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Linninger AA, Ventimiglia T, Jamshidi M, Pascal Suisse M, Alaraj A, Lesage F, Li X, Schwartz DL, Rooney WD. Vascular synthesis based on hemodynamic efficiency principle recapitulates measured cerebral circulation properties in the human brain. J Cereb Blood Flow Metab 2024; 44:801-816. [PMID: 37988131 PMCID: PMC11197140 DOI: 10.1177/0271678x231214840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/20/2023] [Accepted: 10/21/2023] [Indexed: 11/22/2023]
Abstract
Quantifying anatomical and hemodynamical properties of the brain vasculature in vivo is difficult due to limited spatiotemporal resolution neuroimaging, variability between subjects, and bias between acquisition techniques. This work introduces a metabolically inspired vascular synthesis algorithm for creating a digital representation of the cortical blood supply in humans. Spatial organization and segment resistances of a cortical vascular network were generated. Cortical folding and macroscale arterial and venous vessels were reconstructed from anatomical MRI and MR angiography. The remaining network, including ensembles representing the parenchymal capillary bed, were synthesized following a mechanistic principle based on hydrodynamic efficiency of the cortical blood supply. We evaluated the digital model by comparing its simulated values with in vivo healthy human brain measurements of macrovessel blood velocity from phase contrast MRI and capillary bed transit times and bolus arrival times from dynamic susceptibility contrast. We find that measured and simulated values reasonably agree and that relevant neuroimaging observables can be recapitulated in silico. This work provides a basis for describing and testing quantitative aspects of the cerebrovascular circulation that are not directly observable. Future applications of such digital brains include the investigation of the organ-wide effects of simulated vascular and metabolic pathologies.
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Affiliation(s)
- Andreas A Linninger
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL, USA
- Department of Neurosurgery, University of Illinois at Chicago, Chicago, IL, USA
| | - Thomas Ventimiglia
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Mohammad Jamshidi
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Mathieu Pascal Suisse
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Ali Alaraj
- Department of Neurosurgery, University of Illinois at Chicago, Chicago, IL, USA
| | - Frédéric Lesage
- Department of Electrical Engineering, Polytechnique Montréal, Montréal, QC, Canada
| | - Xin Li
- Advanced Imaging Research Center, Oregon Health & Science University, Portland, OR, USA
| | - Daniel L Schwartz
- Advanced Imaging Research Center, Oregon Health & Science University, Portland, OR, USA
- Department of Neurology, Oregon Health & Science University, Portland, OR, USA
| | - William D Rooney
- Advanced Imaging Research Center, Oregon Health & Science University, Portland, OR, USA
- Department of Neurology, Oregon Health & Science University, Portland, OR, USA
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2
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Cui Y, Huang H, Liu J, Zhao M, Li C, Han X, Luo N, Gao J, Yan DM, Zhang C, Jiang T, Yu S. FFCM-MRF: An accurate and generalizable cerebrovascular segmentation pipeline for humans and rhesus monkeys based on TOF-MRA. Comput Biol Med 2024; 170:107996. [PMID: 38266465 DOI: 10.1016/j.compbiomed.2024.107996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/14/2023] [Accepted: 01/13/2024] [Indexed: 01/26/2024]
Abstract
PURPOSE Cerebrovascular segmentation and quantification of vascular morphological features in humans and rhesus monkeys are essential for prevention, diagnosis, and treatment of brain diseases. However, current automated whole-brain vessel segmentation methods are often not generalizable to independent datasets, limiting their usefulness in real-world environments with their heterogeneity in participants, scanners, and species. MATERIALS AND METHODS In this study, we proposed an automated, accurate and generalizable segmentation method for magnetic resonance angiography images called FFCM-MRF. This method integrated fast fuzzy c-means clustering and Markov random field optimization by vessel shape priors and spatial constraints. We used a total of 123 human and 44 macaque MRA images scanned at 1.5 T, 3 T, and 7 T MRI from 9 datasets to develop and validate the method. RESULTS FFCM-MRF achieved average Dice similarity coefficients ranging from 69.16 % to 89.63 % across multiple independent datasets, with improvements ranging from 3.24 % to 7.3 % compared to state-of-the-art methods. Quantitative analysis showed that FFCM-MRF can accurately segment major arteries in the Circle of Willis at the base of the brain and small distal pial arteries while effectively reducing noise. Test-retest analysis showed that the model yielded high vascular volume and diameter reliability. CONCLUSIONS Our results have demonstrated that FFCM-MRF is highly accurate and reliable and largely independent of variations in field strength, scanner platforms, acquisition parameters, and species. The macaque MRA data and user-friendly open-source toolbox are freely available at OpenNeuro and GitHub to facilitate studies of imaging biomarkers for cerebrovascular and neurodegenerative diseases.
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Affiliation(s)
- Yue Cui
- Laboratory of Brain Atlas and Brain-inspired Intelligence, Institute of Automation, Chinese Academy of Sciences, Beijing, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China.
| | - Haibin Huang
- Laboratory of Brain Atlas and Brain-inspired Intelligence, Institute of Automation, Chinese Academy of Sciences, Beijing, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Jialu Liu
- Laboratory of Brain Atlas and Brain-inspired Intelligence, Institute of Automation, Chinese Academy of Sciences, Beijing, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Mingyang Zhao
- Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong, China
| | - Chengyi Li
- Laboratory of Brain Atlas and Brain-inspired Intelligence, Institute of Automation, Chinese Academy of Sciences, Beijing, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Xinyong Han
- Laboratory of Brain Atlas and Brain-inspired Intelligence, Institute of Automation, Chinese Academy of Sciences, Beijing, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Na Luo
- Brainnetome Center, Laboratory of Brain Atlas and Brain-inspired Intelligence, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Jinquan Gao
- Model R&D Center, Beijing Life Biosciences Company Limited, Beijing, China; Technology Management Center, SAFE Pharmaceutical Technology Company Limited, Beijing, China
| | - Dong-Ming Yan
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China; State Key Laboratory of Multimodal Artificial Intelligence Systems (MAIS), Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Chen Zhang
- Department of Neurobiology, School of Basic Medical Sciences, Beijing Key Laboratory of Neural Regeneration and Repair, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China
| | - Tianzi Jiang
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China; Brainnetome Center, Laboratory of Brain Atlas and Brain-inspired Intelligence, Institute of Automation, Chinese Academy of Sciences, Beijing, China; Research Center for Augmented Intelligence, Zhejiang Lab, Hangzhou, China
| | - Shan Yu
- Laboratory of Brain Atlas and Brain-inspired Intelligence, Institute of Automation, Chinese Academy of Sciences, Beijing, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China.
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3
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Galts A, Hammi A. FLASH radiotherapy sparing effect on the circulating lymphocytes in pencil beam scanning proton therapy: impact of hypofractionation and dose rate. Phys Med Biol 2024; 69:025006. [PMID: 38081067 DOI: 10.1088/1361-6560/ad144e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/11/2023] [Indexed: 01/06/2024]
Abstract
Purpose. The sparing effect of ultra-high dose rate (FLASH) radiotherapy has been reported, but its potential to mitigate depletion of circulating blood and lymphocytes (CL) has not been investigated in pencil-beam scanning-based (PBS) proton therapy, which could potentially reduce the risk of radiation-induced lymphopenia.Material and methods. A time-dependent framework was used to score the dose to the CL during the course of radiotherapy. For brain patients, cerebral vasculatures were semi-automatic segmented from 3T MR-angiography data. A dynamic beam delivery system was developed capable of simulating spatially varying instantaneous dose rates of PBS treatment plans, and which is based on realistic beam delivery parameters that are available clinically. We simulated single and different hypofractionated PBS intensity modulated proton therapy (IMPT) FLASH schemes using 600 nA beam current along with conventionally fractionated IMPT treatment plan at 2 nA beam current. The dosimetric impact of treatment schemes on CL was quantified, and we also evaluated the depletion in subsets of CL based on their radiosensitivity.Results. The proton FLASH sparing effect on CL was observed. In single-fraction PBS FLASH, just 1.5% of peripheral blood was irradiated, whereas hypofractionated FLASH irradiated 7.3% of peripheral blood. In contrast, conventional fractionated IMPT exposed 42.4% of peripheral blood to radiation. PBS FLASH reduced the depletion rate of CL by 69.2% when compared to conventional fractionated IMPT.Conclusion. Our dosimetric blood flow model provides quantitative measures of the PBS FLASH sparing effect on the CL in radiotherapy for brain cancer. FLASH Single treatment fraction offers superior CL sparing when compared to hypofractionated FLASH and conventional IMPT, supporting assumptions about reducing risks of lymphopenia compared to proton therapy at conventional dose rates. The results also indicate that faster conformal FLASH delivery, such as passive patient-specific energy modulation, may further enhance the sparing of the immune system.
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Karperien AL, Jelinek HF. ImageJ in Computational Fractal-Based Neuroscience: Pattern Extraction and Translational Research. ADVANCES IN NEUROBIOLOGY 2024; 36:795-814. [PMID: 38468064 DOI: 10.1007/978-3-031-47606-8_40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
To explore questions asked in neuroscience, neuroscientists rely heavily on the tools available. One such toolset is ImageJ, open-source, free, biological digital image analysis software. Open-source software has matured alongside of fractal analysis in neuroscience, and today ImageJ is not a niche but a foundation relied on by a substantial number of neuroscientists for work in diverse fields including fractal analysis. This is largely owing to two features of open-source software leveraged in ImageJ and vital to vigorous neuroscience: customizability and collaboration. With those notions in mind, this chapter's aim is threefold: (1) it introduces ImageJ, (2) it outlines ways this software tool has influenced fractal analysis in neuroscience and shaped the questions researchers devote time to, and (3) it reviews a few examples of ways investigators have developed and used ImageJ for pattern extraction in fractal analysis. Throughout this chapter, the focus is on fostering a collaborative and creative mindset for translating knowledge of the fractal geometry of the brain into clinical reality.
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Affiliation(s)
| | - Herbert F Jelinek
- Department of Medical Sciences and Biotechnology Center, Khalifa University, Abu Dhabi, UAE
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Yoon HS, Oh J, Kim YC. Assessing Machine Learning Models for Predicting Age with Intracranial Vessel Tortuosity and Thickness Information. Brain Sci 2023; 13:1512. [PMID: 38002472 PMCID: PMC10669197 DOI: 10.3390/brainsci13111512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
This study aimed to develop and validate machine learning (ML) models that predict age using intracranial vessels' tortuosity and diameter features derived from magnetic resonance angiography (MRA) data. A total of 171 subjects' three-dimensional (3D) time-of-flight MRA image data were considered for analysis. After annotations of two endpoints in each arterial segment, tortuosity features such as the sum of the angle metrics, triangular index, relative length, and product of the angle distance, as well as the vessels' diameter features, were extracted and used to train and validate the ML models for age prediction. Features extracted from the right and left internal carotid arteries (ICA) and basilar arteries were considered as the inputs to train and validate six ML regression models with a four-fold cross validation. The random forest regression model resulted in the lowest root mean square error of 14.9 years and the highest average coefficient of determination of 0.186. The linear regression model showed the lowest average mean absolute percentage error (MAPE) and the highest average Pearson correlation coefficient (0.532). The mean diameter of the right ICA vessel segment was the most important feature contributing to prediction of age in two out of the four regression models considered. An ML of tortuosity descriptors and diameter features extracted from MRA data showed a modest correlation between real age and ML-predicted age. Further studies are warranted for the assessment of the model's age predictions in patients with intracranial vessel diseases.
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Affiliation(s)
| | | | - Yoon-Chul Kim
- Division of Digital Healthcare, College of Software and Digital Healthcare Convergence, Yonsei University, Wonju 26493, Republic of Korea; (H.-S.Y.); (J.O.)
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Decroocq M, Frindel C, Rougé P, Ohta M, Lavoué G. Modeling and hexahedral meshing of cerebral arterial networks from centerlines. Med Image Anal 2023; 89:102912. [PMID: 37549612 DOI: 10.1016/j.media.2023.102912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 06/12/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023]
Abstract
Computational fluid dynamics (CFD) simulation provides valuable information on blood flow from the vascular geometry. However, it requires extracting precise models of arteries from low-resolution medical images, which remains challenging. Centerline-based representation is widely used to model large vascular networks with small vessels, as it encodes both the geometric and topological information and facilitates manual editing. In this work, we propose an automatic method to generate a structured hexahedral mesh suitable for CFD directly from centerlines. We addressed both the modeling and meshing tasks. We proposed a vessel model based on penalized splines to overcome the limitations inherent to the centerline representation, such as noise and sparsity. The bifurcations are reconstructed using a parametric model based on the anatomy that we extended to planar n-furcations. Finally, we developed a method to produce a volume mesh with structured, hexahedral, and flow-oriented cells from the proposed vascular network model. The proposed method offers better robustness to the common defects of centerlines and increases the mesh quality compared to state-of-the-art methods. As it relies on centerlines alone, it can be applied to edit the vascular model effortlessly to study the impact of vascular geometry and topology on hemodynamics. We demonstrate the efficiency of our method by entirely meshing a dataset of 60 cerebral vascular networks. 92% of the vessels and 83% of the bifurcations were meshed without defects needing manual intervention, despite the challenging aspect of the input data. The source code is released publicly.
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Affiliation(s)
- Méghane Decroocq
- CREATIS, Université Lyon1, CNRS UMR5220, INSERM U1206, INSA-Lyon, 69621 Villeurbanne, France; LIRIS, CNRS UMR 5205, F-69621, France; ELyTMaX IRL3757, CNRS, INSA Lyon, Centrale Lyon, Université Claude Bernard Lyon 1, Tohoku University, 980-8577, Sendai, Japan; Institute of Fluid Science, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; Graduate School of Biomedical Engineering, Tohoku University, 6-6 Aramaki-aza-aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Carole Frindel
- CREATIS, Université Lyon1, CNRS UMR5220, INSERM U1206, INSA-Lyon, 69621 Villeurbanne, France; Institute of Fluid Science, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
| | - Pierre Rougé
- ELyTMaX IRL3757, CNRS, INSA Lyon, Centrale Lyon, Université Claude Bernard Lyon 1, Tohoku University, 980-8577, Sendai, Japan; Université de Reims Champagne Ardenne, CReSTIC, 51100 Reims, France
| | - Makoto Ohta
- ELyTMaX IRL3757, CNRS, INSA Lyon, Centrale Lyon, Université Claude Bernard Lyon 1, Tohoku University, 980-8577, Sendai, Japan; Institute of Fluid Science, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Guillaume Lavoué
- LIRIS, CNRS UMR 5205, F-69621, France; Ecole Centrale de Lyon, France
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7
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Bae J, Li C, Masurkar A, Ge Y, Kim SG. Improving measurement of blood-brain barrier permeability with reduced scan time using deep-learning-derived capillary input function. Neuroimage 2023; 278:120284. [PMID: 37507078 PMCID: PMC10475161 DOI: 10.1016/j.neuroimage.2023.120284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
PURPOSE In Dynamic contrast-enhanced MRI (DCE-MRI), Arterial Input Function (AIF) has been shown to be a significant contributor to uncertainty in the estimation of kinetic parameters. This study is to assess the feasibility of using a deep learning network to estimate local Capillary Input Function (CIF) to estimate blood-brain barrier (BBB) permeability, while reducing the required scan time. MATERIALS AND METHOD A total of 13 healthy subjects (younger (<40 y/o): 8, older (> 67 y/o): 5) were recruited and underwent 25-min DCE-MRI scans. The 25 min data were retrospectively truncated to 10 min to simulate a reduced scan time of 10 min. A deep learning network was trained to predict the CIF using simulated tissue contrast dynamics with two vascular transport models. The BBB permeability (PS) was measured using 3 methods: (i) Ca-25min, using DCE-MRI data of 25 min with individually sampled AIF (Ca); (ii) Ca-10min, using truncated 10min data with AIF (Ca); and (iii) Cp-10min, using truncated 10 min data with CIF (Cp). The PS estimates from the Ca-25min method were used as reference standard values to assess the accuracy of the Ca-10min and Cp-10min methods in estimating the PS values. RESULTS When compared to the reference method(Ca-25min), the Ca-10min and Cp-10min methods resulted in an overestimation of PS by 217 ± 241 % and 48.0 ± 30.2 %, respectively. The Bland Altman analysis showed that the mean difference from the reference was 8.85 ± 1.78 (x10-4 min-1) with the Ca-10min, while it was reduced to 1.63 ± 2.25 (x10-4 min-1) with the Cp-10min, resulting in an average reduction of 81%. The limits of agreement also reduced by up to 39.2% with the Cp-10min. We found a 75% increase of BBB permeability in the gray matter and a 35% increase in the white matter, when comparing the older group to the younger group. CONCLUSIONS We demonstrated the feasibility of estimating the capillary-level input functions using a deep learning network. We also showed that this method can be used to estimate subtle age-related changes in BBB permeability with reduced scan time, without compromising accuracy. Moreover, the trained deep learning network can automatically select CIF, reducing the potential uncertainty resulting from manual user-intervention.
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Affiliation(s)
- Jonghyun Bae
- Vilcek Institute of Graduate Biomedical Science, New York University School of Medicine; Center for Biomedical Imaging, Radiology, New York University School of Medicine; Center for Advanced Imaging Innovation and Research, Radiology, New York University School of Medicine; Department of Radiology, Weill Cornell Medical College.
| | - Chenyang Li
- Vilcek Institute of Graduate Biomedical Science, New York University School of Medicine; Center for Biomedical Imaging, Radiology, New York University School of Medicine; Center for Advanced Imaging Innovation and Research, Radiology, New York University School of Medicine.
| | - Arjun Masurkar
- Center for Cognitive Neurology, Department of Neurology, New York University School of Medicine; Department of Neuroscience & Physiology, New York University School of Medicine; Neuroscience Institute, New York University School of Medicine.
| | - Yulin Ge
- Center for Biomedical Imaging, Radiology, New York University School of Medicine; Center for Advanced Imaging Innovation and Research, Radiology, New York University School of Medicine.
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8
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Keto L, Manninen T. CellRemorph: A Toolkit for Transforming, Selecting, and Slicing 3D Cell Structures on the Road to Morphologically Detailed Astrocyte Simulations. Neuroinformatics 2023; 21:483-500. [PMID: 37133688 PMCID: PMC10406679 DOI: 10.1007/s12021-023-09627-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2023] [Indexed: 05/04/2023]
Abstract
Understanding functions of astrocytes can be greatly enhanced by building and simulating computational models that capture their morphological details. Novel computational tools enable utilization of existing morphological data of astrocytes and building models that have appropriate level of details for specific simulation purposes. In addition to analyzing existing computational tools for constructing, transforming, and assessing astrocyte morphologies, we present here the CellRemorph toolkit implemented as an add-on for Blender, a 3D modeling platform increasingly recognized for its utility for manipulating 3D biological data. To our knowledge, CellRemorph is the first toolkit for transforming astrocyte morphologies from polygonal surface meshes into adjustable surface point clouds and vice versa, precisely selecting nanoprocesses, and slicing morphologies into segments with equal surface areas or volumes. CellRemorph is an open-source toolkit under the GNU General Public License and easily accessible via an intuitive graphical user interface. CellRemorph will be a valuable addition to other Blender add-ons, providing novel functionality that facilitates the creation of realistic astrocyte morphologies for different types of morphologically detailed simulations elucidating the role of astrocytes both in health and disease.
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Affiliation(s)
- Laura Keto
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
| | - Tiina Manninen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
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9
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Sung D, Rejimon A, Allen JW, Fedorov AG, Fleischer CC. Predicting brain temperature in humans using bioheat models: Progress and outlook. J Cereb Blood Flow Metab 2023; 43:833-842. [PMID: 36883416 PMCID: PMC10196749 DOI: 10.1177/0271678x231162173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 03/09/2023]
Abstract
Brain temperature, regulated by the balance between blood circulation and metabolic heat generation, is an important parameter related to neural activity, cerebral hemodynamics, and neuroinflammation. A key challenge for integrating brain temperature into clinical practice is the lack of reliable and non-invasive brain thermometry. The recognized importance of brain temperature and thermoregulation in both health and disease, combined with limited availability of experimental methods, has motivated the development of computational thermal models using bioheat equations to predict brain temperature. In this mini-review, we describe progress and the current state-of-the-art in brain thermal modeling in humans and discuss potential avenues for clinical applications.
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Affiliation(s)
- Dongsuk Sung
- Department of Biomedical
Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA,
USA
- Department of Radiology and Imaging
Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Abinand Rejimon
- Department of Biomedical
Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA,
USA
- Department of Radiology and Imaging
Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Jason W Allen
- Department of Biomedical
Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA,
USA
- Department of Radiology and Imaging
Sciences, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory
University School of Medicine, Atlanta, GA, USA
| | - Andrei G Fedorov
- Woodruff School of Mechanical
Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- Petit Institute for Bioengineering
and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Candace C Fleischer
- Department of Biomedical
Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA,
USA
- Department of Radiology and Imaging
Sciences, Emory University School of Medicine, Atlanta, GA, USA
- Petit Institute for Bioengineering
and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
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10
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Xia Y, Ravikumar N, Lassila T, Frangi AF. Virtual high-resolution MR angiography from non-angiographic multi-contrast MRIs: synthetic vascular model populations for in-silico trials. Med Image Anal 2023; 87:102814. [PMID: 37196537 DOI: 10.1016/j.media.2023.102814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/04/2023] [Accepted: 04/08/2023] [Indexed: 05/19/2023]
Abstract
Despite success on multi-contrast MR image synthesis, generating specific modalities remains challenging. Those include Magnetic Resonance Angiography (MRA) that highlights details of vascular anatomy using specialised imaging sequences for emphasising inflow effect. This work proposes an end-to-end generative adversarial network that can synthesise anatomically plausible, high-resolution 3D MRA images using commonly acquired multi-contrast MR images (e.g. T1/T2/PD-weighted MR images) for the same subject whilst preserving the continuity of vascular anatomy. A reliable technique for MRA synthesis would unleash the research potential of very few population databases with imaging modalities (such as MRA) that enable quantitative characterisation of whole-brain vasculature. Our work is motivated by the need to generate digital twins and virtual patients of cerebrovascular anatomy for in-silico studies and/or in-silico trials. We propose a dedicated generator and discriminator that leverage the shared and complementary features of multi-source images. We design a composite loss function for emphasising vascular properties by minimising the statistical difference between the feature representations of the target images and the synthesised outputs in both 3D volumetric and 2D projection domains. Experimental results show that the proposed method can synthesise high-quality MRA images and outperform the state-of-the-art generative models both qualitatively and quantitatively. The importance assessment reveals that T2 and PD-weighted images are better predictors of MRA images than T1; and PD-weighted images contribute to better visibility of small vessel branches towards the peripheral regions. In addition, the proposed approach can generalise to unseen data acquired at different imaging centres with different scanners, whilst synthesising MRAs and vascular geometries that maintain vessel continuity. The results show the potential for use of the proposed approach to generating digital twin cohorts of cerebrovascular anatomy at scale from structural MR images typically acquired in population imaging initiatives.
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Affiliation(s)
- Yan Xia
- Centre for Computational Imaging and Simulation Technologies in Biomedicine (CISTIB), School of Computing, University of Leeds, Leeds, UK.
| | - Nishant Ravikumar
- Centre for Computational Imaging and Simulation Technologies in Biomedicine (CISTIB), School of Computing, University of Leeds, Leeds, UK
| | - Toni Lassila
- Centre for Computational Imaging and Simulation Technologies in Biomedicine (CISTIB), School of Computing, University of Leeds, Leeds, UK
| | - Alejandro F Frangi
- Centre for Computational Imaging and Simulation Technologies in Biomedicine (CISTIB), School of Computing, University of Leeds, Leeds, UK; Leeds Institute for Cardiovascular and Metabolic Medicine (LICAMM), School of Medicine, University of Leeds, Leeds, UK; Medical Imaging Research Center (MIRC), Cardiovascular Science and Electronic Engineering Departments, KU Leuven, Leuven, Belgium; Alan Turing Institute, London, UK
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11
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Tong S, Zhong J, Chen X, Deng X, Huang J, Zhang Y, Qin M, Li Z, Cheng H, Zhang W, Zheng L, Xie W, Qiu P, Wang K. In Vivo Deep-Brain 3- and 4-Photon Fluorescence Imaging of Subcortical Structures Labeled by Quantum Dots Excited at the 2200 nm Window. ACS NANO 2023; 17:3686-3695. [PMID: 36799427 DOI: 10.1021/acsnano.2c10724] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Multiphoton microscopy (MPM) is an enabling technology for visualizing deep-brain structures at high spatial resolution in vivo. Within the low tissue absorption window, shifting to longer excitation wavelengths reduces tissue scattering and boosts penetration depth. Recently, the 2200 nm excitation window has emerged as the last and longest window suitable for deep-brain MPM. However, multiphoton fluorescence imaging at this window has not been demonstrated, due to the lack of characterization of multiphoton properties of fluorescent labels. Here we demonstrate technologies for measuring both the multiphoton excitation and emission properties of fluorescent labels at the 2200 nm window, using (1) 3-photon (ησ3) and 4-photon action cross sections (ησ4) and (2) 3-photon and 4-photon emission spectra both ex vivo and in vivo of quantum dots. Our results show that quantum dots have exceptionally large ησ3 and ησ4 for efficient generation of multiphoton fluorescence. Besides, the 3-photon and 4-photon emission spectra of quantum dots are essentially identical to those of one-photon emission, which change negligibly subject to the local environment of circulating blood. Based on these characterization results, we further demonstrate deep-brain vasculature imaging in vivo. Due to the superb multiphoton properties of quantum dots, 3-photon and 4-photon fluorescence imaging reaches a maximum brain imaging depth of 1060 and 940 μm below the surface of a mouse brain, respectively, which enables the imaging of subcortical structures. We thus fill the last gap in multiphoton fluorescence imaging in terms of wavelength selection.
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Affiliation(s)
- Shen Tong
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Jincheng Zhong
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Xinlin Chen
- Advanced Life Imaging Lab, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Xiangquan Deng
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Jie Huang
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Yingxian Zhang
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Mengyuan Qin
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Zhenhui Li
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Hui Cheng
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Wanjian Zhang
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Lei Zheng
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Weixin Xie
- College of Electronics and Information Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Ping Qiu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Ke Wang
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
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12
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Liu CF, Hsu J, Xu X, Kim G, Sheppard SM, Meier EL, Miller MI, Hillis AE, Faria AV. Digital 3D Brain MRI Arterial Territories Atlas. Sci Data 2023; 10:74. [PMID: 36739282 PMCID: PMC9899211 DOI: 10.1038/s41597-022-01923-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 12/21/2022] [Indexed: 02/06/2023] Open
Abstract
The locus and extent of brain damage in the event of vascular insult can be quantitatively established quickly and easily with vascular atlases. Although highly anticipated by clinicians and clinical researchers, no digital MRI arterial atlas is readily available for automated data analyses. We created a digital arterial territory atlas based on lesion distributions in 1,298 patients with acute stroke. The lesions were manually traced in the diffusion-weighted MRIs, binary stroke masks were mapped to a common space, probability maps of lesions were generated and the boundaries for each arterial territory was defined based on the ratio between probabilistic maps. The atlas contains the definition of four major supra- and infra-tentorial arterial territories: Anterior, Middle, Posterior Cerebral Arteries and Vertebro-Basilar, and sub-territories (thalamoperforating, lenticulostriate, basilar and cerebellar arterial territories), in two hierarchical levels. This study provides the first publicly-available, digital, 3D deformable atlas of arterial brain territories, which may serve as a valuable resource for large-scale, reproducible processing and analysis of brain MRIs of patients with stroke and other conditions.
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Affiliation(s)
- Chin-Fu Liu
- Center for Imaging Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Johnny Hsu
- Department of Radiology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Xin Xu
- Department of Radiology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ganghyun Kim
- Center for Imaging Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA
| | - Shannon M Sheppard
- Department of Communication Sciences & Disorders, Chapman University, Orange, CA, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Erin L Meier
- Department of Communication Sciences & Disorders, Northeastern University, Boston, MA, USA
| | - Michael I Miller
- Center for Imaging Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Argye E Hillis
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Physical Medicine & Rehabilitation, and Department of Cognitive Science, Johns Hopkins University, Baltimore, MD, USA
| | - Andreia V Faria
- Department of Radiology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
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13
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Ni R, Deán-Ben XL, Treyer V, Gietl A, Hock C, Klohs J, Nitsch RM, Razansky D. Coregistered transcranial optoacoustic and magnetic resonance angiography of the human brain. OPTICS LETTERS 2023; 48:648-651. [PMID: 36723554 DOI: 10.1364/ol.475578] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/17/2022] [Indexed: 06/18/2023]
Abstract
Imaging modalities capable of visualizing the human brain have led to major advances in neurology and brain research. Multi-spectral optoacoustic tomography (MSOT) has gained importance for studying cerebral function in rodent models due to its unique capability to map changes in multiple hemodynamic parameters and to directly visualize neural activity within the brain. The technique further provides molecular imaging capabilities that can facilitate early disease diagnosis and treatment monitoring. However, transcranial imaging of the human brain is hampered by acoustic attenuation and other distortions introduced by the skull. Here, we demonstrate non-invasive transcranial MSOT angiography of pial veins through the temporal bone of an adult healthy volunteer. Time-of-flight (TOF) magnetic resonance angiography (MRA) and T1-weighted structural magnetic resonance imaging (MRI) were further acquired to facilitate anatomical registration and interpretation. The superior middle cerebral vein in the temporal cortex was identified in the MSOT images, matching its location observed in the TOF-MRA images. These initial results pave the way toward the application of MSOT in clinical brain imaging.
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14
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Abdellah M, Cantero JJG, Guerrero NR, Foni A, Coggan JS, Calì C, Agus M, Zisis E, Keller D, Hadwiger M, Magistretti PJ, Markram H, Schürmann F. Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience. Brief Bioinform 2022; 24:6847753. [PMID: 36434788 PMCID: PMC9851302 DOI: 10.1093/bib/bbac491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/27/2022] [Accepted: 10/14/2022] [Indexed: 11/27/2022] Open
Abstract
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.
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Affiliation(s)
- Marwan Abdellah
- Corresponding authors. Marwan Abdellah, Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland. E-mail: ; Felix Schürmann, Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland. E-mail:
| | | | - Nadir Román Guerrero
- Blue Brain Project (BBP) École Polytecnique Fédérale de Lausanne (EPFL) Geneva, Switzerland
| | - Alessandro Foni
- Blue Brain Project (BBP) École Polytecnique Fédérale de Lausanne (EPFL) Geneva, Switzerland
| | - Jay S Coggan
- Blue Brain Project (BBP) École Polytecnique Fédérale de Lausanne (EPFL) Geneva, Switzerland
| | - Corrado Calì
- Biological and Environmental Sciences and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal, Saudi Arabia,Neuroscience Institute Cavalieri Ottolenghi (NICO) Orbassano, Italy,Department of Neuroscience, University of Torino Torino, Italy
| | - Marco Agus
- Visual Computing Center King Abdullah University of Science and Technology (KAUST) Thuwal, Saudi Arabia,College of Science and Engineering Hamad Bin Khalifa University Doha, Qatar
| | - Eleftherios Zisis
- Blue Brain Project (BBP) École Polytecnique Fédérale de Lausanne (EPFL) Geneva, Switzerland
| | - Daniel Keller
- Blue Brain Project (BBP) École Polytecnique Fédérale de Lausanne (EPFL) Geneva, Switzerland
| | - Markus Hadwiger
- Visual Computing Center King Abdullah University of Science and Technology (KAUST) Thuwal, Saudi Arabia
| | - Pierre J Magistretti
- Biological and Environmental Sciences and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal, Saudi Arabia
| | - Henry Markram
- Blue Brain Project (BBP) École Polytecnique Fédérale de Lausanne (EPFL) Geneva, Switzerland
| | - Felix Schürmann
- Corresponding authors. Marwan Abdellah, Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland. E-mail: ; Felix Schürmann, Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland. E-mail:
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15
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Padmos RM, Arrarte Terreros N, Józsa TI, Závodszky G, Marquering HA, Majoie CBLM, Payne SJ, Hoekstra AG. Modelling collateral flow and thrombus permeability during acute ischaemic stroke. J R Soc Interface 2022; 19:20220649. [PMID: 36195117 PMCID: PMC9532024 DOI: 10.1098/rsif.2022.0649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The presence of collaterals and high thrombus permeability are associated with good functional outcomes after an acute ischaemic stroke. We aim to understand the combined effect of the collaterals and thrombus permeability on cerebral blood flow during an acute ischaemic stroke. A cerebral blood flow model including the leptomeningeal collateral circulation is used to simulate cerebral blood flow during an acute ischaemic stroke. The collateral circulation is varied to capture the collateral scores: absent, poor, moderate and good. Measurements of the transit time, void fraction and thrombus length in acute ischaemic stroke patients are used to estimate thrombus permeability. Estimated thrombus permeability ranges between 10-7 and 10-4 mm2. Measured flow rates through the thrombus are small and the effect of a permeable thrombus on brain perfusion during stroke is small compared with the effect of collaterals. Our simulations suggest that the collaterals are a dominant factor in the resulting infarct volume after a stroke.
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Affiliation(s)
- Raymond M. Padmos
- Computational Science Laboratory, Informatics Institute, Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098, The Netherlands,Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Mekelweg 2, Delft 2628, The Netherlands
| | - Nerea Arrarte Terreros
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, location AMC, Amsterdam, The Netherlands,Department of Biomedical Engineering and Physics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Tamás I. Józsa
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK,Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Location VUmc, Amsterdam, The Netherlands
| | - Gábor Závodszky
- Computational Science Laboratory, Informatics Institute, Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098, The Netherlands
| | - Henk A. Marquering
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, location AMC, Amsterdam, The Netherlands,Department of Biomedical Engineering and Physics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Charles B. L. M. Majoie
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Stephen J. Payne
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK,Institute of Applied Mechanics, National Taiwan University, Taiwan
| | - Alfons G. Hoekstra
- Computational Science Laboratory, Informatics Institute, Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098, The Netherlands
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16
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Pochechuev MS, Bilan DS, Fedotov IV, Kelmanson IV, Solotenkov MA, Stepanov EA, Kotova DA, Ivanova AD, Kostyuk AI, Raevskii RI, Lanin AA, Fedotov AB, Belousov VV, Zheltikov AM. Real-time fiber-optic recording of acute-ischemic-stroke signatures. JOURNAL OF BIOPHOTONICS 2022; 15:e202200050. [PMID: 35654757 DOI: 10.1002/jbio.202200050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/24/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
We present an experimental framework and methodology for in vivo studies on rat stroke models that enable a real-time fiber-optic recording of stroke-induced hydrogen peroxide and pH transients in ischemia-affected brain areas. Arrays of reconnectable implantable fiber probes combined with advanced optogenetic fluorescent protein sensors are shown to enable a quantitative multisite time-resolved study of oxidative-stress and acidosis buildup dynamics as the key markers, correlates and possible drivers of ischemic stroke. The fiber probes designed for this work provide a wavelength-multiplex forward-propagation channel for a spatially localized, dual-pathway excitation of genetically encoded fluorescence-protein sensors along with a back-propagation channel for the fluorescence return from optically driven fluorescence sensors. We show that the spectral analysis of the fiber-probe-collected fluorescence return provides means for a high-fidelity autofluorescence background subtraction, thus enhancing the sensitivity of real-time detection of stroke-induced transients and significantly reducing measurement uncertainties in in vivo acute-stroke studies as inherently statistical experiments operating with outcomes of multiply repeated measurements on large populations of individually variable animal stroke models.
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Affiliation(s)
| | - Dmitry S Bilan
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ilya V Fedotov
- Physics Department, M.V. Lomonosov Moscow State University, Moscow, Russia
- Department of Physics and Astronomy, Texas A&M University, College Station, Texas, USA
- Russian Quantum Center, Skolkovo, Moscow, Russia
| | - Ilya V Kelmanson
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Maxim A Solotenkov
- Physics Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Evgeny A Stepanov
- Physics Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Daria A Kotova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexandra D Ivanova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander I Kostyuk
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Roman I Raevskii
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Aleksandr A Lanin
- Physics Department, M.V. Lomonosov Moscow State University, Moscow, Russia
- Russian Quantum Center, Skolkovo, Moscow, Russia
| | - Andrei B Fedotov
- Physics Department, M.V. Lomonosov Moscow State University, Moscow, Russia
- Russian Quantum Center, Skolkovo, Moscow, Russia
- National University of Science and Technology "MISiS", Moscow, Russia
| | - Vsevolod V Belousov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, Russia
| | - Aleksei M Zheltikov
- Department of Physics and Astronomy, Texas A&M University, College Station, Texas, USA
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17
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Deshpande A, Elliott J, Kari N, Jiang B, Michel P, Toosizadeh N, Fahadan PT, Kidwell C, Wintermark M, Laksari K. Novel imaging markers for altered cerebrovascular morphology in aging, stroke, and Alzheimer's disease. J Neuroimaging 2022; 32:956-967. [PMID: 35838658 PMCID: PMC9474631 DOI: 10.1111/jon.13023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 06/26/2022] [Accepted: 06/29/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND AND PURPOSE Altered brain vasculature is a key phenomenon in several neurologic disorders. This paper presents a quantitative assessment of the anatomical variations in the Circle of Willis (CoW) and vascular morphology in healthy aging, acute ischemic stroke (AIS) and Alzheimer's Disease (AD). METHODS We used our novel automatic method to segment and extract geometric features of the cerebral vasculature from MR angiography scans of 175 healthy subjects, which were used to create a probabilistic atlas of cerebrovasculature and to study normal aging and intersubject variations in CoW anatomy. Subsequently, we quantified and analyzed vascular alterations in 45AIS and 50 AD patients, two prominent cerebrovascular and neurodegenerative disorders. RESULTS In the sampled cohort, we determined that the CoW is fully formed in only 35% of healthy adults and found significantly (p < .05) increased tortuosity and fractality, with increasing age and also with disease in both AIS and AD. We also found significantly lower vessel length, volume, and number of branches in AIS patients, as expected. The AD cerebral vessels exhibited significantly smaller diameter and more complex branching patterns, compared to age-matched healthy adults. These changes were significantly heightened (p < .05) among healthy, early onset mild AD, and moderate/severe dementia groups. CONCLUSION Although our study does not include longitudinal data due to paucity of such datasets, the specific geometric features and quantitative comparisons demonstrate the potential for using vascular morphology as a noninvasive imaging biomarker for neurologic disorders.
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Affiliation(s)
| | - Jordan Elliott
- Department of Biomedical Engineering, University of Arizona
| | - Nitya Kari
- Department of Biomedical Engineering, University of Arizona
| | - Bin Jiang
- Department of Radiology, Stanford University
| | - Patrik Michel
- Department of Neurology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Nima Toosizadeh
- Department of Biomedical Engineering, University of Arizona
- Arizona Center on Aging, Department of Medicine, University of Arizona
| | - Pouya Tahsili Fahadan
- Neuroscience Intensive Care Unit, Medical Critical Care Service and Department of Medical Education, University of Virginia School of Medicine, Inova Fairfax Medical Campus
- Departments of Neurology, Johns Hopkins University School of Medicine
| | | | | | - Kaveh Laksari
- Department of Biomedical Engineering, University of Arizona
- Department of Aerospace and Mechanical Engineering, University of Arizona
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18
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Hadad S, Pradhan A, Kadirvel R, Kallmes D, Cebral JR, Mut F. Flow reversal in distal collaterals as a possible mechanism of delayed intraparenchymal hemorrhage after flow diversion treatment of cerebral aneurysms. Front Physiol 2022; 13:881627. [PMID: 35923225 PMCID: PMC9339966 DOI: 10.3389/fphys.2022.881627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/01/2022] [Indexed: 11/17/2022] Open
Abstract
Background and Purpose: Delayed intraparenchymal hemorrhages (DIPHs) are one of the most serious complications of cerebral aneurysm treatment with flow diverters (FD), yet their causes are largely unknown. This study analyzes distal hemodynamic alterations induced by the treatment of intracranial aneurysms with FDs. Methods: A realistic model of the brain arterial network was constructed from MRA images and extended with a constrained constructive optimization technique down to vessel diameters of approximately 50μm. Different variants of the circle of Willis were created by alternatively occluding communicating arteries. Collateral vessels connecting different arterial trees were then added to the model, and a distributed lumped parameter approach was used to model the pulsatile blood flow in the arterial network. The treatment of an ICA aneurysm was modeled by changing the local resistance, flow inertia, and compliance of the aneurysmal segment. Results: The maximum relative change in distal pressure induced by the aneurysm treatment was below 1%. However, for certain combinations of the circle of Willis and distal collateralization, important flow reversals (with a wall shear stress larger than approximately 1.0 dyne/cm2) were observed in collateral vessels, both ipsilaterally and contralaterally to the treated aneurysm. Conclusion: This study suggests the hypothesis that flow diverters treatment of intracranial aneurysms could cause important flow reversal in distal collaterals. Flow reversal has previously been shown to be pro-inflammatory and pro-atherogenic and could therefore have a detrimental effect on these collateral vessels, and thus could be a suitable explanation of DIPHs, while the small distal pressure increase is not.
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Affiliation(s)
- Sara Hadad
- Bioengineering Department, George Mason University, Fairfax, VA, United States
- *Correspondence: Sara Hadad, mailto:
| | - Aseem Pradhan
- Bioengineering Department, George Mason University, Fairfax, VA, United States
| | | | - David Kallmes
- Interventional Neuroradiology, Mayo Clinic, Rochester, MN, United States
| | - Juan R. Cebral
- Bioengineering Department, George Mason University, Fairfax, VA, United States
| | - Fernando Mut
- Bioengineering Department, George Mason University, Fairfax, VA, United States
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19
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Decroocq M, Lavoue G, Ohta M, Frindel C. A Software to Visualize, Edit, Model and Mesh Vascular Networks. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2022; 2022:2208-2214. [PMID: 36085963 DOI: 10.1109/embc48229.2022.9871365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Computational fluid dynamics (CFD) is a key tool for a wide range of research areas, beyond the computer science community. In particular, CFD is used in medicine to measure blood flow from patient specific models of arteries. In this field, the creation of accurate meshes remains the most challenging step, as it is based on the segmentation of medical images, a time-consuming task which often requires manual intervention by medical doctors. In this context, user-friendly, interactive softwares are valuable. They enable to spread the new advances in numerical treatment to the medical community and enrich them with the expert knowledge (e.g anatomical knowledge) of clinicians. In this work, we present a user interface dedicated to the meshing of vascular networks from centerlines. It allows for the 3D visualization and edition of input centerlines, which constitute a simplified, easy-to-manipulate representation of vascular networks. The surface of the artery can be reconstructed from the modified centerlines by an editable parametric model and then meshed with high quality hexahedral elements. At every step of the process, the network can be confronted with medical images with enhanced visualization. The software will be released publicly. Clinical relevance- This tool facilitates the manual extraction and editing of vascular networks by medical doctors. It opens the generation of hexahedral meshes for computational fluid dynamics studies to non-expert users.
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20
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Zhang B, Huo Y, Yang Z, Lv H, Wang Y, Feng J, Han Y, Wang H. Day to Day Blood Pressure Variability Associated With Cerebral Arterial Dilation and White Matter Hyperintensity. Hypertension 2022; 79:1455-1465. [PMID: 35502669 PMCID: PMC9172904 DOI: 10.1161/hypertensionaha.122.19269] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Previous studies suggested blood pressure variability (BPV) might help reveal interactions between blood pressure fluctuation and white matter lesions, and the impact of elevated BPV on white matter hyperintensity (WMH) or cerebral arterial dilation is unclear.
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Affiliation(s)
- Boyu Zhang
- Institute of Science and Technology for Brain-Inspired Intelligence (B.Z., Z.Y., J.F., H.W.), Fudan University, Shanghai, China.,Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, China (B.Z., Z.Y., J.F., H.W.)
| | - Yajing Huo
- Department of Neurology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China (Y. Huo, H.L., Y. Han)
| | - Zidong Yang
- Institute of Science and Technology for Brain-Inspired Intelligence (B.Z., Z.Y., J.F., H.W.), Fudan University, Shanghai, China.,Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, China (B.Z., Z.Y., J.F., H.W.)
| | - Huihui Lv
- Department of Neurology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China (Y. Huo, H.L., Y. Han)
| | - Yilin Wang
- Georgetown Preparatory School, Washington DC (Y.W.)
| | - Jianfeng Feng
- Institute of Science and Technology for Brain-Inspired Intelligence (B.Z., Z.Y., J.F., H.W.), Fudan University, Shanghai, China.,Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, China (B.Z., Z.Y., J.F., H.W.)
| | - Yan Han
- Department of Neurology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China (Y. Huo, H.L., Y. Han)
| | - He Wang
- Institute of Science and Technology for Brain-Inspired Intelligence (B.Z., Z.Y., J.F., H.W.), Fudan University, Shanghai, China.,Department of Neurology, Zhongshan Hospital (H.W.), Fudan University, Shanghai, China.,Human Phenome Institute (H.W.), Fudan University, Shanghai, China.,Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, China (B.Z., Z.Y., J.F., H.W.)
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21
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Bollmann S, Mattern H, Bernier M, Robinson SD, Park DJ, Speck O, Polimeni JR. Imaging of the pial arterial vasculature of the human brain in vivo using high-resolution 7T time-of-flight angiography. eLife 2022; 11:71186. [PMID: 35486089 PMCID: PMC9150892 DOI: 10.7554/elife.71186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 04/28/2022] [Indexed: 11/30/2022] Open
Abstract
The pial arterial vasculature of the human brain is the only blood supply to the neocortex, but quantitative data on the morphology and topology of these mesoscopic arteries (diameter 50–300 µm) remains scarce. Because it is commonly assumed that blood flow velocities in these vessels are prohibitively slow, non-invasive time-of-flight magnetic resonance angiography (TOF-MRA)—which is well suited to high 3D imaging resolutions—has not been applied to imaging the pial arteries. Here, we provide a theoretical framework that outlines how TOF-MRA can visualize small pial arteries in vivo, by employing extremely small voxels at the size of individual vessels. We then provide evidence for this theory by imaging the pial arteries at 140 µm isotropic resolution using a 7 Tesla (T) magnetic resonance imaging (MRI) scanner and prospective motion correction, and show that pial arteries one voxel width in diameter can be detected. We conclude that imaging pial arteries is not limited by slow blood flow, but instead by achievable image resolution. This study represents the first targeted, comprehensive account of imaging pial arteries in vivo in the human brain. This ultra-high-resolution angiography will enable the characterization of pial vascular anatomy across the brain to investigate patterns of blood supply and relationships between vascular and functional architecture.
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Affiliation(s)
- Saskia Bollmann
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia
| | - Hendrik Mattern
- Department of Biomedical Magnetic Resonance, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Michaël Bernier
- Athinoula A Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, United States
| | - Simon D Robinson
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia
| | - Daniel J Park
- Athinoula A Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, United States
| | - Oliver Speck
- German Center for Neurodegenerative Diseases, Magdeburg, Germany
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22
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Zhu J, Teolis S, Biassou N, Tabb A, Jabin PE, Lavi O. Tracking the Adaptation and Compensation Processes of Patients' Brain Arterial Network to an Evolving Glioblastoma. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2022; 44:488-501. [PMID: 32750811 DOI: 10.1109/tpami.2020.3008379] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The brain's vascular network dynamically affects its development and core functions. It rapidly responds to abnormal conditions by adjusting properties of the network, aiding stabilization and regulation of brain activities. Tracking prominent arterial changes has clear clinical and surgical advantages. However, the arterial network functions as a system; thus, local changes may imply global compensatory effects that could impact the dynamic progression of a disease. We developed automated personalized system-level analysis methods of the compensatory arterial changes and mean blood flow behavior from a patient's clinical images. By applying our approach to data from a patient with aggressive brain cancer compared with healthy individuals, we found unique spatiotemporal patterns of the arterial network that could assist in predicting the evolution of glioblastoma over time. Our personalized approach provides a valuable analysis tool that could augment current clinical assessments of the progression of glioblastoma and other neurological disorders affecting the brain.
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23
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Bijari K, Valera G, López-Schier H, Ascoli GA. Quantitative neuronal morphometry by supervised and unsupervised learning. STAR Protoc 2021; 2:100867. [PMID: 34647039 PMCID: PMC8496329 DOI: 10.1016/j.xpro.2021.100867] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We present a protocol to characterize the morphological properties of individual neurons reconstructed from microscopic imaging. We first describe a simple procedure to extract relevant morphological features from digital tracings of neural arbors. Then, we provide detailed steps on classification, clustering, and statistical analysis of the traced cells based on morphological features. We illustrate the pipeline design using specific examples from zebrafish anatomy. Our approach can be readily applied and generalized to the characterization of axonal, dendritic, or glial geometry. For complete context and scientific motivation for the studies and datasets used here, refer to Valera et al. (2021).
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Affiliation(s)
- Kayvan Bijari
- Center for Neural Informatics, Structures, & Plasticity and Neuroscience Program, Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA 22030, USA
| | - Gema Valera
- Sensory Biology and Organogenesis, Helmholtz Zentrum Munich, 85764 Neuherberg, Germany
| | - Hernán López-Schier
- Sensory Biology and Organogenesis, Helmholtz Zentrum Munich, 85764 Neuherberg, Germany
| | - Giorgio A. Ascoli
- Center for Neural Informatics, Structures, & Plasticity and Neuroscience Program, Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA 22030, USA
- Bioengineering Department, Volgenau School of Engineering, George Mason University, Fairfax, VA 22032, USA
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24
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Ciulla C. Inverse Fourier transformation of combined first order derivative and intensity-curvature functional of magnetic resonance angiography of the human brain. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2021; 211:106384. [PMID: 34537491 DOI: 10.1016/j.cmpb.2021.106384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 08/26/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND OBJECTIVE This paper reports a novel image processing technique based on inverse Fourier transformation and its validation procedure. METHODS Magnetic Resonance Angiography (MRA) data of the human brain is fitted on a pixel-by-pixel basis with bivariate linear model polynomial function. Polynomial fitting allows the formulation of two measures: the first order derivative (FOD), which is an edge finder, and the intensity-curvature functional (ICF), which is a high pass filter. The calculation of FOD and ICF uses knowledge provided by existing research and is performed through resampling. ICF and FOD are direct Fourier transformed, and their k-space is combined through a nonlinear convolution of terms. The resulting k-space is inverse Fourier transformed so to obtain a novel image called Fourier Convolution Image (FCI). RESULTS FCI possesses the characteristics of an edge finder (FOD) and a high pass filter (ICF). CONCLUSIONS FC images yield the following properties versus MRA: 1. Change of the contrast; 2. Increased sharpness in the proximity of human brain vessels; 3. Increased visualization of vessel connectivity. The implication of this study is to provide FCI as another viable option for MRA evaluation.
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Affiliation(s)
- Carlo Ciulla
- Department of Computer Engineering, Epoka University, Rr. Tiranë-Rinas, Km. 12, Vorë, Tirana 1032, Albania.
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25
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Abstract
Biological allometries, such as the scaling of metabolism to mass, are hypothesized to result from natural selection to maximize how vascular networks fill space yet minimize internal transport distances and resistance to blood flow. Metabolic scaling theory argues two guiding principles—conservation of fluid flow and space-filling fractal distributions—describe a diversity of biological networks and predict how the geometry of these networks influences organismal metabolism. Yet, mostly absent from past efforts are studies that directly, and independently, measure metabolic rate from respiration and vascular architecture for the same organ, organism, or tissue. Lack of these measures may lead to inconsistent results and conclusions about metabolism, growth, and allometric scaling. We present simultaneous and consistent measurements of metabolic scaling exponents from clinical images of lung cancer, serving as a first-of-its-kind test of metabolic scaling theory, and identifying potential quantitative imaging biomarkers indicative of tumor growth. We analyze data for 535 clinical PET-CT scans of patients with non-small cell lung carcinoma to establish the presence of metabolic scaling between tumor metabolism and tumor volume. Furthermore, we use computer vision and mathematical modeling to examine predictions of metabolic scaling based on the branching geometry of the tumor-supplying blood vessel networks in a subset of 56 patients diagnosed with stage II-IV lung cancer. Examination of the scaling of maximum standard uptake value with metabolic tumor volume, and metabolic tumor volume with gross tumor volume, yield metabolic scaling exponents of 0.64 (0.20) and 0.70 (0.17), respectively. We compare these to the value of 0.85 (0.06) derived from the geometric scaling of the tumor-supplying vasculature. These results: (1) inform energetic models of growth and development for tumor forecasting; (2) identify imaging biomarkers in vascular geometry related to blood volume and flow; and (3) highlight unique opportunities to develop and test the metabolic scaling theory of ecology in tumors transitioning from avascular to vascular geometries.
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26
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Abdellah M, Foni A, Zisis E, Guerrero NR, Lapere S, Coggan JS, Keller D, Markram H, Schürmann F. Metaball skinning of synthetic astroglial morphologies into realistic mesh models for visual analytics and in silico simulations. Bioinformatics 2021; 37:i426-i433. [PMID: 34252950 PMCID: PMC8275327 DOI: 10.1093/bioinformatics/btab280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Motivation Astrocytes, the most abundant glial cells in the mammalian brain, have an instrumental role in developing neuronal circuits. They contribute to the physical structuring of the brain, modulating synaptic activity and maintaining the blood–brain barrier in addition to other significant aspects that impact brain function. Biophysically, detailed astrocytic models are key to unraveling their functional mechanisms via molecular simulations at microscopic scales. Detailed, and complete, biological reconstructions of astrocytic cells are sparse. Nonetheless, data-driven digital reconstruction of astroglial morphologies that are statistically identical to biological counterparts are becoming available. We use those synthetic morphologies to generate astrocytic meshes with realistic geometries, making it possible to perform these simulations. Results We present an unconditionally robust method capable of reconstructing high fidelity polygonal meshes of astroglial cells from algorithmically-synthesized morphologies. Our method uses implicit surfaces, or metaballs, to skin the different structural components of astrocytes and then blend them in a seamless fashion. We also provide an end-to-end pipeline to produce optimized two- and three-dimensional meshes for visual analytics and simulations, respectively. The performance of our pipeline has been assessed with a group of 5000 astroglial morphologies and the geometric metrics of the resulting meshes are evaluated. The usability of the meshes is then demonstrated with different use cases. Availability and implementation Our metaball skinning algorithm is implemented in Blender 2.82 relying on its Python API (Application Programming Interface). To make it accessible to computational biologists and neuroscientists, the implementation has been integrated into NeuroMorphoVis, an open source and domain specific package that is primarily designed for neuronal morphology visualization and meshing. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Marwan Abdellah
- Blue Brain Project (BBP), École polytechnique fédérale de Lausanne (EPFL), Geneva 1202, Switzerland
| | - Alessandro Foni
- Blue Brain Project (BBP), École polytechnique fédérale de Lausanne (EPFL), Geneva 1202, Switzerland
| | - Eleftherios Zisis
- Blue Brain Project (BBP), École polytechnique fédérale de Lausanne (EPFL), Geneva 1202, Switzerland
| | - Nadir Román Guerrero
- Blue Brain Project (BBP), École polytechnique fédérale de Lausanne (EPFL), Geneva 1202, Switzerland
| | - Samuel Lapere
- Blue Brain Project (BBP), École polytechnique fédérale de Lausanne (EPFL), Geneva 1202, Switzerland
| | - Jay S Coggan
- Blue Brain Project (BBP), École polytechnique fédérale de Lausanne (EPFL), Geneva 1202, Switzerland
| | - Daniel Keller
- Blue Brain Project (BBP), École polytechnique fédérale de Lausanne (EPFL), Geneva 1202, Switzerland
| | - Henry Markram
- Blue Brain Project (BBP), École polytechnique fédérale de Lausanne (EPFL), Geneva 1202, Switzerland
| | - Felix Schürmann
- Blue Brain Project (BBP), École polytechnique fédérale de Lausanne (EPFL), Geneva 1202, Switzerland
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27
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Chen L, Shaw DWW, Dager SR, Corrigan NM, Chu B, Kleinhans NM, Kuhl PK, Hwang JN, Yuan C. Quantitative Assessment of the Intracranial Vasculature of Infants and Adults Using iCafe (Intracranial Artery Feature Extraction). Front Neurol 2021; 12:668298. [PMID: 34122310 PMCID: PMC8193571 DOI: 10.3389/fneur.2021.668298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/16/2021] [Indexed: 11/13/2022] Open
Abstract
Comprehensive quantification of intracranial artery features may help to assess and understand regional variations of blood supply during early brain development and aging. We analyzed vasculature features of 27 healthy infants during natural sleep, 13 infants at 7-months (7.3 ± 1.0 month), and 14 infants at 12-months (11.7 ± 0.4 month), and 13 older healthy, awake adults (62.8 ± 8.7 years) to investigate age-related vascular differences as a preliminary study of vascular changes associated with brain development. 3D time-of-flight (TOF) magnetic resonance angiography (MRA) acquisitions were processed in iCafe, a technique to quantify arterial features (http://icafe.clatfd.cn), to characterize intracranial vasculature. Overall, adult subjects were found to have increased ACA length, tortuosity, and vasculature density compared to both 7-month-old and 12-month-old infants, as well as MCA length compared to 7-month-old infants. No brain laterality differences were observed for any vascular measures in either infant or adult age groups. Reduced skull and brain sharpness, indicative of increased head motion and brain/vascular pulsation, respectively, were observed in infants but not correlated with length, tortuosity, or vasculature density measures. Quantitative analysis of TOF MRA using iCafe may provide an objective approach for systematic study of infant brain vascular development and for clinical assessment of adult and pediatric brain vascular diseases.
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Affiliation(s)
- Li Chen
- University of Washington, Seattle, WA, United States
| | | | | | | | | | | | | | | | - Chun Yuan
- University of Washington, Seattle, WA, United States
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28
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Padmos RM, Terreros NA, Józsa TI, Závodszky G, Marquering HA, Majoie CBLM, Hoekstra AG. Modelling the leptomeningeal collateral circulation during acute ischaemic stroke. Med Eng Phys 2021; 91:1-11. [PMID: 34074460 DOI: 10.1016/j.medengphy.2021.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/26/2021] [Accepted: 03/10/2021] [Indexed: 10/21/2022]
Abstract
A novel model of the leptomeningeal collateral circulation is created by combining data from multiple sources with statistical scaling laws. The extent of the collateral circulation is varied by defining a collateral vessel probability. Blood flow and pressure are simulated using a one-dimensional steady state blood flow model. The leptomeningeal collateral vessels provide significant flow during a stroke. The pressure drop over an occlusion predicted by the model ranges between 60 and 85 mmHg depending on the extent of the collateral circulation. The linear transport of contrast material was simulated in the circulatory network. The time delay of peak contrast over an occlusion is 3.3 s in the model, and 2.1 s (IQR 0.8-4.0 s) when measured in dynamic CTA data of acute ischaemic stroke patients. Modelling the leptomeningeal collateral circulation could lead to better estimates of infarct volume and patient outcome.
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Affiliation(s)
- Raymond M Padmos
- Computational Science Laboratory, Informatics Institute, Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, the Netherlands.
| | - Nerea Arrarte Terreros
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, location AMC, Amsterdam, the Netherlands; Department of Biomedical Engineering and Physics, Amsterdam UMC, location AMC, Amsterdam, the Netherlands
| | - Tamás I Józsa
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Gábor Závodszky
- Computational Science Laboratory, Informatics Institute, Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, the Netherlands
| | - Henk A Marquering
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, location AMC, Amsterdam, the Netherlands; Department of Biomedical Engineering and Physics, Amsterdam UMC, location AMC, Amsterdam, the Netherlands
| | - Charles B L M Majoie
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, location AMC, Amsterdam, the Netherlands
| | - Alfons G Hoekstra
- Computational Science Laboratory, Informatics Institute, Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, the Netherlands
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29
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Zhang R, He X, Jiang JM, Li PP, Wang HY, Li L, Yang JX, Kong L. A computational and experimental investigation of donor-acceptor BODIPY based near-infrared fluorophore for in vivo imaging. Bioorg Chem 2021; 110:104789. [PMID: 33714760 DOI: 10.1016/j.bioorg.2021.104789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/01/2021] [Accepted: 02/28/2021] [Indexed: 12/27/2022]
Abstract
TD-DFT quantum calculation was performed to predict and/or illustrate the electronic transition, the related absorption and emission maxima of some pyrrole-difluoroboron derivatives with different electron donor-acceptor unit or π-conjugated degree. Upon the calculated results, a new near infrared (NIR) fluorophore (abbreviated as TPBD-BP) was designed and fabricated through linking triphenylamine and pyrrole-difluoroboron units to benzothiadiazole (BTD) backbone. The fluorescence of TPBD-BP in solid state centered at 932 nm, which was 985 nm for TPBD-BP nanoparticles (TPBD-BP dots) encapsulated in PEG-6000. The fluorescence of TPBD-BP in both solid state and dots exhibited off-peak tail emission to NIR-II region (extended to 1300 nm). The TPBD-BP dots showed excellent water solubility, biocompatibility and aggregation induced emission (AIE), which was suitable to be applied in vivo imaging. NIR-II emission signal of TPBD-BP dots can be observed in the reproductive organ of normal nude mice after tail vein injection. This attractive combination of computational and experimental investigation would help to develop new-typed small-molecular NIR fluorophores.
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Affiliation(s)
- Rui Zhang
- College of Chemistry and Chemical Engineering, Key Laboratory of Functional Inorganic Materials of Anhui Province, Anhui University, Hefei 230039, PR China
| | - Xuan He
- Institutes of Physical Science and Information Technology, Anhui University, PR China
| | - Jia-Min Jiang
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, PR China
| | - Pan-Pan Li
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, PR China
| | - Hai-Yan Wang
- Institutes of Physical Science and Information Technology, Anhui University, PR China
| | - Lin Li
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, PR China
| | - Jia-Xiang Yang
- College of Chemistry and Chemical Engineering, Key Laboratory of Functional Inorganic Materials of Anhui Province, Anhui University, Hefei 230039, PR China
| | - Lin Kong
- College of Chemistry and Chemical Engineering, Key Laboratory of Functional Inorganic Materials of Anhui Province, Anhui University, Hefei 230039, PR China.
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30
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Padmos RM, Józsa TI, El-Bouri WK, Konduri PR, Payne SJ, Hoekstra AG. Coupling one-dimensional arterial blood flow to three-dimensional tissue perfusion models for in silico trials of acute ischaemic stroke. Interface Focus 2021; 11:20190125. [PMID: 33335706 PMCID: PMC7739918 DOI: 10.1098/rsfs.2019.0125] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2020] [Indexed: 01/08/2023] Open
Abstract
An acute ischaemic stroke is due to the sudden blockage of an intracranial blood vessel by an embolized thrombus. In the context of setting up in silico trials for the treatment of acute ischaemic stroke, the effect of a stroke on perfusion and metabolism of brain tissue should be modelled to predict final infarcted brain tissue. This requires coupling of blood flow and tissue perfusion models. A one-dimensional intracranial blood flow model and a method to couple this to a brain tissue perfusion model for patient-specific simulations is presented. Image-based patient-specific data on the anatomy of the circle of Willis are combined with literature data and models for vessel anatomy not visible in the images, to create an extended model for each patient from the larger vessels down to the pial surface. The coupling between arterial blood flow and tissue perfusion occurs at the pial surface through the estimation of perfusion territories. The coupling method is able to accurately estimate perfusion territories. Finally, we argue that blood flow can be approximated as steady-state flow at the interface between arterial blood flow and tissue perfusion to reduce the cost of organ-scale simulations.
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Affiliation(s)
- Raymond M. Padmos
- Computational Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Tamás I. Józsa
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Wahbi K. El-Bouri
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Praneeta R. Konduri
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, Location AMC, 1105 AZ Amsterdam, The Netherlands
- Biomedical Engineering and Physics, Amsterdam UMC, Location AMC, 1105 AZ Amsterdam, The Netherlands
| | - Stephen J. Payne
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Alfons G. Hoekstra
- Computational Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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31
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Deshpande A, Jamilpour N, Jiang B, Michel P, Eskandari A, Kidwell C, Wintermark M, Laksari K. Automatic segmentation, feature extraction and comparison of healthy and stroke cerebral vasculature. Neuroimage Clin 2021; 30:102573. [PMID: 33578323 PMCID: PMC7875826 DOI: 10.1016/j.nicl.2021.102573] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 01/13/2021] [Accepted: 01/16/2021] [Indexed: 02/01/2023]
Abstract
Accurate segmentation of cerebral vasculature and a quantitative assessment of its morphology is critical to various diagnostic and therapeutic purposes and is pertinent to studying brain health and disease. However, this is still a challenging task due to the complexity of the vascular imaging data. We propose an automated method for cerebral vascular segmentation without the need of any manual intervention as well as a method to skeletonize the binary segmented map to extract vascular geometric features and characterize vessel structure. We combine a Hessian-based probabilistic vessel-enhancing filtering with an active-contour-based technique to segment magnetic resonance and computed tomography angiograms (MRA and CTA) and subsequently extract the vessel centerlines and diameters to calculate the geometrical properties of the vasculature. Our method was validated using a 3D phantom of the Circle-of-Willis region, demonstrating 84% mean Dice similarity coefficient (DSC) and 85% mean Pearson's correlation coefficient (PCC) with minimal modified Hausdorff distance (MHD) error (3 surface pixels at most), and showed superior performance compared to existing segmentation algorithms upon quantitative comparison using DSC, PCC and MHD. We subsequently applied our algorithm to a dataset of 40 subjects, including 1) MRA scans of healthy subjects (n = 10, age = 30 ± 9), 2) MRA scans of stroke patients (n = 10, age = 51 ± 15), 3) CTA scans of healthy subjects (n = 10, age = 62 ± 12), and 4) CTA scans of stroke patients (n = 10, age = 68 ± 11), and obtained a quantitative comparison between the stroke and normal vasculature for both imaging modalities. The vascular network in stroke patients compared to age-adjusted healthy subjects was found to have a significantly (p < 0.05) higher tortuosity (3.24 ± 0.88 rad/cm vs. 7.17 ± 1.61 rad/cm for MRA, and 4.36 ± 1.32 rad/cm vs. 7.80 ± 0.92 rad/cm for CTA), higher fractal dimension (1.36 ± 0.28 vs. 1.71 ± 0.14 for MRA, and 1.56 ± 0.05 vs. 1.69 ± 0.20 for CTA), lower total length (3.46 ± 0.99 m vs. 2.20 ± 0.67 m for CTA), lower total volume (61.80 ± 18.79 ml vs. 34.43 ± 22.9 ml for CTA), lower average diameter (2.4 ± 0.21 mm vs. 2.18 ± 0.07 mm for CTA), and lower average branch length (4.81 ± 1.97 mm vs. 8.68 ± 2.03 mm for MRA), respectively. We additionally studied the change in vascular features with respect to aging and imaging modality. While we observed differences between features as a result of aging, statistical analysis did not show any significant differences, whereas we found that the number of branches were significantly different (p < 0.05) between the two imaging modalities (201 ± 73 for MRA vs. 189 ± 69 for CTA). Our segmentation and feature extraction algorithm can be applied on any imaging modality and can be used in the future to automatically obtain the 3D segmented vasculature for diagnosis and treatment planning as well as to study morphological changes due to stroke and other cerebrovascular diseases (CVD) in the clinic.
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Affiliation(s)
- Aditi Deshpande
- Department of Biomedical Engineering, University of Arizona, United States
| | - Nima Jamilpour
- Department of Biomedical Engineering, University of Arizona, United States
| | - Bin Jiang
- Department of Radiology, Stanford University, United States
| | - Patrik Michel
- Department of Neurology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Ashraf Eskandari
- Department of Neurology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Chelsea Kidwell
- Department of Neurology, University of Arizona, United States
| | - Max Wintermark
- Department of Radiology, Stanford University, United States
| | - Kaveh Laksari
- Department of Biomedical Engineering, University of Arizona, United States; Department of Aerospace and Mechanical Engineering, University of Arizona, United States.
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32
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Tucker T. Arterial stiffness as a vascular contribution to cognitive impairment: a fluid dynamics perspective. Biomed Phys Eng Express 2021; 7. [PMID: 33482655 DOI: 10.1088/2057-1976/abdf36] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/22/2021] [Indexed: 11/11/2022]
Abstract
A model of cerebral pulsatile blood through multiple arterial bifurcations is developed, based on the physics of wave propagation in compliant vessels. The model identifies the conditions for the optimum antegrade flow of blood into the arterioles as a function of the areas and stiffnesses of the arteries. The model predicts and quantifies the reduction in vessel diameter which occurs in progressing from the large central arteries into the arterioles. It also predicts and quantifies the change in vessel compliance which occurs in progressing from the large central arteries, through the small arteries, into the arterioles. Physics predicts that the clinically observed compliance changes are consistent with the efficient delivery of blood to the cerebral capillary bed. The model predicts that increasing arterial stiffening with age, reduces pulsatile cerebral blood flow substantially, potentially resulting in ischemia, hypoperfusion and hypoxia, with attendant neurological and cognition consequences. The model predicts that while central pulse pressure increases with aging, small vessel pulse pressure reduces, contrary to the concept of a pressure wave tsunami in the small vessels. The model also predicts that increased luminal diameters with increasing age, mitigate, somewhat the negative consequences of arterial stiffening, a form of adaptive arterial remodelling.
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Affiliation(s)
- Trevor Tucker
- Independent Researcher, Independent Researcher, Ottawa, Ontario, CANADA
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33
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Hindenes LB, Håberg AK, Johnsen LH, Mathiesen EB, Robben D, Vangberg TR. Variations in the Circle of Willis in a large population sample using 3D TOF angiography: The Tromsø Study. PLoS One 2020; 15:e0241373. [PMID: 33141840 PMCID: PMC7608873 DOI: 10.1371/journal.pone.0241373] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/14/2020] [Indexed: 11/18/2022] Open
Abstract
The main arteries that supply blood to the brain originate from the Circle of Willis (CoW). The CoW exhibits considerable anatomical variations which may have clinical importance, but the variability is insufficiently characterised in the general population. We assessed the anatomical variability of CoW variants in a community-dwelling sample (N = 1,864, 874 men, mean age = 65.4, range 40–87 years), and independent and conditional frequencies of the CoW’s artery segments. CoW segments were classified as present or missing/hypoplastic (w/1mm diameter threshold) on 3T time-of-flight magnetic resonance angiography images. We also examined whether age and sex were associated with CoW variants. We identified 47 unique CoW variants, of which five variants constituted 68.5% of the sample. The complete variant was found in 11.9% of the subjects, and the most common variant (27.8%) was missing both posterior communicating arteries. Conditional frequencies showed patterns of interdependence across most missing segments in the CoW. CoW variants were associated with mean-split age (P = .0147), and there was a trend showing more missing segments with increasing age. We found no association with sex (P = .0526). Our population study demonstrated age as associated with CoW variants, suggesting reduced collateral capacity with older age.
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Affiliation(s)
- Lars B. Hindenes
- Department of Clinical Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
- PET Centre, University Hospital of North Norway, Tromsø, Norway
- * E-mail:
| | - Asta K. Håberg
- Department of Radiology and Nuclear Medicine, St. Olav University Hospital, Trondheim, Norway
- Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Liv Hege Johnsen
- Department of Clinical Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ellisiv B. Mathiesen
- Department of Clinical Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
- Department of Neurology, University Hospital of North Norway, Tromsø, Norway
| | - David Robben
- ESAT-PSI, Department of Electrical Engineering, KU Leuven, Leuven, Belgium
- Icometrix, Leuven, Belgium
| | - Torgil R. Vangberg
- Department of Clinical Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
- PET Centre, University Hospital of North Norway, Tromsø, Norway
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Phan TG, Ma H, Goyal M, Hilton J, Sinnott M, Srikanth V, Beare R. Computer Modeling of Clot Retrieval-Circle of Willis. Front Neurol 2020; 11:773. [PMID: 32849226 PMCID: PMC7427049 DOI: 10.3389/fneur.2020.00773] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/24/2020] [Indexed: 12/22/2022] Open
Abstract
Endovascular clot retrieval, often referred to as mechanical thrombectomy, has transformed the treatment of patients with ischemic stroke based on an underlying large cerebral vessel occlusion, ranging from the extracranial internal carotid artery (ICA) to the M1 (proximal) segment of the middle cerebral artery (MCA). The aim of this study was to evaluate the effect of a progressive occlusion of the extracranial portion of the ICA on the cerebral blood flow either with a conventional guiding catheter or a balloon-guiding catheter, which enables the operator to completely occlude the parent artery by inflating the balloon around the tip of this type of guiding catheter. We evaluated the impact of flow reduction in the ICA in the setting of ipsilateral MCA occlusion given the different configurations of the circle of Willis (CoW). The computer model of cerebral arteries was based on anatomical works by Rhoton (1) and van der Eecken (2). The interactive experimental results are available on the web at https://gntem3.shinyapps.io/ecrsim. In the setting of left MCA occlusion, compensation from the anterior and posterior communicating artery preserved the flow in the left anterior cerebral artery (ACA) but not the left MCA branches. Under selected CoW configurations, such as classic, missing Acom, or missing A1 segment of the ACA and concurrent right ICA occlusion, there was a progressive decrease of flow in the left ACA to a minimum of 78% when the simulated catheter fully occluded the left ICA. Flow collapsed (<10%) in the left ACA and MCA branches under CoW configurations, such as bilateral fetal PCA. In summary, compensatory flow collapsed under certain clot retrieval scenarios and unusual configurations of CoW.
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Affiliation(s)
- Thanh G Phan
- Stroke and Aging Research Group, Clinical Trials, Imaging and Informatics Division, School of Clinical Sciences at Monash Health, Monash University, Melbourne, VIC, Australia.,Department of Neurology, Monash Health, Melbourne, VIC, Australia
| | - Henry Ma
- Stroke and Aging Research Group, Clinical Trials, Imaging and Informatics Division, School of Clinical Sciences at Monash Health, Monash University, Melbourne, VIC, Australia.,Department of Neurology, Monash Health, Melbourne, VIC, Australia
| | - Mayank Goyal
- Departments of Clinical Neuroscience and Radiology, Cummings School of Medicine, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - James Hilton
- Data 61, CSIRO, Innovation Hub, Docklands, VIC, Australia
| | | | - Velandai Srikanth
- Department of Medicine, Peninsula Clinical School, Central Clinical School, Frankston Hospital, Monash University, Melbourne, VIC, Australia
| | - Richard Beare
- Departments of Clinical Neuroscience and Radiology, Cummings School of Medicine, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
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Lutz Y, Meiner T, Krames L, Cattaneo G, Meckel S, Dossel O, Loewe A. Selective Brain Hypothermia for Ischemic MCA-M1 Stroke: Influence of Cerebral Arterial Circulation in a 3D Brain Temperature Model. IEEE Trans Biomed Eng 2020; 68:404-415. [PMID: 32746020 DOI: 10.1109/tbme.2020.3000521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Acute ischemic stroke is a major health problem with a high mortality rate and a high risk for permanent disabilities. Selective brain hypothermia has the neuroprotective potential to possibly lower cerebral harm. A recently developed catheter system enables to combine endovascular blood cooling and thrombectomy using the same endovascular access. By using the penumbral perfusion via leptomeningeal collaterals, the catheter aims at enabling a cold reperfusion, which mitigates the risk of a reperfusion injury. However, cerebral circulation is highly patient-specific and can vary greatly. Since direct measurement of remaining perfusion and temperature decrease induced by the catheter is not possible without additional harm to the patient, computational modeling provides an alternative to gain knowledge about resulting cerebral temperature decrease. In this work, we present a brain temperature model with a realistic division into gray and white matter and consideration of spatially resolved perfusion. Furthermore, it includes detailed anatomy of cerebral circulation with possibility of personalizing on base of real patient anatomy. For evaluation of catheter performance in terms of cold reperfusion and to analyze its general performance, we calculated the decrease in brain temperature in case of a large vessel occlusion in the middle cerebral artery (MCA) for different scenarios of cerebral arterial anatomy. Congenital arterial variations in the circle of Willis had a distinct influence on the cooling effect and the resulting spatial temperature distribution before vessel recanalization. Independent of the branching configurations, the model predicted a cold reperfusion due to a strong temperature decrease after recanalization (1.4-2.2 °C after 25 min of cooling, recanalization after 20 min of cooling). Our model illustrates the effectiveness of endovascular cooling in combination with mechanical thrombectomy and its results serve as an adequate substitute for temperature measurement in a clinical setting in the absence of direct intraparenchymal temperature probes.
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Abdellah M, Guerrero NR, Lapere S, Coggan JS, Keller D, Coste B, Dagar S, Courcol JD, Markram H, Schürmann F. Interactive visualization and analysis of morphological skeletons of brain vasculature networks with VessMorphoVis. Bioinformatics 2020; 36:i534-i541. [PMID: 32657395 PMCID: PMC7355309 DOI: 10.1093/bioinformatics/btaa461] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
MOTIVATION Accurate morphological models of brain vasculature are key to modeling and simulating cerebral blood flow in realistic vascular networks. This in silico approach is fundamental to revealing the principles of neurovascular coupling. Validating those vascular morphologies entails performing certain visual analysis tasks that cannot be accomplished with generic visualization frameworks. This limitation has a substantial impact on the accuracy of the vascular models employed in the simulation. RESULTS We present VessMorphoVis, an integrated suite of toolboxes for interactive visualization and analysis of vast brain vascular networks represented by morphological graphs segmented originally from imaging or microscopy stacks. Our workflow leverages the outstanding potentials of Blender, aiming to establish an integrated, extensible and domain-specific framework capable of interactive visualization, analysis, repair, high-fidelity meshing and high-quality rendering of vascular morphologies. Based on the initial feedback of the users, we anticipate that our framework will be an essential component in vascular modeling and simulation in the future, filling a gap that is at present largely unfulfilled. AVAILABILITY AND IMPLEMENTATION VessMorphoVis is freely available under the GNU public license on Github at https://github.com/BlueBrain/VessMorphoVis. The morphology analysis, visualization, meshing and rendering modules are implemented as an add-on for Blender 2.8 based on its Python API (application programming interface). The add-on functionality is made available to users through an intuitive graphical user interface, as well as through exhaustive configuration files calling the API via a feature-rich command line interface running Blender in background mode. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Marwan Abdellah
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, 1202 Geneva, Switzerland
| | - Nadir Román Guerrero
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, 1202 Geneva, Switzerland
| | - Samuel Lapere
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, 1202 Geneva, Switzerland
| | - Jay S Coggan
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, 1202 Geneva, Switzerland
| | - Daniel Keller
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, 1202 Geneva, Switzerland
| | - Benoit Coste
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, 1202 Geneva, Switzerland
| | - Snigdha Dagar
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, 1202 Geneva, Switzerland
| | - Jean-Denis Courcol
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, 1202 Geneva, Switzerland
| | - Henry Markram
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, 1202 Geneva, Switzerland
| | - Felix Schürmann
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, 1202 Geneva, Switzerland
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Su J, Wolff L, van Es ACGM, van Zwam W, Majoie C, W J Dippel D, van der Lugt A, J Niessen W, Van Walsum T. Automatic Collateral Scoring From 3D CTA Images. IEEE TRANSACTIONS ON MEDICAL IMAGING 2020; 39:2190-2200. [PMID: 31944937 DOI: 10.1109/tmi.2020.2966921] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The collateral score is an important biomarker in decision making for endovascular treatment (EVT) of patients with ischemic stroke. The existing collateral grading systems are based on visual inspection and prone to subjective interpretation and interobserver variation. The purpose of our work is the development of an automatic collateral scoring method. In this work, we present a method that is inspired by human collateral scoring. Firstly, we define an anatomical region by atlas-based registration and extract vessel structures using a deep convolutional neural network. From this, high-level features based on the ratios of vessel length and volume of the occluded and the contralateral side are defined. Multi-class classification models are used to map the feature space to a four-grade collateral score and a quantitative score. The dataset used for training, validation and testing is from a registry of images acquired in clinical routine at multiple medical centers. The model performance is tested on 269 subjects, achieving an accuracy of 0.8. The dichotomized collateral score accuracy is 0.9. The error is comparable to the interobserver variation, the results are comparable to the performance of two radiologists with 10 to 30 years of experience.
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A novel algorithm for refining cerebral vascular measurements in infants and adults. J Neurosci Methods 2020; 340:108751. [PMID: 32344044 DOI: 10.1016/j.jneumeth.2020.108751] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/03/2020] [Accepted: 04/21/2020] [Indexed: 01/11/2023]
Abstract
BACKGROUND Comprehensive quantification of intracranial vascular characteristics by vascular tracing provides an objective clinical assessment of vascular structure. However, weak signal or low contrast in small distal arteries, artifacts due to volitional motion, and vascular pulsation are challenges for accurate vessel tracing from 3D time-of-flight (3D-TOF) magnetic resonance angiography (MRA) images. NEW METHOD A vascular measurement refinement algorithm is developed and validated for robust quantification of intracranial vasculature from 3D-TOF MRA. After automated vascular tracing, centerline positions, lumen radii and centerline deviations are jointly optimized to restrict traces to within vascular regions in the straightened curved planar reformation (CPR) views. The algorithm is validated on simulated vascular images and on repeat 3D-TOF MRA acquired from infants and adults. RESULTS The refinement algorithm can reliably estimate vascular radius and correct deviated centerlines. For the simulated vascular image with noise level of 1 and deviation of centerline of 3, the mean radius difference is below 15.3 % for scan-rescan reliability. Vascular features from repeated clinical scans show significantly improved measurement agreement, with intra-class correlation coefficient (ICC) improvement from 0.55 to 0.7 for infants and from 0.59 to 0.92 for adults. COMPARISON WITH EXISTING METHODS The refinement algorithm is novel because it utilizes straightened CPR views that incorporate information from the entire artery. In addition, the optimization corrects centerline positions, lumen radii and centerline deviations simultaneously. CONCLUSIONS Intracranial vasculature quantification using a novel refinement algorithm for vascular tracing improves the reliability of vascular feature measurements in both infants and adults.
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Pandey A, Shukla H, Young GS, Qin L, Zamani AA, Hsu L, Huang R, Dunne C, Borkin MA. CerebroVis: Designing an Abstract yet Spatially Contextualized Cerebral Artery Network Visualization. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2020; 26:938-948. [PMID: 31545730 DOI: 10.1109/tvcg.2019.2934402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Blood circulation in the human brain is supplied through a network of cerebral arteries. If a clinician suspects a patient has a stroke or other cerebrovascular condition, they order imaging tests. Neuroradiologists visually search the resulting scans for abnormalities. Their visual search tasks correspond to the abstract network analysis tasks of browsing and path following. To assist neuroradiologists in identifying cerebral artery abnormalities, we designed CerebroVis, a novel abstract-yet spatially contextualized-cerebral artery network visualization. In this design study, we contribute a novel framing and definition of the cerebral artery system in terms of network theory and characterize neuroradiologist domain goals as abstract visualization and network analysis tasks. Through an iterative, user-centered design process we developed an abstract network layout technique which incorporates cerebral artery spatial context. The abstract visualization enables increased domain task performance over 3D geometry representations, while including spatial context helps preserve the user's mental map of the underlying geometry. We provide open source implementations of our network layout technique and prototype cerebral artery visualization tool. We demonstrate the robustness of our technique by successfully laying out 61 open source brain scans. We evaluate the effectiveness of our layout through a mixed methods study with three neuroradiologists. In a formative controlled experiment our study participants used CerebroVis and a conventional 3D visualization to examine real cerebral artery imaging data to identify a simulated intracranial artery stenosis. Participants were more accurate at identifying stenoses using CerebroVis (absolute risk difference 13%). A free copy of this paper, the evaluation stimuli and data, and source code are available at osf.io/e5sxt.
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40
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Keelan J, Chung EML, Hague JP. Development of a globally optimised model of the cerebral arteries. Phys Med Biol 2019; 64:125021. [PMID: 31226100 DOI: 10.1088/1361-6560/ab2479] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The cerebral arteries are difficult to reproduce from first principles, featuring interwoven territories, and intricate layers of grey and white matter with differing metabolic demand. The aim of this study was to identify the ideal configuration of arteries required to sustain an entire brain hemisphere based on minimisation of the energy required to supply the tissue. The 3D distribution of grey and white matter within a healthy human brain was first segmented from magnetic resonance images. A novel simulated annealing algorithm was then applied to determine the optimal configuration of arteries required to supply brain tissue. The model was validated through comparison of this ideal, entirely optimised, brain vasculature with the structure and properties of real arteries. This analysis established that the human cerebral vasculature is highly optimised; closely resembling the most energy efficient arrangement of vessels. In addition to local adherence to fluid dynamical optimisation principles, the optimised vasculature reproduced expected brain perfusion territories, featuring well-defined boundaries between anterior, middle and posterior regions. This validated brain vascular model and algorithm can be used for patient-specific modelling of stroke and cerebral haemodynamics, identification of sub-optimal conditions associated with vascular disease, and optimising vascular structures for tissue engineering applications and artificial organ design.
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Affiliation(s)
- Jonathan Keelan
- School of Physical Sciences, The Open University, MK7 6AA, United Kingdom
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Chen L, Sun J, Hippe DS, Balu N, Yuan Q, Yuan I, Zhao X, Li R, He L, Hatsukami TS, Hwang JN, Yuan C. Quantitative assessment of the intracranial vasculature in an older adult population using iCafe. Neurobiol Aging 2019; 79:59-65. [PMID: 31026623 DOI: 10.1016/j.neurobiolaging.2019.02.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/04/2019] [Accepted: 02/28/2019] [Indexed: 01/11/2023]
Abstract
Comprehensive quantification of intracranial artery features may help us assess and understand variations of blood supply during brain development and aging. We analyzed vasculature features of 163 participants (age 56-85 years, mean of 71) from a community study to investigate if any of the features varied with age. Three-dimensional time-of-flight magnetic resonance angiography images of these participants were processed in IntraCranial artery feature extraction technique (a recently developed technique to obtain quantitative features of arteries) to divide intracranial vasculatures into anatomical segments and generate 8 morphometry and intensity features for each segment. Overall, increase in age was found negatively associated with number of branches and average order of intracranial arteries while positively associated with tortuosity, which remained after adjusting for cardiovascular risk factors. The associations with number of branches and average order were consistently found between 3 main intracranial artery regions, whereas the association with tortuosity appeared to be present only in middle cerebral artery/distal arteries. The combination of time-of-flight magnetic resonance angiography and IntraCranial artery feature extraction technique may provide an effective way to study vascular conditions and changes in the aging brain.
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Affiliation(s)
- Li Chen
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA
| | - Jie Sun
- Department of Radiology, University of Washington, Seattle, WA, USA
| | - Daniel S Hippe
- Department of Radiology, University of Washington, Seattle, WA, USA
| | - Niranjan Balu
- Department of Radiology, University of Washington, Seattle, WA, USA
| | - Quan Yuan
- Department of Neurology, Xuanwu hospital, Capital Medical University, Beijing, China
| | | | - Xihai Zhao
- Biomedical Engineering, Tsinghua University, Beijing, China
| | - Rui Li
- Biomedical Engineering, Tsinghua University, Beijing, China
| | - Le He
- Biomedical Engineering, Tsinghua University, Beijing, China
| | | | - Jenq-Neng Hwang
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA
| | - Chun Yuan
- Department of Radiology, University of Washington, Seattle, WA, USA.
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Hsu C, Li Y, Han Y, Elijovich L, Sabin ND, Abuelem T, Torabi R, Faught A, Hua C, Klimo P, Merchant TE, Lucas JT. Automatic image processing pipeline for tracking longitudinal vessel changes in magnetic resonance angiography. J Magn Reson Imaging 2019; 50:1063-1074. [DOI: 10.1002/jmri.26699] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 11/07/2022] Open
Affiliation(s)
- Chih‐Yang Hsu
- Department of Radiation OncologySt. Jude Children's Research Hospital Memphis Tennessee USA (Work Origin)
| | - Yimei Li
- Department of BiostatisticsSt. Jude Children's Research Hospital Memphis Tennessee USA
| | - Yuanyuan Han
- Department of BiostatisticsSt. Jude Children's Research Hospital Memphis Tennessee USA
| | - Lucas Elijovich
- Vascular Anomalies CenterLe Bonheur Children's Hospital Memphis Tennessee USA
| | - Noah D. Sabin
- Department of Diagnostic ImagingSt. Jude Children's Research Hospital Memphis Tennessee USA
| | | | | | - Austin Faught
- Department of Radiation OncologySt. Jude Children's Research Hospital Memphis Tennessee USA (Work Origin)
| | - Chia‐Ho Hua
- Department of Radiation OncologySt. Jude Children's Research Hospital Memphis Tennessee USA (Work Origin)
| | | | - Thomas E. Merchant
- Department of Radiation OncologySt. Jude Children's Research Hospital Memphis Tennessee USA (Work Origin)
| | - John T. Lucas
- Department of Radiation OncologySt. Jude Children's Research Hospital Memphis Tennessee USA (Work Origin)
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Li Y, Zeng S, Hao J. Non-Invasive Optical Guided Tumor Metastasis/Vessel Imaging by Using Lanthanide Nanoprobe with Enhanced Down-Shifting Emission beyond 1500 nm. ACS NANO 2019; 13:248-259. [PMID: 30604961 DOI: 10.1021/acsnano.8b05431] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Visualization of tumor vessels/metastasis and cerebrovascular architecture is vitally important for analyzing pathological states of brain diseases and a tumor's abnormal blood vessels to improve cancer diagnoses. In vivo fluorescence imaging using second near-infrared emission beyond 1500 nm (NIR-IIb) has emerged as a next generation optical imaging method with significant improvement in imaging sensitivity and spatial resolution. Unfortunately, a highly biocompatible probe capable of generating NIR-IIb emission with sufficient brightness and uniformed size is still scarce. Here, we have proposed the poly(acrylic acid) (PAA)-modified NaLnF4:40Gd/20Yb/2Er nanorods (Ln = Y, Yb, Lu, PAA-Ln-NRs) with enhanced downshifting NIR-IIb emission, high quantum yield (QY), relatively narrow bandwidth (∼160 nm), and high biocompatibility via Ce3+ doping for high performance NIR-IIb bioimaging. The downshifting emission beyond 1500 nm is improved by 1.75-2.2 times with simultaneously suppressing the upconversion (UC) path in Y, Yb, and Lu hosts via Ce3+ doping. Moreover, compared with the traditionally used Y-based host, the QY of NIR-IIb emission in the Lu-based probe in water is improved from 2.2% to 3.6%. The explored bright NIR-IIb emitted PAA-Lu-NRs were used for high sensitivity small tumor (∼4 mm)/metastatic tiny tumor detection (∼3 mm), tumor vessel visualization with high spatial resolution (41 μm), and brain vessel imaging. Therefore, our findings open up the opportunity of utilizing the lanthanide based NIR-IIb probe with bright 1525 nm emission for in vivo optical-guided tumor vessel/metastasis and noninvasive brain vascular imaging.
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Affiliation(s)
- Youbin Li
- Synergetic Innovation Center for Quantum Effects and Application, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control of Ministry of Education, School of Physics and Electronics , Hunan Normal University , Changsha 410081 , P.R. China
| | - Songjun Zeng
- Synergetic Innovation Center for Quantum Effects and Application, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control of Ministry of Education, School of Physics and Electronics , Hunan Normal University , Changsha 410081 , P.R. China
| | - Jianhua Hao
- Department of Applied Physics , The Hong Kong Polytechnic University , Hong Kong , China
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Chen L, Mossa-Basha M, Sun J, Hippe DS, Balu N, Yuan Q, Pimentel K, Hatsukami TS, Hwang JN, Yuan C. Quantification of morphometry and intensity features of intracranial arteries from 3D TOF MRA using the intracranial artery feature extraction (iCafe): A reproducibility study. Magn Reson Imaging 2018; 57:293-302. [PMID: 30580079 DOI: 10.1016/j.mri.2018.12.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/22/2018] [Accepted: 12/19/2018] [Indexed: 11/27/2022]
Abstract
BACKGROUND Accurate and reliable vascular features extracted from 3D time-of-flight (TOF) magnetic resonance angiography (MRA) can help evaluate cerebral vascular diseases and conditions. The goal of this study was to evaluate the reproducibility of an intracranial artery feature extraction (iCafe) algorithm for quantitative analysis of intracranial arteries from TOF MRA. METHODS Twenty-four patients with known intracranial artery stenosis were recruited and underwent two separate MRA scans within 2 weeks of each other. Each dataset was blinded to associated imaging and clinical data and then processed independently using iCafe. Inter-scan reproducibility analysis was performed on the 24 pairs of scans while intra-/inter-operator reproducibility and stenosis detection were assessed on 8 individual MRA scans. After tracing the vessels visualized on TOF MRA, iCafe was used to automatically extract the locations with stenosis and eight other vascular features. The vascular features included the following six morphometry and two signal intensity features: artery length (total, distal, and proximal), volume, number of branches, average radius of the M1 segment of the middle cerebral artery, and average normalized intensity of all arteries and large vertical arteries. A neuroradiologist independently reviewed the images to identify locations of stenosis for the reference standard. Reproducibility of stenosis detection and vascular features was assessed using Cohen's kappa, the intra-class correlation coefficient (ICC), and within-subject coefficient of variation (CV). RESULTS The segment-based sensitivity of iCafe for stenosis detection ranged from 83.3-91.7% while specificity was 97.4%. Kappa values for inter-scan and intra-operator reproducibility were 0.73 and 0.77, respectively. All vascular features demonstrated excellent inter-scan and intra-operator reproducibility (ICC = 0.91-1.00, and CV = 1.21-8.78% for all markers), and good to excellent inter-operator reproducibility (ICC = 0.76-0.99, and CV = 3.27-15.79% for all markers). CONCLUSION Intracranial artery features can be reliably quantified from TOF MRA using iCafe to provide both clinical diagnostic assistance and facilitate future investigative quantitative analyses.
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Affiliation(s)
- Li Chen
- Department of Electrical Engineering, University of Washington, Seattle, WA 98195, USA.
| | - Mahmud Mossa-Basha
- Department of Radiology, University of Washington, Seattle, WA 98195, USA.
| | - Jie Sun
- Department of Radiology, University of Washington, Seattle, WA 98195, USA.
| | - Daniel S Hippe
- Department of Radiology, University of Washington, Seattle, WA 98195, USA.
| | - Niranjan Balu
- Department of Radiology, University of Washington, Seattle, WA 98195, USA.
| | - Quan Yuan
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Kristi Pimentel
- Department of Radiology, University of Washington, Seattle, WA 98195, USA.
| | - Thomas S Hatsukami
- Department of Surgery, University of Washington, Seattle, WA 98195, USA.
| | - Jenq-Neng Hwang
- Department of Electrical Engineering, University of Washington, Seattle, WA 98195, USA.
| | - Chun Yuan
- Department of Radiology, University of Washington, Seattle, WA 98195, USA.
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Aliaga Maraver JJ, Mata S, Benavides-Piccione R, DeFelipe J, Pastor L. A Method for the Symbolic Representation of Neurons. Front Neuroanat 2018; 12:106. [PMID: 30618651 PMCID: PMC6305400 DOI: 10.3389/fnana.2018.00106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/20/2018] [Indexed: 11/13/2022] Open
Abstract
The field of neuroanatomy has progressed considerably in recent decades, thanks to the emergence of novel methods which provide new insights into the organization of the nervous system. These new methods have produced a wealth of data that needs to be analyzed, shifting the bottleneck from the acquisition to the analysis of data. In other disciplines, such as in many engineering areas, scientists and engineers are dealing with increasingly complex systems, using hierarchical decompositions, graphical models and simplified schematic diagrams for analysis and design processes. This approach makes it possible for users to simultaneously combine global system views and very detailed representations of specific areas of interest, by selecting appropriate representations for each of these views. In this way, users can concentrate on specific details while also maintaining a general system overview - a capability that is essential for understanding structure and function whenever complexity is an issue. Following this approach, this paper focuses on a graphical tool designed to help neuroanatomists to better understand and detect morphological characteristics of neuronal cells. The method presented here, based on a symbolic representation that can be tailored to enhance a particular range of features of a neuron or neuron set, has proven to be useful for highlighting particular geometries that may be hidden due to the complexity of the analysis tasks and the richness of neuronal morphologies. A software tool has been developed to generate graphical representations of neurons from 3D computer-aided reconstruction files.
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Affiliation(s)
- Jose Juan Aliaga Maraver
- Departamento de Aeronaves y Vehículos Espaciales, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Susana Mata
- Department of Computer Engineering, Universidad Rey Juan Carlos, Madrid, Spain.,Center for Computational Simulation, Universidad Politécnica de Madrid, Madrid, Spain
| | - Ruth Benavides-Piccione
- Cajal Institute (CSIC), Madrid, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Madrid, Spain.,Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Madrid, Spain
| | - Javier DeFelipe
- Cajal Institute (CSIC), Madrid, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Madrid, Spain.,Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Madrid, Spain
| | - Luis Pastor
- Department of Computer Engineering, Universidad Rey Juan Carlos, Madrid, Spain.,Center for Computational Simulation, Universidad Politécnica de Madrid, Madrid, Spain
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Ghaffari M, Sanchez L, Xu G, Alaraj A, Zhou XJ, Charbel FT, Linninger AA. Validation of parametric mesh generation for subject-specific cerebroarterial trees using modified Hausdorff distance metrics. Comput Biol Med 2018; 100:209-220. [PMID: 30048917 DOI: 10.1016/j.compbiomed.2018.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 01/19/2023]
Abstract
Accurate subject-specific vascular network reconstruction is a critical task for the hemodynamic analysis of cerebroarterial circulation. Vascular skeletonization and computational mesh generation for large sections of cerebrovascular trees from magnetic resonance angiography (MRA) is an error-prone, operator-dependent, and very time-consuming task. Validation of reconstructed computational models is essential to ascertain their accuracy and precision, which directly relates to the confidence of CFD computations performed on these meshes. The aim of this study is to generate an imaging segmentation pipeline to validate and quantify the spatial accuracy of computational models of subject-specific cerebral arterial trees. We used a recently introduced parametric structured mesh (PSM) generation method to automatically reconstruct six subject-specific cerebral arterial trees containing 1364 vessels and 571 bifurcations. By automatically extracting sampling frames for all vascular segments and bifurcations, we quantify the spatial accuracy of PSM against the original MRA images. Our comprehensive study correlates lumen area, pixel-based statistical analysis, area overlap and centerline accuracy measurements. In addition, we propose a new metric, the pointwise offset surface distance metric (PSD), to quantify the spatial alignment between dimensions of reconstructed arteries and bifurcations with in-vivo data with the ability to quantify the over- and under-approximation of the reconstructed models. Accurate reconstruction of vascular trees can a practical process tool for morphological analysis of large patient data banks, such as medical record files in hospitals, or subject-specific hemodynamic simulations of the cerebral arterial circulation.
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Affiliation(s)
- Mahsa Ghaffari
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Lea Sanchez
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Guoren Xu
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Ali Alaraj
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA; Department of Neurosurgery, University of Illinois at Chicago, Chicago, IL, USA.
| | - Xiaohong Joe Zhou
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA; Department of Neurosurgery, University of Illinois at Chicago, Chicago, IL, USA; Department of Radiology and Center for MR Research, University of Illinois at Chicago, Chicago, IL, USA
| | - Fady T Charbel
- Department of Neurosurgery, University of Illinois at Chicago, Chicago, IL, USA
| | - Andreas A Linninger
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA; Department of Neurosurgery, University of Illinois at Chicago, Chicago, IL, USA.
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Xue Z, Zeng S, Hao J. Non-invasive through-skull brain vascular imaging and small tumor diagnosis based on NIR-II emissive lanthanide nanoprobes beyond 1500 nm. Biomaterials 2018; 171:153-163. [DOI: 10.1016/j.biomaterials.2018.04.037] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 04/09/2018] [Accepted: 04/14/2018] [Indexed: 01/08/2023]
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How does blood regulate cerebral temperatures during hypothermia? Sci Rep 2018; 8:7877. [PMID: 29777174 PMCID: PMC5959945 DOI: 10.1038/s41598-018-26063-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/27/2018] [Indexed: 11/30/2022] Open
Abstract
Macro-modeling of cerebral blood flow can help determine the impact of thermal intervention during instances of head trauma to mitigate tissue damage. This work presents a bioheat model using a 3D fluid-porous domain coupled with intersecting 1D arterial and venous vessel trees. This combined vascular porous (VaPor) model resolves both cerebral blood flow and energy equations, including heat generated by metabolism, using vasculature extracted from MRI data and is extended using a tree generation algorithm. Counter-current flows are expected to increase thermal transfer within the brain and are enforced using either the vascular structure or flow reversal, represented by a flow reversal constant, CR. These methods exhibit larger average brain cooling (from 0.56 °C ± <0.01 °C to 0.58 °C ± <0.01 °C) compared with previous models (0.39 °C) when scalp temperature is reduced. An greater reduction in core brain temperature is observed (from 0.29 °C ± <0.01 °C to 0.45 °C ± <0.01 °C) compared to previous models (0.11 °C) due to the inclusion of counter-current cooling effects. The VaPor model also predicts that a hypothermic average temperature (<36 °C) can be reached in core regions of neonatal models using scalp cooling alone.
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Bulant C, Blanco P, Clausse A, Bezerra C, Lima T, Ávila L, Lemos P, Feijóo R. Thermodynamic analogies for the characterization of 3D human coronary arteries. Biomed Signal Process Control 2018. [DOI: 10.1016/j.bspc.2017.09.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Mattern H, Sciarra A, Godenschweger F, Stucht D, Lüsebrink F, Rose G, Speck O. Prospective motion correction enables highest resolution time-of-flight angiography at 7T. Magn Reson Med 2017; 80:248-258. [PMID: 29230871 DOI: 10.1002/mrm.27033] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 11/10/2017] [Accepted: 11/13/2017] [Indexed: 12/15/2022]
Abstract
PURPOSE Higher magnetic field strengths enable time-of-flight (TOF) angiography with higher resolution to depict small-vessel pathologies. However, this potential is limited by the subject's ability to remain motionless. Even small-scale, involuntary motion can degrade vessel depiction, thus limiting the effective resolution. The aim of this study was to overcome this resolution limit by deploying prospectively motion-corrected (PMC) TOF. METHODS An optical, marker-based, in-bore tracking system was used to update the imaging volume prospectively according to the subject's head motion. PMC TOF was evaluated in 12 healthy, cooperative subjects at isotropic resolution of up to 150 μm. Image quality was assessed qualitatively through reader rating and quantitatively with the average edge-strength metric. RESULTS PMC significantly increased the average edge strength and qualitatively improved the vessel depiction in nine out of 11 cases. Image quality was never degraded by motion correction. PMC also enabled acquisition of the highest resolution human brain in vivo TOF angiography to date. CONCLUSION With PMC enabled, high-resolution TOF is able to visualize brain vasculature beyond the effective resolution limit. Magn Reson Med 80:248-258, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
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Affiliation(s)
- Hendrik Mattern
- Department of Biomedical Magnetic Resonance, Institute of Experimental Physics, Otto-von-Guericke-University, Magdeburg, Germany
| | - Alessandro Sciarra
- Department of Biomedical Magnetic Resonance, Institute of Experimental Physics, Otto-von-Guericke-University, Magdeburg, Germany
| | - Frank Godenschweger
- Department of Biomedical Magnetic Resonance, Institute of Experimental Physics, Otto-von-Guericke-University, Magdeburg, Germany
| | - Daniel Stucht
- Department of Biomedical Magnetic Resonance, Institute of Experimental Physics, Otto-von-Guericke-University, Magdeburg, Germany
| | - Falk Lüsebrink
- Department of Biomedical Magnetic Resonance, Institute of Experimental Physics, Otto-von-Guericke-University, Magdeburg, Germany
| | - Georg Rose
- Chair for Healthcare Telematics and Medical Engineering, Otto-von-Guericke-University, Magdeburg, Germany
| | - Oliver Speck
- Department of Biomedical Magnetic Resonance, Institute of Experimental Physics, Otto-von-Guericke-University, Magdeburg, Germany.,German Center for Neurodegenerative Diseases, Magdeburg, Germany.,Center for Behavioral Brain Sciences, Magdeburg, Germany.,Leibniz Institute for Neurobiology, Magdeburg, Germany
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