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A quasi-3D model of the whole lung: airway extension to the tracheobronchial limit using the constrained constructive optimization and alveolar modeling, using a sac-trumpet model

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JOURNAL OF COMPUTATIONAL DESIGN AND ENGINEERING 2021年第2期8卷 691-704页

作者： Kannan, Ravishekar (Ravi) Singh, Narender Przekwas, Andrzej Zhou, Xianlian Alex Walenga, Ross Babiskin, Andrew CFD Res Corp 701 McMillian Way NWSuite D Huntsville AL 35806 USA New Jersey Inst Technol 323 Martin Luther King Blvd Newark NJ 07102 USA US FDA Ctr Drug Evaluat Res Silver Spring MD 20993 USA

Existing computational models used for simulating the flow and species transport in the human airways are zero-dimensional (0D) compartmental, three-dimensional (3D) computational fluid dynamics (CFD), or the recently developed quasi-3D (Q3D) models. Unlike compartmental models, the full CFD and Q3D models are physiologically and anatomically consistent in the mouth and the upper airways, since the starting point of these models is the mouth-lung surface geometry, typically created from computed tomography (CT) scans. However, the current resolution of CT scans limits the airway detection between the 3rd-4th and 7th-9th generations. Consequently, CFD and the Q3D models developed using these scans are generally limited to these generations. In this study, we developed a method to extend the conducting airways from the end of the truncated Q3D lung to the tracheobronchial (TB) limit. We grew the lung generations within the closed lung lobes using the modified constrained constructive optimization, creating an aerodynamically optimized network aiming to produce equal pressure at the distal ends of the terminal segments. This resulted in a TB volume and lateral area of similar to 165 cc and similar to 2000 cm(2), respectively. We created a "sac-trumpet" model at each of the TB outlets to represent the alveoli. The volumes of the airways and the individual alveolar generations match the anatomical values by design: with the functional residual capacity at 2611 cc. Lateral surface areas were scaled to match the physiological values. These generated Q3D whole lung models can be efficiently used for conducting multiple breathing cycles of drug transport and deposition simulations.

关键词： CFD quasi-3D (Q3D) Q3D lung airway constrained constructive optimization sac-trumpet CCO

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In Silico Design of Heterogeneous Microvascular Trees Using Generative Adversarial Networks and constrained constructive optimization

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MICROCIRCULATION 2024年第5期31卷 e12854-e12854页

作者： Pan, Qing Shen, Huanghui Li, Peilun Lai, Biyun Jiang, Akang Huang, Wenjie Lu, Fei Peng, Hong Fang, Luping Kuebler, Wolfgang M. Pries, Axel R. Ning, Gangmin Zhejiang Univ Technol Coll Informat Engn Hangzhou Peoples R China Zhejiang Univ Dept Biomed Engn Key Lab Biomed Engn MOE Hangzhou Peoples R China Charite Univ Med Berlin Inst Physiol Berlin Germany Free Univ Berlin Berlin Germany Humboldt Univ Berlin Germany Danube Private Univ Fac Med & Dent Dept Med Krems Austria

ObjectiveDesigning physiologically adequate microvascular trees is of crucial relevance for bioengineering functional tissues and organs. Yet, currently available methods are poorly suited to replicate the morphological and topological heterogeneity of real microvascular trees because the parameters used to control tree generation are too simplistic to mimic results of the complex angiogenetic and structural adaptation processes in *** propose a method to overcome this limitation by integrating a conditional deep convolutional generative adversarial network (cDCGAN) with a local fractal dimension-oriented constrained constructive optimization (LFDO-CCO) strategy. The cDCGAN learns the patterns of real microvascular bifurcations allowing for their artificial replication. The LFDO-CCO strategy connects the generated bifurcations hierarchically to form microvascular trees with a vessel density corresponding to that observed in healthy *** generated artificial microvascular trees are consistent with real microvascular trees regarding characteristics such as fractal dimension, vascular density, and coefficient of variation of diameter, length, and *** results support the adoption of the proposed strategy for the generation of artificial microvascular trees in tissue engineering as well as for computational modeling and simulations of microcirculatory physiology.

关键词： constrained constructive optimization generative adversarial network microvascular tree tissue engineering

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3D Printable Vascular Networks Generated by Accelerated constrained constructive optimization for Tissue Engineering

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IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING 2020年第6期67卷 1650-1663页

作者： Guy, Andrew A. Justin, Alexander W. Aguilar-Garza, Dulce M. Markaki, Athina E. Univ Cambridge Dept Engn Cambridge CB2 1PZ England

One of the greatest challenges in fabricating artificial tissues and organs is the incorporation of vascular networks to support the biological requirements of the embedded cells, encouraging tissue formation and maturation. With the advent of 3D printing technology, significant progress has been made with respect to generating vascularized artificial tissues. Current algorithms to generate arterial/venous trees are computationally expensive and offer limited freedom to optimize the resulting structures. Furthermore, there is no method for algorithmic generation of vascular networks that can recapitulate the complexity of the native vasculature for more than two trees, and export directly to a 3D printing format. Here, we report such a method, using an accelerated constructive constrained optimization approach, by decomposing the process into construction, optimization, and collision resolution stages. The new approach reduces computation time to minutes at problem sizes where previous implementations have reported days. With the optimality criterion of maximizing the volume of useful tissue which could be grown around such a network, an approach of alternating stages of construction and batch optimization of all node positions is introduced and shown to yield consistently more optimal networks. The approach does not place a limit on the number of interpenetrating networks that can be constructed in a given space;indeed we demonstrate a biomimetic, liver-like tissue model. Methods to account for the limitations of 3D printing are provided, notably the minimum feature size and infill at sharp angles, through padding and angle reduction, respectively.

关键词： optimization Bifurcation Three-dimensional printing Biological system modeling Solid modeling Physiology Three-dimensional displays constrained constructive optimization vascular networks tissue engineering 3D printing

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Convex optimization for Binary Tree-Based Transport Networks 3rd

Convex Optimization for Binary Tree-Based Transport Networks

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3rd International Joint Conference on Discrete Geometry and Mathematical Morphology (DGM)

作者： de Chou, Raoul Salle Srir, Mohamed Ali Najman, Laurent Passat, Nicolas Talbot, Hugues Vignon-Clementel, Irene INRIA Palaiseau France Univ Paris Saclay INRIA CentraleSupelec Gif Sur Yvette France Univ Gustave Eiffel CNRS LIGM Champs Sur Marne France Univ Reims CReSTIC Reims France

ISBN: (纸本)9783031577925;9783031577932

Optimizing transport networks is a well-known class of problems that have been extensively studied, with application in many domains. Here we are interested in a generalization of the Steiner problem, which entails finding a graph minimizing a cost function associated with connecting a given set of points. In this paper, we concentrate on a specific formulation of this problem which is applied to the generation of synthetic vascular trees. More precisely, we focus on the constrained constructive optimization (CCO) tree algorithm, which constructs a vascular network iteratively, optimizing a blood transport energy efficiency. We show that the classical incremental construction method often leads to sub-optimal results, and that a better global solution can be reached.

关键词： constrained constructive optimization Discrete optimal transport Binary trees Convex optimization Numerical twin

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Generation of Patient-Specific Cardiac Vascular Networks: A Hybrid Image-Based and Synthetic Geometric Model

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IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING 2019年第4期66卷 946-955页

作者： Jaquet, Clara Najman, Laurent Talbot, Hugues Grady, Leo Schaap, Michiel Spain, Buzzy Kim, Hyun Jin Vignon-Clementel, Irene Taylor, Charles A. Univ Paris Est ESIEE Paris F-93162 Noisy Le Grand France Univ Paris Saclay Cent Supelec Gif Sur Yvette France Univ Paris Est ESIEE Noisy Le Grand France HeartFlow Inc Redwood City CA USA INRIA Paris France Sorbonne Univ Paris France

Objective: In this paper, we propose an algorithm for the generation of a patient-specific cardiac vascular network starting from segmented epicardial vessels down to the arterioles. Method: We extend a tree generation method based on satisfaction of functional principles, named constrained constructive optimization, to account for multiple, competing vascular trees. The algorithm simulates angiogenesis under vascular volume minimization with flow-related and geometrical constraints adapting the simultaneous tree growths to patient priors. The generated trees fill the entire left ventricle myocardium up to the arterioles. Results: From actual vascular tree models segmented from CT images, we generated networks with 6000 terminal segments for six patients. These networks contain between 33 and 62 synthetic trees. All vascular models match morphometry properties previously described. Conclusion and significance: Image-based models derived from CT angiography are being used clinically to simulate blood flow in the coronary arteries of individual patients to aid in the diagnosis of disease and planning treatments. However, image resolution limits vessel segmentation to larger epicardial arteries. The generated model can be used to simulate the blood flow and derived quantities from the aorta into the myocardium. This is an important step for diagnosis and treatment planning of coronary artery disease.

关键词： Arterial morphometry constrained constructive optimization coronary arteries patient-specific modeling

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Modeling sphere dynamics in blood vessels for SIRT pre-planning - To fathom the potential and limitations

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ZEITSCHRIFT FUR MEDIZINISCHE PHYSIK 2019年第1期29卷 5-15页

作者： Kretzi, Dominik Hesser, Juergen Glatting, Gerhard Diehl, Steffen Wenz, Frederik He, Wanji Zheng, Lei Heidelberg Univ Univ Med Ctr Mannheim Dept Radiat Oncol Expt Radiat Oncol Heidelberg Germany Heidelberg Univ Interdisciplinary Ctr Sci Comp IWR Heidelberg Germany Cent Inst Mental Hlth ZI Mannheim Germany Heidelberg Univ Univ Med Ctr Mannheim Med Fac Mannheim Med Radiat Phys Radiat ProtectDept Radiat Oncol Heidelberg Germany Heidelberg Univ Univ Med Ctr Mannheim Dept Clin Radiol & Nucl Med Heidelberg Germany Heidelberg Univ Univ Med Ctr Mannheim Dept Radiat Oncol Heidelberg Germany

For selective internal radiation therapy (SIRT) the calculation of the 3D distribution of spheres based on individual blood flow properties is still an open and relevant research question. The purpose of this work is to develop and analyze a new treatment planning method for SIRT to calculate the absorbed dose distribution. For this intention, flow dynamics of the SIRT-spheres inside the blood vessels was simulated. The challenge is treatment planning solely using high-resolution imaging data available before treatment. The resolution required to reliably predict the sphere distribution and hence the dose was investigated. For this purpose, arteries of the liver were segmented from a contrast-enhanced angiographic CT. Due to the limited resolution of the given CT smaller vessels were generated via a vessel model. A combined 1D/3D-flow simulation model was implemented to simulate the final 3D distribution of spheres and dose. Results were evaluated against experimental data from Y-90-PET. Analysis showed that the resolution of the vessels within the angiographic CT of about 0.5 mm should be improved to a limit of about 150 mu m to reach a reliable prediction.

关键词： Treatment planning Blood flow simulation Smoothed particle hydrodynamics Vessel segmentation constrained constructive optimization Y-90-PET

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Algorithmically generated rodent hepatic vascular trees in arbitrary detail

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JOURNAL OF THEORETICAL BIOLOGY 2015年 365卷 289-300页

作者： Schwen, Lars Ole Wei, Weiwei Gremse, Felix Ehling, Josef Wang, Lei Dahmen, Uta Preusser, Tobias Fraunhofer MEVIS D-28359 Bremen Germany Univ Hosp Jena Dept Gen Visceral & Vasc Surg D-07747 Jena Germany Rhein Westfal TH Aachen D-52074 Aachen Germany Univ Bremen Sch Sci & Engn D-28759 Bremen Germany

Physiologically realistic geometric models of the vasculature in the liver are indispensable for modelling hepatic blood flow, the main connection between the liver and the organism. Current in vivo imaging techniques do not provide sufficiently detailed vascular trees for many simulation applications, so it is necessary to use algorithmic refinement methods. The method of constrained constructive optimization (CCO) (Schreiner et al., 2006) is well suited for this purpose. Its results after calibration have been previously compared to experimentally acquired human vascular trees (Schwen and Preusser, 2012). The goal of this paper is to extend this calibration to the case of rodents (mice and rats), the most commonly used animal models in liver research. Based on in vivo and ex vivo micro-CT scans of rodent livers and their vasculature, we performed an analysis of various geometric features of the vascular trees. Starting from pruned versions of the original vascular trees, we applied the CCO procedure and compared these algorithmic results to the original vascular trees using a suitable similarity measure. The calibration of the postprocessing improved the algorithmic results compared to those obtained using standard CCO. In terms of angular features, the average similarity increased from 027 to 0.61, improving the total similarity from 028 to 0.40. Finally, we applied the calibrated algorithm to refine measured vascular trees to the (higher) level of detail desired for specific applications. Having successfully adapted the CCO algorithm to the rodent model organism, the resulting individual-specific refined hepatic vascular trees can now be used for advanced modeling involving, e.g., detailed blood flow simulations. (C) 2014 Elsevier Ltd. All rights reserved.

关键词： constrained constructive optimization Hepatic portal vein Hepatic vein

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Simulation and Analysis of Three-dimensional Arterial Trees

Simulation and Analysis of Three-dimensional Arterial Trees

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2nd International Conference on Sensors, Measurement and Intelligent Materials (ICSMIM 2013)

作者： Zhang, Yan Xie, Haiwei Tianjin Univ Commerce Tianjin Key Lab Refrigerat Technol Sch Mech Engn Tianjin Peoples R China

ISBN: (纸本)9783037859711

For hemodynamic simulation and heat transfer analysis of blood, it is necessary to generate a three-dimensional model of arterial tree. Referring to the approach of constrained constructive optimization (CCO), a new method based on bifurcation law, Poiseuille's law and mass conservation was proposed to model arterial trees directly in simulation objects. The formulas for calculating the bifurcation ratios and the way to determine the location of bifurcation point were presented in the paper. In this model, the radius of the root segment was constant, the terminal pressure was unknown and the bifurcation exponent was variable. In order to demonstrate the feasibility of this method, an arterial tree was constructed in a spherical tissue.

关键词： Artery Vascular trees Computer simulation constrained constructive optimization

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Investigation of Pulmonary Acoustic Simulation: Comparing Airway Model Generation Techniques

Investigation of Pulmonary Acoustic Simulation: Comparing Ai...

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Conference on Medical Imaging - Biomedical Applications in Molecular, Structural, and Functional Imaging

作者： Henry, Brian Dai, Zoujun Peng, Ying Mansy, Hansen A. Sandler, Richard H. Royston, Thomas Univ Illinois Dept Bioengn Chicago IL 60607 USA Rush Univ Med Ctr Chicago IL 60612 USA Univ Cent Florida Orlando FL 32816 USA Nemours Childrens Hosp Orlando FL 32827 USA

ISBN: (纸本)9780819498311

Alterations in the structure and function of the pulmonary system that occur in disease or injury often give rise to measurable spectral, spatial and/or temporal changes in lung sound production and transmission. These changes, if properly quantified, might provide additional information about the etiology, severity and location of trauma, injury, or pathology. With this in mind, the authors are developing a comprehensive computer simulation model of pulmonary acoustics, known as The Audible Human Project T. Its purpose is to improve our understanding of pulmonary acoustics and to aid in interpreting measurements of sound and vibration in the lungs generated by airway insonification, natural breath sounds, and external stimuli on the chest surface, such as that used in elastography. As a part of this development process, finite element (FE) models were constructed of an excised pig lung that also underwent experimental studies. Within these models, the complex airway structure was created via two methods: x-ray CT image segmentation and through an algorithmic means called constrained constructive optimization (CCO). CCO was implemented to expedite the segmentation process, as airway segments can be grown digitally. These two approaches were used in FE simulations of the surface motion on the lung as a result of sound input into the trachea. Simulation results were compared to experimental measurements. By testing how close these models are to experimental measurements, we are evaluating whether CCO can be used as a means to efficiently construct physiologically relevant airway trees.

关键词： Pulmonary structure acoustics constrained constructive optimization image segmentation elastography

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Error estimation of geometrical data obtained by histomorphometry of oblique vessel sections: a computer model study

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COMPUTERS IN BIOLOGY AND MEDICINE 2005年第9期35卷 829-844页

作者： Nadler, BA Karch, R Neumann, M Neumann, F Aharinejad, S Schreiner, W Med Univ Vienna Dept Med Comp Sci A-1090 Vienna Austria Med Univ Vienna Inst Expt Phys A-1090 Vienna Austria Med Univ Vienna Dept Anat Cardiovasc Res Lab A-1090 Vienna Austria

The errors of radius and wall thickness of a single vessel due to oblique sectioning in histomorphometry are expressed as a function of the circular shape factor (CSF) of the section's lumen, assuming cylindrical geometry and the absence of tissue deformation. Using computer model trees generated by constrained constructive optimization, mean errors are estimated for an ensemble of vessel segments. A geometrical exclusion criterion for segments cut too obliquely is defined on the basis of a CSF-cutoff value. It is shown that CSF-values ranging from 0.95 to 0.9 are reasonable choices for a cutoff and lead to mean errors of the same order of magnitude (9.6% [9.3%] to 15.4% [14.8%] for the radius [wall thickness]) as errors due to histological tissue processing. (c) 2004 Elsevier Ltd. All rights reserved.

关键词： vascular trees arterial geometry shape factor cutting angle constrained constructive optimization

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