these efforts could enhance the assessment of concussion risks and design of protective headgear. Therefore, this work contributes to improved strategies for concussion detection, mitigation, and prevention.

A Human Brain Map of Mitochondrial Respiratory Capacity and Diversity.

Mitochondrial oxidative phosphorylation (OxPhos) powers brain activity1,2, and mitochondrial defects are linked to neurodegenerative and neuropsychiatric disorders3,4, underscoring the need to define the brain's molecular energetic landscape5-10. To bridge the cognitive neuroscience and cell biology scale gap, we developed a physical voxelization approach to partition a frozen human coronal hemisphere section into 703 voxels comparable to neuroimaging resolution (3×3×3 mm). In each cortical and subcortical brain voxel, we profiled mitochondrial phenotypes including OxPhos enzyme activities, mitochondrial DNA and volume density, and mitochondria-specific respiratory capacity. We show that the human brain contains a diversity of mitochondrial phenotypes driven by both topology and cell types. Compared to white matter, grey matter contains >50% more mitochondria. We show that the more abundant grey matter mitochondria also are biochemically optimized for energy transformation, particularly among recently evolved cortical brain regions. Scaling these data to the whole brain, we created a backward linear regression model integrating several neuroimaging modalities11, thereby generating a brain-wide map of mitochondrial distribution and specialization that predicts mitochondrial characteristics in an independent brain region of the same donor brain. This new approach and the resulting MitoBrainMap of mitochondrial phenotypes provide a foundation for exploring the molecular energetic landscape that enables normal brain functions, relating it to neuroimaging data, and defining the subcellular basis for regionalized brain processes relevant to neuropsychiatric and neurodegenerative disorders.

A Human Brain Map of Mitochondrial Respiratory Capacity and Diversity.

Mitochondrial oxidative phosphorylation (OxPhos) powers brain activity1,2, and mitochondrial defects are linked to neurodegenerative and neuropsychiatric disorders3,4, underscoring the need to define the brain's molecular energetic landscape5-10. To bridge the cognitive neuroscience and cell biology scale gap, we developed a physical voxelization approach to partition a frozen human coronal hemisphere section into 703 voxels comparable to neuroimaging resolution (3×3×3 mm). In each cortical and subcortical brain voxel, we profiled mitochondrial phenotypes including OxPhos enzyme activities, mitochondrial DNA and volume density, and mitochondria-specific respiratory capacity. We show that the human brain contains a diversity of mitochondrial phenotypes driven by both topology and cell types. Compared to white matter, grey matter contains >50% more mitochondria. We show that the more abundant grey matter mitochondria also are biochemically optimized for energy transformation, particularly among recently evolved cortical brain regions. Scaling these data to the whole brain, we created a backward linear regression model integrating several neuroimaging modalities11, thereby generating a brain-wide map of mitochondrial distribution and specialization that predicts mitochondrial characteristics in an independent brain region of the same donor brain. This new approach and the resulting MitoBrainMap of mitochondrial phenotypes provide a foundation for exploring the molecular energetic landscape that enables normal brain functions, relating it to neuroimaging data, and defining the subcellular basis for regionalized brain processes relevant to neuropsychiatric and neurodegenerative disorders.

Polymorph segmentation representation for medical image computing.

BACKGROUND AND OBJECTIVE: Segmentation is a ubiquitous operation in medical image computing. Various data representations can describe segmentation results, such as labelmap volumes or surface models. Conversions between them are often required, which typically include complex data processing steps. We identified four challenges related to managing multiple representations: conversion method selection, data provenance, data consistency, and coherence of in-memory objects. METHODS: A complex data container preserves identity and provenance of the contained representations and ensures data coherence. Conversions are executed automatically on-demand. A graph containing the implemented conversion algorithms determines each execution, ensuring consistency between various representations. The design and implementation of a software library are proposed, in order to provide a readily usable software tool to manage segmentation data in multiple data representations. A low-level core library called PolySeg implemented in the Visualization Toolkit (VTK) manages the data objects and conversions. It is used by a high-level application layer, which has been implemented in the medical image visualization and analysis platform 3D Slicer. The application layer provides advanced visualization, transformation, interoperability, and other functions. RESULTS: The core conversion algorithms comprising the graph were validated. Several applications were implemented based on the library, demonstrating advantages in terms of usability and ease of software development in each case. The Segment Editor application provides fast, comprehensive, and easy-to-use manual and semi-automatic segmentation workflows. Clinical applications for gel dosimetry, external beam planning, and MRI-ultrasound image fusion in brachytherapy were rapidly prototyped resulting robust applications that are already in use in clinical research. The conversion algorithms were found to be accurate and reliable using these applications. CONCLUSIONS: A generic software library has been designed and developed for automatic management of multiple data formats in segmentation tasks. It enhances both user and developer experience, enabling fast and convenient manual workflows and quicker and more robust software prototyping. The software's BSD-style open-source license allows complete freedom of use of the library.

Dose distribution prediction in isodose feature-preserving voxelization domain using deep convolutional neural network.

PURPOSE: To implement a framework for dose prediction using a deep convolutional neural network (CNN) based on the concept of isodose feature-preserving voxelization (IFPV) in simplifying the representation of the dose distribution. METHODS: The concept of IFPV was introduced for concise representation of a treatment plan. IFPV is a sparse voxelization scheme that partitions the voxels into subgroups according to their geometric, anatomical, and dosimetric features. In this study a deep CNN was constructed to buildup a dose prediction model in IFPV domain based on 60 volumetric modulated arc therapy (VMAT) treatment plans from a database of previously treated 70 prostate cancer patients. The dose prediction model learns the contour to dose relationship and predicts the dose distribution in IFPV domain given the input contours. Additional ten independent prostate cases were selected as testing data.DVH comparison, dose difference maps, and residual analysis with the sum of absolute residual (SAR) were used to evaluate the performance of the proposed method. RESULTS: The proposed IFPV-based method achieved good prediction performance in terms of DVH comparison and dose difference maps. Statistical results of SARs showed that the IFPV-based method is comparable with voxel-based method even though the number of dose representation points used in the IFPV-based method was substantially reduced. The proposed approach achieved mean SARs of 0.029 ± 0.020 and 0.077 ± 0.030 for bladder and rectum, respectively, compared with mean SARs of 0.039 ± 0.029 and 0.069 ± 0.028 in the conventional voxel-based method. CONCLUSIONS: A novel deep CNN-based dose prediction method in IFPV domain was proposed. The proposed approach has great potential to significantly improve the efficiency of dose prediction and facilitate the treatment planning workflow.

Isodose feature-preserving voxelization (IFPV) for radiation therapy treatment planning.

PURPOSE: Inverse planning involves iterative optimization of a large number of parameters and is known to be a labor-intensive procedure. To reduce the scale of computation and improve characterization of isodose plan, this paper presents an isodose feature-preserving voxelization (IFPV) framework for radiation therapy applications and demonstrates an implementation of inverse planning in the IFPV domain. METHODS: A dose distribution in IFPV scheme is characterized by partitioning the voxels into subgroups according to their geometric and dosimetric values. Computationally, the isodose feature-preserving (IFP) clustering combines the conventional voxels that are spatially and dosimetrically close into physically meaningful clusters. A K-means algorithm and support vector machine (SVM) runs sequentially to group the voxels into IFP clusters. The former generates initial clusters according to the geometric and dosimetric information of the voxels and SVM is invoked to improve the connectivity of the IFP clusters. To illustrate the utility of the formalism, an inverse planning framework in the IFPV domain is implemented, and the resultant plans of three prostate IMRT and one head-and-neck cases are compared quantitatively with that obtained using conventional inverse planning technique. RESULTS: The IFPV generates models with significant dimensionality reduction without compromising the spatial resolution seen in traditional downsampling schemes. The implementation of inverse planning in IFPV domain is demonstrated. In addition to the improved computational efficiency, it is found that, for the cases studied here, the IFPV-domain inverse planning yields better treatment plans than that of DVH-based planning, primarily because of more effective use of both geometric and dose information of the system during plan optimization. CONCLUSIONS: The proposed IFPV provides a low parametric representation of isodose plan without compromising the essential characteristics of the plan, thus providing a practically valuable framework for various applications in radiation therapy.

The Effect of Crystal Defects on 3D High-Resolution Diffraction Peaks: A FFT-Based Method.

Forward modeling of diffraction peaks is a potential way to compare the results of theoretical mechanical simulations and experimental X-ray diffraction (XRD) data recorded during in situ experiments. As the input data are the strain or displacement field within a representative volume of the material containing dislocations, a computer-aided efficient and accurate method to generate these fields is necessary. With this aim, a current and promising numerical method is based on the use of the fast Fourier transform (FFT)-based method. However, classic FFT-based methods present some numerical artifacts due to the Gibbs phenomenon or "aliasing" and to "voxelization" effects. Here, we propose several improvements: first, a consistent discrete Green operator to remove "aliasing" effects; and second, a method to minimize the voxelization artifacts generated by dislocation loops inclined with respect to the computational grid. Then, we show the effect of these improvements on theoretical diffraction peaks.

Voxelization algorithms for geospatial applications: Computational methods for voxelating spatial datasets of 3D city models containing 3D surface, curve and point data models.

Voxel representations have been used for years in scientific computation and medical imaging. The main focus of our research is to provide easy access to methods for making large-scale voxel models of built environment for environmental modelling studies while ensuring they are spatially correct, meaning they correctly represent topological and semantic relations among objects. In this article, we present algorithms that generate voxels (volumetric pixels) out of point cloud, curve, or surface objects. The algorithms for voxelization of surfaces and curves are a customization of the topological voxelization approach [1]; we additionally provide an extension of this method for voxelization of point clouds. The developed software has the following advantages:•It provides easy management of connectivity levels in the resulting voxels.•It is not dependant on any external library except for primitive types and constructs; therefore, it is easy to integrate them in any application.•One of the algorithms is implemented in C++ and C for platform independence and efficiency.