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Sun Q, Yang J, Ma S, Huang Y, Yuan Y, Hou Y. 3D vessel extraction using a scale-adaptive hybrid parametric tracker. Med Biol Eng Comput 2023; 61:2467-2480. [PMID: 37184591 DOI: 10.1007/s11517-023-02815-0] [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: 08/11/2022] [Accepted: 02/28/2023] [Indexed: 05/16/2023]
Abstract
3D vessel extraction has great significance in the diagnosis of vascular diseases. However, accurate extraction of vessels from computed tomography angiography (CTA) data is challenging. For one thing, vessels in different body parts have a wide range of scales and large curvatures; for another, the intensity distributions of vessels in different CTA data vary considerably. Besides, surrounding interfering tissue, like bones or veins with similar intensity, also seriously affects vessel extraction. Considering all the above imaging and structural features of vessels, we propose a new scale-adaptive hybrid parametric tracker (SAHPT) to extract arbitrary vessels of different body parts. First, a geometry-intensity parametric model is constructed to calculate the geometry-intensity response. While geometry parameters are calculated to adapt to the variation in scale, intensity parameters can also be estimated to meet non-uniform intensity distributions. Then, a gradient parametric model is proposed to calculate the gradient response based on a multiscale symmetric normalized gradient filter which can effectively separate the target vessel from surrounding interfering tissue. Last, a hybrid parametric model that combines the geometry-intensity and gradient parametric models is constructed to evaluate how well it fits a local image patch. In the extraction process, a multipath spherical sampling strategy is used to solve the problem of anatomical complexity. We have conducted many quantitative experiments using the synthetic and clinical CTA data, asserting its superior performance compared to traditional or deep learning-based baselines.
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Affiliation(s)
- Qi Sun
- Key Laboratory of Intelligent Computing in Medical Image, Ministry of Education, Northeastern University, Shenyang, Liaoning, China
- School of Computer Science and Engineering, Northeastern University, Shenyang, Liaoning, China
| | - Jinzhu Yang
- Key Laboratory of Intelligent Computing in Medical Image, Ministry of Education, Northeastern University, Shenyang, Liaoning, China.
- School of Computer Science and Engineering, Northeastern University, Shenyang, Liaoning, China.
| | - Shuang Ma
- Key Laboratory of Intelligent Computing in Medical Image, Ministry of Education, Northeastern University, Shenyang, Liaoning, China
- School of Computer Science and Engineering, Northeastern University, Shenyang, Liaoning, China
| | - Yan Huang
- Key Laboratory of Intelligent Computing in Medical Image, Ministry of Education, Northeastern University, Shenyang, Liaoning, China
- School of Computer Science and Engineering, Northeastern University, Shenyang, Liaoning, China
| | - Yuliang Yuan
- Key Laboratory of Intelligent Computing in Medical Image, Ministry of Education, Northeastern University, Shenyang, Liaoning, China
- School of Computer Science and Engineering, Northeastern University, Shenyang, Liaoning, China
| | - Yang Hou
- Department of Radiology, ShengJing Hospital of China Medical University, Shenyang, Liaoning, China
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Zhao J, Feng Q. Automatic Aortic Dissection Centerline Extraction Via Morphology-Guided CRN Tracker. IEEE J Biomed Health Inform 2021; 25:3473-3485. [PMID: 33755572 DOI: 10.1109/jbhi.2021.3068420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Aortic dissection (AD) centerline extraction has important clinical value in the quantitative diagnosis and treatment of AD disease. However, AD centerline extraction is a difficult task and quantitative evaluation is rarely studied. In this work, we propose a fully automatic algorithm to extract AD centerline based on a convolutional regression network (CRN) and the morphological properties of AD. To this end, we first design a topological model to describe the complex topology of AD. With this model, CRNs are trained to estimate the position, tangential vector, and scale of the centerline. The tracking accuracy is further improved by centerline continuity and a gradient-based penalty function. In addition, seed points are extracted on the basis of random regression and line clustering to ensure automated vessel tracking. The proposed method has been evaluated on an AD database and a public aortic database, and achieved high overlapping ratios of 0.9610 and 1.0000, respectively. The tracked centerline is very close to the ground truth and shows good stability, with low average distance errors of 1.4720 mm and 1.8748 mm, respectively.
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He Y, Yang G, Yang J, Chen Y, Kong Y, Wu J, Tang L, Zhu X, Dillenseger JL, Shao P, Zhang S, Shu H, Coatrieux JL, Li S. Dense biased networks with deep priori anatomy and hard region adaptation: Semi-supervised learning for fine renal artery segmentation. Med Image Anal 2020; 63:101722. [DOI: 10.1016/j.media.2020.101722] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 05/02/2020] [Accepted: 05/06/2020] [Indexed: 12/24/2022]
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5
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Tensor-cut: A tensor-based graph-cut blood vessel segmentation method and its application to renal artery segmentation. Med Image Anal 2020; 60:101623. [DOI: 10.1016/j.media.2019.101623] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 11/18/2019] [Accepted: 11/25/2019] [Indexed: 11/19/2022]
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6
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Belciug S. Pathologist at work. Artif Intell Cancer 2020. [DOI: 10.1016/b978-0-12-820201-2.00003-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Merveille O, Naegel B, Talbot H, Passat N. n D Variational Restoration of Curvilinear Structures With Prior-Based Directional Regularization. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2019; 28:3848-3859. [PMID: 30835221 DOI: 10.1109/tip.2019.2901706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Curvilinear structure restoration in image processing procedures is a difficult task, which can be compounded when these structures are thin, i.e., when their smallest dimension is close to the resolution of the sensor. Many recent restoration methods involve considering a local gradient-based regularization term as prior, assuming gradient sparsity. An isotropic gradient operator is typically not suitable for thin curvilinear structures, since gradients are not sparse for these. In this paper, we propose a mixed gradient operator that combines a standard gradient in the isotropic image regions, and a directional gradient in the regions where specific orientations are likely. In particular, such information can be provided by curvilinear structure detectors (e.g., RORPO or Frangi filters). Our proposed mixed gradient operator, that can be viewed as a companion tool of such detectors, is proposed in a discrete framework and its formulation/computation holds in any dimension; in other words, it is valid in [Formula: see text], n ≥ 1 . We show how this mixed gradient can be used to construct image priors that take edge orientation, as well as intensity, into account, and then involved in various image processing tasks while preserving curvilinear structures. The experiments carried out on 2D, 3D, real, and synthetic images illustrate the relevance of the proposed gradient, and its use in variational frameworks for both denoising and segmentation tasks.
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Kitrungrotsakul T, Han XH, Iwamoto Y, Lin L, Foruzan AH, Xiong W, Chen YW. VesselNet: A deep convolutional neural network with multi pathways for robust hepatic vessel segmentation. Comput Med Imaging Graph 2019; 75:74-83. [DOI: 10.1016/j.compmedimag.2019.05.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 03/20/2019] [Accepted: 05/13/2019] [Indexed: 11/26/2022]
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Zhao J, Ai D, Yang Y, Song H, Huang Y, Wang Y, Yang J. Deep feature regression (DFR) for 3D vessel segmentation. ACTA ACUST UNITED AC 2019; 64:115006. [DOI: 10.1088/1361-6560/ab0eee] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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10
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Directional fast-marching and multi-model strategy to extract coronary artery centerlines. Comput Biol Med 2019; 108:67-77. [DOI: 10.1016/j.compbiomed.2019.03.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 03/29/2019] [Accepted: 03/30/2019] [Indexed: 11/18/2022]
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Vigneshwaran V, Sands GB, LeGrice IJ, Smaill BH, Smith NP. Reconstruction of coronary circulation networks: A review of methods. Microcirculation 2019; 26:e12542. [DOI: 10.1111/micc.12542] [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: 01/25/2019] [Accepted: 02/27/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Vibujithan Vigneshwaran
- Auckland Bioengineering Institute University of Auckland Auckland New Zealand
- Faculty of Engineering University of Auckland Auckland New Zealand
| | - Gregory B. Sands
- Auckland Bioengineering Institute University of Auckland Auckland New Zealand
| | - Ian J. LeGrice
- Department of Physiology University of Auckland Auckland New Zealand
| | - Bruce H. Smaill
- Auckland Bioengineering Institute University of Auckland Auckland New Zealand
| | - Nicolas P. Smith
- Auckland Bioengineering Institute University of Auckland Auckland New Zealand
- Faculty of Engineering University of Auckland Auckland New Zealand
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12
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Hu X, Ding D, Chu D. Multiple Hidden Markov Model for Pathological Vessel Segmentation. BIOMED RESEARCH INTERNATIONAL 2018; 2018:9868215. [PMID: 30643827 PMCID: PMC6311274 DOI: 10.1155/2018/9868215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/12/2018] [Accepted: 11/28/2018] [Indexed: 11/27/2022]
Abstract
One of the obstacles that prevent the accurate delineation of vessel boundaries is the presence of pathologies, which results in obscure boundaries and vessel-like structures. Targeting this limitation, we present a novel segmentation method based on multiple Hidden Markov Models. This method works with a vessel axis + cross-section model, which constrains the classifier around the vessel. The vessel axis constraint gives our method the potential to be both physiologically accurate and computationally effective. Focusing on pathological vessels, we reap the benefits of the redundant information embedded in multiple vessel-specific features and the good statistical properties coming with Hidden Markov Model, to cover the widest possible spectrum of complex situations. The performance of our method is evaluated on synthetic complex-structured datasets, where we achieve a 91% high overlap ratio. We also validate the proposed method on a real challenging case, segmentation of pathological abdominal arteries. The performance of our method is promising, since our method yields better results than two state-of-the-art methods on both synthetic datasets and real clinical datasets.
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Affiliation(s)
- Xin Hu
- School of Computer Science and Technology, Harbin Institute of Technology at Weihai, Weihai 264209, China
| | - Deqiong Ding
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Dianhui Chu
- School of Computer Science and Technology, Harbin Institute of Technology at Weihai, Weihai 264209, China
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13
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Nowak MR, Choe Y. Towards An Open-Source Framework For The Analysis Of Cerebrovasculature Structure. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2018; 2018:570-573. [PMID: 30440461 DOI: 10.1109/embc.2018.8512331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The use of graphs to analyze cerebrovascular networks is quite common in studies of the microcirculation. While we have learned a lot from studies utilizing graphs as a tool for the analysis of microvessels, most methodologies for these procedures have only been described in brief and most are not publicly accessible. In this work, we introduce the foundation for an anticipated open-source framework that we hope will streamline the analysis of cerebrovascular structure. We believe that a standardized and accessible framework for the analysis vascular filaments is not only needed, but is necessary, for studies charting the microcirculation on image volumes spanning several grains of tissue. We set forth the foundations for a comprehensive and complete framework in our current work.
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Michael R N, Choe Y. Data-Driven Synthetic Cerebrovascular Models For Validation Of Segmentation Algorithms. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2018; 2018:5154-5157. [PMID: 30441500 DOI: 10.1109/embc.2018.8513456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We introduce a novel method to generate biologically grounded synthetic cerebrovasculature models in a datadriven fashion. First, the centerlines of vascular filaments embedded in an acquired imaging volume are obtained by a segmentation algorithm. That imaging volume is reconstructed from a graph encoding of the centerline (i.e., generating the model's ground truth) and the segmentation algorithm is applied to the resultant volume. As the location and characteristics of the vasculature embedded in this volume are known,theaccuracyofthesegmentationalgorithmcanbeassessed. Moreover, because the synthetic volume was reconstructed directly from biological data, an assessment is made on embedded filaments that are representative of the topologicalandgeometricalcharacteristicsofthedataset. Webelieve thatsuchmodels will provide the means necessary for the enhanced evaluation of vascular segmentation algorithms.
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Hu X, Cheng Y, Ding D, Chu D. Axis-Guided Vessel Segmentation Using a Self-Constructing Cascade-AdaBoost-SVM Classifier. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3636180. [PMID: 29750151 PMCID: PMC5884412 DOI: 10.1155/2018/3636180] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 02/04/2018] [Accepted: 02/13/2018] [Indexed: 11/23/2022]
Abstract
One major limiting factor that prevents the accurate delineation of vessel boundaries has been the presence of blurred boundaries and vessel-like structures. Overcoming this limitation is exactly what we are concerned about in this paper. We describe a very different segmentation method based on a cascade-AdaBoost-SVM classifier. This classifier works with a vessel axis + cross-section model, which constrains the classifier around the vessel. This has the potential to be both physiologically accurate and computationally effective. To further increase the segmentation accuracy, we organize the AdaBoost classifiers and the Support Vector Machine (SVM) classifiers in a cascade way. And we substitute the AdaBoost classifier with the SVM classifier under special circumstances to overcome the overfitting issue of the AdaBoost classifier. The performance of our method is evaluated on synthetic complex-structured datasets, where we obtain high overlap ratios, around 91%. We also validate the proposed method on one challenging case, segmentation of carotid arteries over real clinical datasets. The performance of our method is promising, since our method yields better results than two state-of-the-art methods on both synthetic datasets and real clinical datasets.
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Affiliation(s)
- Xin Hu
- School of Computer Science and Technology, Harbin Institute of Technology at Weihai, Weihai 264209, China
| | - Yuanzhi Cheng
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Deqiong Ding
- Department of Mathematics, Harbin Institute of Technology at Weihai, Weihai 264209, China
| | - Dianhui Chu
- School of Computer Science and Technology, Harbin Institute of Technology at Weihai, Weihai 264209, China
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16
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Singh PK, Hernandez-Herrera P, Labate D, Papadakis M. Automated 3-D Detection of Dendritic Spines from In Vivo Two-Photon Image Stacks. Neuroinformatics 2017; 15:303-319. [DOI: 10.1007/s12021-017-9332-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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17
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Blood vessel modeling for interactive simulation of interventional neuroradiology procedures. Med Image Anal 2017; 35:685-698. [DOI: 10.1016/j.media.2016.10.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 10/03/2016] [Accepted: 10/08/2016] [Indexed: 11/19/2022]
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18
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Lu N, Miao H. Clustering Tree-Structured Data on Manifold. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2016; 38:1956-1968. [PMID: 26660696 PMCID: PMC5027669 DOI: 10.1109/tpami.2015.2505282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Tree-structured data usually contain both topological and geometrical information, and are necessarily considered on manifold instead of euclidean space for appropriate data parameterization and analysis. In this study, we propose a novel tree-structured data parameterization, called Topology-Attribute matrix (T-A matrix), so the data clustering task can be conducted on matrix manifold. We incorporate the structure constraints embedded in data into the non-negative matrix factorization method to determine meta-trees from the T-A matrix, and the signature vector of each single tree can then be extracted by meta-tree decomposition. The meta-tree space turns out to be a cone space, in which we explore the distance metric and implement the clustering algorithm based on the concepts like Fréchet mean. Finally, the T-A matrix based clustering (TAMBAC) framework is evaluated and compared using both simulated data and real retinal images to illustrate its efficiency and accuracy.
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Affiliation(s)
- Na Lu
- State Key Laboratory for Manufacturing Systems Engineering, Systems Engineering Institute, Xi’an Jiaotong University, Xi’an, Shaanxi,China, 710049.
| | - Hongyu Miao
- Department of Biostatistics, School of Public Health, University of Texas Health Science Center at Houston, , Houston, TX, USA, 77030.
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Gagnon L, Smith AF, Boas DA, Devor A, Secomb TW, Sakadžić S. Modeling of Cerebral Oxygen Transport Based on In vivo Microscopic Imaging of Microvascular Network Structure, Blood Flow, and Oxygenation. Front Comput Neurosci 2016; 10:82. [PMID: 27630556 PMCID: PMC5006088 DOI: 10.3389/fncom.2016.00082] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 07/25/2016] [Indexed: 01/09/2023] Open
Abstract
Oxygen is delivered to brain tissue by a dense network of microvessels, which actively control cerebral blood flow (CBF) through vasodilation and contraction in response to changing levels of neural activity. Understanding these network-level processes is immediately relevant for (1) interpretation of functional Magnetic Resonance Imaging (fMRI) signals, and (2) investigation of neurological diseases in which a deterioration of neurovascular and neuro-metabolic physiology contributes to motor and cognitive decline. Experimental data on the structure, flow and oxygen levels of microvascular networks are needed, together with theoretical methods to integrate this information and predict physiologically relevant properties that are not directly measurable. Recent progress in optical imaging technologies for high-resolution in vivo measurement of the cerebral microvascular architecture, blood flow, and oxygenation enables construction of detailed computational models of cerebral hemodynamics and oxygen transport based on realistic three-dimensional microvascular networks. In this article, we review state-of-the-art optical microscopy technologies for quantitative in vivo imaging of cerebral microvascular structure, blood flow and oxygenation, and theoretical methods that utilize such data to generate spatially resolved models for blood flow and oxygen transport. These “bottom-up” models are essential for the understanding of the processes governing brain oxygenation in normal and disease states and for eventual translation of the lessons learned from animal studies to humans.
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Affiliation(s)
- Louis Gagnon
- Optics Division, Department of Radiology, MHG/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School Charlestown, MA, USA
| | - Amy F Smith
- Institut de Mécanique des Fluides de ToulouseToulouse, France; Department of Physiology, University of ArizonaTucson, AZ, USA
| | - David A Boas
- Optics Division, Department of Radiology, MHG/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School Charlestown, MA, USA
| | - Anna Devor
- Optics Division, Department of Radiology, MHG/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical SchoolCharlestown, MA, USA; Departments of Neurosciences and Radiology, University of California, San DiegoLa Jolla, CA, USA
| | | | - Sava Sakadžić
- Optics Division, Department of Radiology, MHG/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School Charlestown, MA, USA
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20
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Nowak MR. Learning to distinguish cerebral vasculature data from mechanical chatter in India-ink images acquired using knife-edge scanning microscopy. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2016; 2016:3989-3992. [PMID: 28269159 DOI: 10.1109/embc.2016.7591601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We introduce a simple, yet effective, procedure for accurate classification of connected components embedded in biological images. In our method, a training set is generated from user-delineated features of manually-labeled examples; we subsequently train a classifier using the resultant training set. The overall process is described using imaging data acquired from an India-ink perfused C57BL/6J mouse brain using Knife Edge Scanning Microscopy. We illustrate the procedure through segmentation of cerebral vasculature structures from mechanical noise using trained classifiers. The features extracted by our procedure show high discriminatory power between classes; the classifiers (linear SVM, Gaussian SVM, and GentleBoost decision tree ensemble) trained using these features achieved high performance: F1-scores reported for linear SVM, Gaussian SVM, and GentleBoost decision tree ensemble were 0.963, 0.956, and 0.963 respectively.
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Implementation and use of 3D pairwise geodesic distance fields for seeding abdominal aortic vessels. Int J Comput Assist Radiol Surg 2015; 11:803-16. [PMID: 26567091 DOI: 10.1007/s11548-015-1321-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 10/26/2015] [Indexed: 12/16/2022]
Abstract
PURPOSE Precise extraction of aorta and the vessels departing from it (i.e. coeliac, renal, and iliac) is vital for correct positioning of a graft prior to abdominal aortic surgery. To perform this task, most of the segmentation algorithms rely on seed points, and better-located seed points provide better initial positions for cross-sectional methods. Under non-optimal acquisition characteristics of daily clinical routine and complex morphology of these vessels, inserting seed points to all these small, but critically important vessels is a tedious, time-consuming, and error-prone task. Thus, in this paper, a novel strategy is developed to generate pathways between user-inserted seed points in order to initialize segmentation methods effectively. METHOD The proposed method requires only a single user-inserted seed for each vessel of interest for initializations. Starting from these initial seeds, it automatically generates pathways that span all vessels in between. To accomplish this, first, a geodesic mask is generated by adaptive thresholding, which reinforces the initial seeds to be kept in the vascular tree. Then, a novel implementation of 3D pairwise geodesic distance field (3D-PGDF) is utilized. It is shown that the minimal-valued geodesic of 3D-PGDF successfully defines a path linking the initial seeds as being the shortest geodesic. Moreover, the robustness of the minimum level set of the 3D-PGDF to local variations and regions of high curvature is increased by a region classification strategy, which adds partial geodesics to these critical regions. RESULTS The proposed method was applied to 19 challenging CT data sets obtained from four different scanners and compared to two benchmark methods. The first method is a high-precision technique with very long processing time (subvoxel precise multi-stencil fast marching-MSFM), while the second is a very fast method with lower accuracy (3D fast marching). The results, which are obtained using various measures, show that the pathways generated by the developed technique enable significantly higher segmentation performance than 3D fast marching and require much less computational power and time than MSFM. CONCLUSION The developed technique offers a useful tool for generating pathways between seed points with minimal user interaction. It guarantees to include all important vessels in a computationally effective manner and thus, it can be used to initialize segmentation methods for abdominal aortic tree.
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Tamura S. Accurate vessel segmentation with constrained B-snake. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2015; 24:2440-2455. [PMID: 25861085 DOI: 10.1109/tip.2015.2417683] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We describe an active contour framework with accurate shape and size constraints on the vessel cross-sectional planes to produce the vessel segmentation. It starts with a multiscale vessel axis tracing in a 3D computed tomography (CT) data, followed by vessel boundary delineation on the cross-sectional planes derived from the extracted axis. The vessel boundary surface is deformed under constrained movements on the cross sections and is voxelized to produce the final vascular segmentation. The novelty of this paper lies in the accurate contour point detection of thin vessels based on the CT scanning model, in the efficient implementation of missing contour points in the problematic regions and in the active contour model with accurate shape and size constraints. The main advantage of our framework is that it avoids disconnected and incomplete segmentation of the vessels in the problematic regions that contain touching vessels (vessels in close proximity to each other), diseased portions (pathologic structure attached to a vessel), and thin vessels. It is particularly suitable for accurate segmentation of thin and low contrast vessels. Our method is evaluated and demonstrated on CT data sets from our partner site, and its results are compared with three related methods. Our method is also tested on two publicly available databases and its results are compared with the recently published method. The applicability of the proposed method to some challenging clinical problems, the segmentation of the vessels in the problematic regions, is demonstrated with good results on both quantitative and qualitative experimentations; our segmentation algorithm can delineate vessel boundaries that have level of variability similar to those obtained manually.
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Zhao F, Xie X, Roach M. Computer Vision Techniques for Transcatheter Intervention. IEEE JOURNAL OF TRANSLATIONAL ENGINEERING IN HEALTH AND MEDICINE 2015; 3:1900331. [PMID: 27170893 PMCID: PMC4848047 DOI: 10.1109/jtehm.2015.2446988] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 04/10/2015] [Accepted: 06/09/2015] [Indexed: 12/02/2022]
Abstract
Minimally invasive transcatheter technologies have demonstrated substantial promise for the diagnosis and the treatment of cardiovascular diseases. For example, transcatheter aortic valve implantation is an alternative to aortic valve replacement for the treatment of severe aortic stenosis, and transcatheter atrial fibrillation ablation is widely used for the treatment and the cure of atrial fibrillation. In addition, catheter-based intravascular ultrasound and optical coherence tomography imaging of coronary arteries provides important information about the coronary lumen, wall, and plaque characteristics. Qualitative and quantitative analysis of these cross-sectional image data will be beneficial to the evaluation and the treatment of coronary artery diseases such as atherosclerosis. In all the phases (preoperative, intraoperative, and postoperative) during the transcatheter intervention procedure, computer vision techniques (e.g., image segmentation and motion tracking) have been largely applied in the field to accomplish tasks like annulus measurement, valve selection, catheter placement control, and vessel centerline extraction. This provides beneficial guidance for the clinicians in surgical planning, disease diagnosis, and treatment assessment. In this paper, we present a systematical review on these state-of-the-art methods. We aim to give a comprehensive overview for researchers in the area of computer vision on the subject of transcatheter intervention. Research in medical computing is multi-disciplinary due to its nature, and hence, it is important to understand the application domain, clinical background, and imaging modality, so that methods and quantitative measurements derived from analyzing the imaging data are appropriate and meaningful. We thus provide an overview on the background information of the transcatheter intervention procedures, as well as a review of the computer vision techniques and methodologies applied in this area.
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Affiliation(s)
- Feng Zhao
- Department of Computer ScienceSwansea UniversitySwanseaSA2 8PPU.K.
| | - Xianghua Xie
- Department of Computer ScienceSwansea UniversitySwanseaSA2 8PPU.K.
| | - Matthew Roach
- Department of Computer ScienceSwansea UniversitySwanseaSA2 8PPU.K.
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Zhao F, Liang J, Chen D, Wang C, Yang X, Chen X, Cao F. Automatic segmentation method for bone and blood vessel in murine hindlimb. Med Phys 2015; 42:4043-54. [DOI: 10.1118/1.4922200] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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25
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Kulkarni PM, Barton E, Savelonas M, Padmanabhan R, Lu Y, Trett K, Shain W, Leasure JL, Roysam B. Quantitative 3-D analysis of GFAP labeled astrocytes from fluorescence confocal images. J Neurosci Methods 2015; 246:38-51. [DOI: 10.1016/j.jneumeth.2015.02.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/13/2015] [Accepted: 02/14/2015] [Indexed: 12/31/2022]
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26
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Skibbe H, Reisert M, Maeda SI, Koyama M, Oba S, Ito K, Ishii S. Efficient Monte Carlo image analysis for the location of vascular entity. IEEE TRANSACTIONS ON MEDICAL IMAGING 2015; 34:628-643. [PMID: 25347876 DOI: 10.1109/tmi.2014.2364404] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Tubular shaped networks appear not only in medical images like X-ray-, time-of-flight MRI- or CT-angiograms but also in microscopic images of neuronal networks. We present EMILOVE (Efficient Monte-carlo Image-analysis for the Location Of Vascular Entity), a novel modeling algorithm for tubular networks in biomedical images. The model is constructed using tablet shaped particles and edges connecting them. The particles encode the intrinsic information of tubular structure, including position, scale and orientation. The edges connecting the particles determine the topology of the networks. For simulated data, EMILOVE was able to accurately extract the tubular network. EMILOVE showed high performance in real data as well; it successfully modeled vascular networks in real cerebral X-ray and time-of-flight MRI angiograms. We also show some promising, preliminary results on microscopic images of neurons.
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Schwen LO, Wei W, Gremse F, Ehling J, Wang L, Dahmen U, Preusser T. Algorithmically generated rodent hepatic vascular trees in arbitrary detail. J Theor Biol 2014; 365:289-300. [PMID: 25451523 DOI: 10.1016/j.jtbi.2014.10.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 10/16/2014] [Accepted: 10/22/2014] [Indexed: 12/13/2022]
Abstract
Physiologically realistic geometric models of the vasculature in the liver are indispensable for modelling hepatic blood flow, the main connection between the liver and the organism. Current in vivo imaging techniques do not provide sufficiently detailed vascular trees for many simulation applications, so it is necessary to use algorithmic refinement methods. The method of Constrained Constructive Optimization (CCO) (Schreiner et al., 2006) is well suited for this purpose. Its results after calibration have been previously compared to experimentally acquired human vascular trees (Schwen and Preusser, 2012). The goal of this paper is to extend this calibration to the case of rodents (mice and rats), the most commonly used animal models in liver research. Based on in vivo and ex vivo micro-CT scans of rodent livers and their vasculature, we performed an analysis of various geometric features of the vascular trees. Starting from pruned versions of the original vascular trees, we applied the CCO procedure and compared these algorithmic results to the original vascular trees using a suitable similarity measure. The calibration of the postprocessing improved the algorithmic results compared to those obtained using standard CCO. In terms of angular features, the average similarity increased from 0.27 to 0.61, improving the total similarity from 0.28 to 0.40. Finally, we applied the calibrated algorithm to refine measured vascular trees to the (higher) level of detail desired for specific applications. Having successfully adapted the CCO algorithm to the rodent model organism, the resulting individual-specific refined hepatic vascular trees can now be used for advanced modeling involving, e.g., detailed blood flow simulations.
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Affiliation(s)
- Lars Ole Schwen
- Fraunhofer MEVIS, Universitätsallee 29, 28359 Bremen, Germany.
| | - Weiwei Wei
- Department of General, Visceral and Vascular Surgery, University Hospital Jena, Drackendorfer Str. 1, 07747 Jena, Germany.
| | - Felix Gremse
- Experimental Molecular Imaging, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany.
| | - Josef Ehling
- Experimental Molecular Imaging, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany.
| | - Lei Wang
- Fraunhofer MEVIS, Universitätsallee 29, 28359 Bremen, Germany.
| | - Uta Dahmen
- Department of General, Visceral and Vascular Surgery, University Hospital Jena, Drackendorfer Str. 1, 07747 Jena, Germany.
| | - Tobias Preusser
- Fraunhofer MEVIS, Universitätsallee 29, 28359 Bremen, Germany; School of Engineering and Science, Jacobs University, Campus Ring 1, 28759 Bremen, Germany.
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Yin X, Chao JR, Wang RK. User-guided segmentation for volumetric retinal optical coherence tomography images. JOURNAL OF BIOMEDICAL OPTICS 2014; 19:086020. [PMID: 25147962 PMCID: PMC4407675 DOI: 10.1117/1.jbo.19.8.086020] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/05/2014] [Accepted: 08/06/2014] [Indexed: 05/18/2023]
Abstract
Despite the existence of automatic segmentation techniques, trained graders still rely on manual segmentation to provide retinal layers and features from clinical optical coherence tomography (OCT) images for accurate measurements. To bridge the gap between this time-consuming need of manual segmentation and currently available automatic segmentation techniques, this paper proposes a user-guided segmentation method to perform the segmentation of retinal layers and features in OCT images. With this method, by interactively navigating three-dimensional (3-D) OCT images, the user first manually defines user-defined (or sketched) lines at regions where the retinal layers appear very irregular for which the automatic segmentation method often fails to provide satisfactory results. The algorithm is then guided by these sketched lines to trace the entire 3-D retinal layer and anatomical features by the use of novel layer and edge detectors that are based on robust likelihood estimation. The layer and edge boundaries are finally obtained to achieve segmentation. Segmentation of retinal layers in mouse and human OCT images demonstrates the reliability and efficiency of the proposed user-guided segmentation method.
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Affiliation(s)
- Xin Yin
- University of Washington, Department of Bioengineering, 3720 15th Avenue NE, Seattle, Washington 98195, United States
| | - Jennifer R. Chao
- University of Washington, Department of Ophthalmology, 325 9th Avenue, Seattle, Washington 98104, United States
| | - Ruikang K. Wang
- University of Washington, Department of Bioengineering, 3720 15th Avenue NE, Seattle, Washington 98195, United States
- University of Washington, Department of Ophthalmology, 325 9th Avenue, Seattle, Washington 98104, United States
- Address all correspondence to: Ruikang K. Wang, E-mail:
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Stamatelos SK, Kim E, Pathak AP, Popel AS. A bioimage informatics based reconstruction of breast tumor microvasculature with computational blood flow predictions. Microvasc Res 2013; 91:8-21. [PMID: 24342178 DOI: 10.1016/j.mvr.2013.12.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 12/04/2013] [Accepted: 12/05/2013] [Indexed: 12/19/2022]
Abstract
Induction of tumor angiogenesis is among the hallmarks of cancer and a driver of metastatic cascade initiation. Recent advances in high-resolution imaging enable highly detailed three-dimensional geometrical representation of the whole-tumor microvascular architecture. This enormous increase in complexity of image-based data necessitates the application of informatics methods for the analysis, mining and reconstruction of these spatial graph data structures. We present a novel methodology that combines ex-vivo high-resolution micro-computed tomography imaging data with a bioimage informatics algorithm to track and reconstruct the whole-tumor vasculature of a human breast cancer model. The reconstructed tumor vascular network is used as an input of a computational model that estimates blood flow in each segment of the tumor microvascular network. This formulation involves a well-established biophysical model and an optimization algorithm that ensures mass balance and detailed monitoring of all the vessels that feed and drain blood from the tumor microvascular network. Perfusion maps for the whole-tumor microvascular network are computed. Morphological and hemodynamic indices from different regions are compared to infer their role in overall tumor perfusion.
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Affiliation(s)
- Spyros K Stamatelos
- Department of Biomedical Engineering, The Johns Hopkins University, School of Medicine, USA.
| | - Eugene Kim
- Department of Biomedical Engineering, The Johns Hopkins University, School of Medicine, USA; Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University, School of Medicine, USA
| | - Arvind P Pathak
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University, School of Medicine, USA; Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University, School of Medicine, USA
| | - Aleksander S Popel
- Department of Biomedical Engineering, The Johns Hopkins University, School of Medicine, USA; Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University, School of Medicine, USA
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Kretschmer J, Godenschwager C, Preim B, Stamminger M. Interactive patient-specific vascular modeling with sweep surfaces. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2013; 19:2828-2837. [PMID: 24051850 DOI: 10.1109/tvcg.2013.169] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The precise modeling of vascular structures plays a key role in medical imaging applications, such as diagnosis, therapy planning and blood flow simulations. For the simulation of blood flow in particular, high-precision models are required to produce accurate results. It is thus common practice to perform extensive manual data polishing on vascular segmentations prior to simulation. This usually involves a complex tool chain which is highly impractical for clinical on-site application. To close this gap in current blood flow simulation pipelines, we present a novel technique for interactive vascular modeling which is based on implicit sweep surfaces. Our method is able to generate and correct smooth high-quality models based on geometric centerline descriptions on the fly. It supports complex vascular free-form contours and consequently allows for an accurate and fast modeling of pathological structures such as aneurysms or stenoses. We extend the concept of implicit sweep surfaces to achieve increased robustness and applicability as required in the medical field. We finally compare our method to existing techniques and provide case studies that confirm its contribution to current simulation pipelines.
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Affiliation(s)
- Jan Kretschmer
- Computer Science Department, FAU Erlangen, and Siemens Healthcare, Computed Tomography
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31
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Abstract
Recent advances in automated high-resolution fluorescence microscopy and robotic handling have made the systematic and cost effective study of diverse morphological changes within a large population of cells possible under a variety of perturbations, e.g., drugs, compounds, metal catalysts, RNA interference (RNAi). Cell population-based studies deviate from conventional microscopy studies on a few cells, and could provide stronger statistical power for drawing experimental observations and conclusions. However, it is challenging to manually extract and quantify phenotypic changes from the large amounts of complex image data generated. Thus, bioimage informatics approaches are needed to rapidly and objectively quantify and analyze the image data. This paper provides an overview of the bioimage informatics challenges and approaches in image-based studies for drug and target discovery. The concepts and capabilities of image-based screening are first illustrated by a few practical examples investigating different kinds of phenotypic changes caEditorsused by drugs, compounds, or RNAi. The bioimage analysis approaches, including object detection, segmentation, and tracking, are then described. Subsequently, the quantitative features, phenotype identification, and multidimensional profile analysis for profiling the effects of drugs and targets are summarized. Moreover, a number of publicly available software packages for bioimage informatics are listed for further reference. It is expected that this review will help readers, including those without bioimage informatics expertise, understand the capabilities, approaches, and tools of bioimage informatics and apply them to advance their own studies.
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Affiliation(s)
- Fuhai Li
- NCI Center for Modeling Cancer Development, Department of Systems Medicine and Bioengineering, The Methodist Hospital Research Institute, Weil Medical College of Cornell University, Houston, Texas, United States of America
| | - Zheng Yin
- NCI Center for Modeling Cancer Development, Department of Systems Medicine and Bioengineering, The Methodist Hospital Research Institute, Weil Medical College of Cornell University, Houston, Texas, United States of America
| | - Guangxu Jin
- NCI Center for Modeling Cancer Development, Department of Systems Medicine and Bioengineering, The Methodist Hospital Research Institute, Weil Medical College of Cornell University, Houston, Texas, United States of America
| | - Hong Zhao
- NCI Center for Modeling Cancer Development, Department of Systems Medicine and Bioengineering, The Methodist Hospital Research Institute, Weil Medical College of Cornell University, Houston, Texas, United States of America
| | - Stephen T. C. Wong
- NCI Center for Modeling Cancer Development, Department of Systems Medicine and Bioengineering, The Methodist Hospital Research Institute, Weil Medical College of Cornell University, Houston, Texas, United States of America
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32
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Abstract
In the context of computer-based simulation, contact management requires an accurate, smooth, but still efficient surface model for the blood vessels. A new implicit model is proposed, consisting of a tree of local implicit surfaces generated by skeletons (blobby models). The surface is reconstructed from data points by minimizing an energy, alternating with an original blob selection and subdivision scheme. The reconstructed models are very efficient for simulation and were shown to provide a sub-voxel approximation of the vessel surface on 5 patients.
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33
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Kajić V, Esmaeelpour M, Glittenberg C, Kraus MF, Honegger J, Othara R, Binder S, Fujimoto JG, Drexler W. Automated three-dimensional choroidal vessel segmentation of 3D 1060 nm OCT retinal data. BIOMEDICAL OPTICS EXPRESS 2013; 4:134-50. [PMID: 23304653 PMCID: PMC3539191 DOI: 10.1364/boe.4.000134] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 12/13/2012] [Accepted: 12/15/2012] [Indexed: 05/19/2023]
Abstract
A fully automated, robust vessel segmentation algorithm has been developed for choroidal OCT, employing multiscale 3D edge filtering and projection of "probability cones" to determine the vessel "core", even in the tomograms with low signal-to-noise ratio (SNR). Based on the ideal vessel response after registration and multiscale filtering, with computed depth related SNR, the vessel core estimate is dilated to quantify the full vessel diameter. As a consequence, various statistics can be computed using the 3D choroidal vessel information, such as ratios of inner (smaller) to outer (larger) choroidal vessels or the absolute/relative volume of choroid vessels. Choroidal vessel quantification can be displayed in various forms, focused and averaged within a special region of interest, or analyzed as the function of image depth. In this way, the proposed algorithm enables unique visualization of choroidal watershed zones, as well as the vessel size reduction when investigating the choroid from the sclera towards the retinal pigment epithelium (RPE). To the best of our knowledge, this is the first time that an automatic choroidal vessel segmentation algorithm is successfully applied to 1060 nm 3D OCT of healthy and diseased eyes.
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Affiliation(s)
- Vedran Kajić
- Center for Medical Physics and Biomedical Engineering, Medical
University Vienna, General Hospital Vienna 4L, Waehringer Guertel 18-20, A-1090 Vienna,
Austria
| | - Marieh Esmaeelpour
- Center for Medical Physics and Biomedical Engineering, Medical
University Vienna, General Hospital Vienna 4L, Waehringer Guertel 18-20, A-1090 Vienna,
Austria
- Ludwig Boltzmann Institute of Retinology and Biomicroscopic Laser
Surgery, Department of Ophthalmology, Rudolf Foundation Clinic, Vienna,
Austria
| | - Carl Glittenberg
- Ludwig Boltzmann Institute of Retinology and Biomicroscopic Laser
Surgery, Department of Ophthalmology, Rudolf Foundation Clinic, Vienna,
Austria
| | - Martin F. Kraus
- Pattern Recognition Lab and School of Advanced Optical
Technologies (SAOT), University Erlangen-Nuremberg, Erlangen, Germany
| | - Joachim Honegger
- Pattern Recognition Lab and School of Advanced Optical
Technologies (SAOT), University Erlangen-Nuremberg, Erlangen, Germany
| | - Richu Othara
- Center for Medical Physics and Biomedical Engineering, Medical
University Vienna, General Hospital Vienna 4L, Waehringer Guertel 18-20, A-1090 Vienna,
Austria
| | - Susanne Binder
- Ludwig Boltzmann Institute of Retinology and Biomicroscopic Laser
Surgery, Department of Ophthalmology, Rudolf Foundation Clinic, Vienna,
Austria
| | - James G. Fujimoto
- Department of Electrical Engineering and Computer Science, MIT,
Cambridge, MA, USA
| | - Wolfgang Drexler
- Center for Medical Physics and Biomedical Engineering, Medical
University Vienna, General Hospital Vienna 4L, Waehringer Guertel 18-20, A-1090 Vienna,
Austria
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Reyes-Aldasoro CC, Björndahl MA, Akerman S, Ibrahim J, Griffiths MK, Tozer GM. Online chromatic and scale-space microvessel-tracing analysis for transmitted light optical images. Microvasc Res 2012; 84:330-9. [PMID: 22982542 DOI: 10.1016/j.mvr.2012.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 07/31/2012] [Accepted: 09/01/2012] [Indexed: 02/08/2023]
Abstract
Limited contrast in transmitted light optical images from intravital microscopy is problematic for analysing tumour vascular morphology. Moreover, in some cases, changes in vasculature are visible to a human observer but are not easy to quantify. In this paper two online algorithms are presented: scale-space vessel tracing and chromatic decomposition for analysis of the vasculature of SW1222 human colorectal carcinoma xenografts growing in dorsal skin-fold "window" chambers in mice. Transmitted light optical images of tumours were obtained from mice treated with the tumour vascular disrupting agent, combretastatin-A-4-phosphate (CA4P), or saline. The tracing algorithm was validated against hand-traced vessels with accurate results. The measurements extracted with the algorithms confirmed the known effects of CA4P on tumour vascular topology. Furthermore, changes in the chromaticity suggest a deoxygenation of the blood with a recovery to initial levels in CA4P-treated tumours relative to the controls. The algorithms can be freely applied to other studies through the CAIMAN website (CAncer IMage ANalysis: http://www.caiman.org.uk).
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Affiliation(s)
- Constantino Carlos Reyes-Aldasoro
- Biomedical Engineering Research Group, Department of Engineering and Design, 2B10 Shawcross Building, University of Sussex, Falmer, Brighton, BN1 9QT, UK.
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35
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Li P, Yin X, Shi L, Rugonyi S, Wang RK. In vivo functional imaging of blood flow and wall strain rate in outflow tract of embryonic chick heart using ultrafast spectral domain optical coherence tomography. JOURNAL OF BIOMEDICAL OPTICS 2012; 17:96006-1. [PMID: 23085907 PMCID: PMC3434623 DOI: 10.1117/1.jbo.17.9.096006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 08/06/2012] [Accepted: 08/08/2012] [Indexed: 05/22/2023]
Abstract
During cardiac development, the cardiac wall and flowing blood are two important cardiac tissues that constantly interact with each other. This dynamic interaction defines appropriate biomechanical environment to which the embryonic heart is exposed. Quantitative assessment of the dynamic parameters of wall tissues and blood flow is required to further our understanding of cardiac development. We report the use of an ultrafast 1310-nm dual-camera spectral domain optical coherence tomography (SDOCT) system to characterize/image, in parallel, the dynamic radial strain rate of the myocardial wall and the Doppler velocity of the underlying flowing blood within an in vivo beating chick embryo. The OCT system operates at 184-kHz line scan rate, providing the flexibility of imaging the fast blood flow and the slow tissue deformation within one scan. The ability to simultaneously characterize tissue motion and blood flow provides a useful approach to better understand cardiac dynamics during early developmental stages.
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Affiliation(s)
- Peng Li
- University of Washington, Department of Bioengineering, Seattle, Washington 98195
| | - Xin Yin
- Oregon Health & Science University, Department of Biomedical Engineering, Portland, Oregon 97239
| | - Liang Shi
- Oregon Health & Science University, Department of Biomedical Engineering, Portland, Oregon 97239
| | - Sandra Rugonyi
- Oregon Health & Science University, Department of Biomedical Engineering, Portland, Oregon 97239
| | - Ruikang K. Wang
- University of Washington, Department of Bioengineering, Seattle, Washington 98195
- Address all correspondence to: Ruikang K. Wang, University of Washington, Department of Bioengineering, Seattle, Washington 98195. E-mail:
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36
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Yin X, Liu A, Thornburg KL, Wang RK, Rugonyi S. Extracting cardiac shapes and motion of the chick embryo heart outflow tract from four-dimensional optical coherence tomography images. JOURNAL OF BIOMEDICAL OPTICS 2012; 17:96005-1. [PMID: 23085906 PMCID: PMC3523643 DOI: 10.1117/1.jbo.17.9.096005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Recent advances in optical coherence tomography (OCT), and the development of image reconstruction algorithms, enabled four-dimensional (4-D) (three-dimensional imaging over time) imaging of the embryonic heart. To further analyze and quantify the dynamics of cardiac beating, segmentation procedures that can extract the shape of the heart and its motion are needed. Most previous studies analyzed cardiac image sequences using manually extracted shapes and measurements. However, this is time consuming and subject to inter-operator variability. Automated or semi-automated analyses of 4-D cardiac OCT images, although very desirable, are also extremely challenging. This work proposes a robust algorithm to semi automatically detect and track cardiac tissue layers from 4-D OCT images of early (tubular) embryonic hearts. Our algorithm uses a two-dimensional (2-D) deformable double-line model (DLM) to detect target cardiac tissues. The detection algorithm uses a maximum-likelihood estimator and was successfully applied to 4-D in vivo OCT images of the heart outflow tract of day three chicken embryos. The extracted shapes captured the dynamics of the chick embryonic heart outflow tract wall, enabling further analysis of cardiac motion.
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Affiliation(s)
- Xin Yin
- Oregon Health & Science University, Department of Biomedical Engineering, Portland, Oregon 97239
| | - Aiping Liu
- University of Wisconsin, Department of Biomedical Engineering, Madison, Wisconsin 53706
| | - Kent L. Thornburg
- Oregon Health & Science University, Heart Research Center, Portland, Oregon 97239
| | - Ruikang K. Wang
- University of Washington, Department of Bioengineering, Seattle, Washington 98195
| | - Sandra Rugonyi
- Oregon Health & Science University, Department of Biomedical Engineering, Portland, Oregon 97239
- Address all correspondence to: Sandra Rugonyi, Oregon Health & Science University, Department of Biomedical Engineering, Mail Code CH13B, Portland, Oregon 97239; E-mail:
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37
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Erdmann G, Volz C, Boutros M. Systematic approaches to dissect biological processes in stem cells by image-based screening. Biotechnol J 2012; 7:768-78. [DOI: 10.1002/biot.201200117] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Gillette TA, Brown KM, Ascoli GA. The DIADEM metric: comparing multiple reconstructions of the same neuron. Neuroinformatics 2012; 9:233-45. [PMID: 21519813 DOI: 10.1007/s12021-011-9117-y] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Digital reconstructions of neuronal morphology are used to study neuron function, development, and responses to various conditions. Although many measures exist to analyze differences between neurons, none is particularly suitable to compare the same arborizing structure over time (morphological change) or reconstructed by different people and/or software (morphological error). The metric introduced for the DIADEM (DIgital reconstruction of Axonal and DEndritic Morphology) Challenge quantifies the similarity between two reconstructions of the same neuron by matching the locations of bifurcations and terminations as well as their topology between the two reconstructed arbors. The DIADEM metric was specifically designed to capture the most critical aspects in automating neuronal reconstructions, and can function in feedback loops during algorithm development. During the Challenge, the metric scored the automated reconstructions of best-performing algorithms against manually traced gold standards over a representative data set collection. The metric was compared with direct quality assessments by neuronal reconstruction experts and with clocked human tracing time saved by automation. The results indicate that relevant morphological features were properly quantified in spite of subjectivity in the underlying image data and varying research goals. The DIADEM metric is freely released open source ( http://diademchallenge.org ) as a flexible instrument to measure morphological error or change in high-throughput reconstruction projects.
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Affiliation(s)
- Todd A Gillette
- Center for Neural Informatics, Structures, & Plasticity, and Molecular Neuroscience Department, Krasnow Institute for Advanced Study, MS2A1 George Mason University, Fairfax, VA 22030, USA
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El-Baz A, Elnakib A, Khalifa F, El-Ghar MA, McClure P, Soliman A, Gimel'farb G. Precise segmentation of 3-D magnetic resonance angiography. IEEE Trans Biomed Eng 2012; 59:2019-29. [PMID: 22547453 DOI: 10.1109/tbme.2012.2196434] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Accurate automatic extraction of a 3-D cerebrovascular system from images obtained by time-of-flight (TOF) or phase contrast (PC) magnetic resonance angiography (MRA) is a challenging segmentation problem due to the small size objects of interest (blood vessels) in each 2-D MRA slice and complex surrounding anatomical structures (e.g., fat, bones, or gray and white brain matter). We show that due to the multimodal nature of MRA data, blood vessels can be accurately separated from the background in each slice using a voxel-wise classification based on precisely identified probability models of voxel intensities. To identify the models, an empirical marginal probability distribution of intensities is closely approximated with a linear combination of discrete Gaussians (LCDG) with alternate signs, using our previous EM-based techniques for precise linear combination of Gaussian-approximation adapted to deal with the LCDGs. The high accuracy of the proposed approach is experimentally validated on 85 real MRA datasets (50 TOF and 35 PC) as well as on synthetic MRA data for special 3-D geometrical phantoms of known shapes.
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Affiliation(s)
- Ayman El-Baz
- Bioengineering Department, University of Louisville, Louisville, KY 40292, USA.
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40
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Schaap M, van Walsum T, Neefjes L, Metz C, Capuano E, de Bruijne M, Niessen W. Robust shape regression for supervised vessel segmentation and its application to coronary segmentation in CTA. IEEE TRANSACTIONS ON MEDICAL IMAGING 2011; 30:1974-1986. [PMID: 21708497 DOI: 10.1109/tmi.2011.2160556] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This paper presents a vessel segmentation method which learns the geometry and appearance of vessels in medical images from annotated data and uses this knowledge to segment vessels in unseen images. Vessels are segmented in a coarse-to-fine fashion. First, the vessel boundaries are estimated with multivariate linear regression using image intensities sampled in a region of interest around an initialization curve. Subsequently, the position of the vessel boundary is refined with a robust nonlinear regression technique using intensity profiles sampled across the boundary of the rough segmentation and using information about plausible cross-sectional vessel shapes. The method was evaluated by quantitatively comparing segmentation results to manual annotations of 229 coronary arteries. On average the difference between the automatically obtained segmentations and manual contours was smaller than the inter-observer variability, which is an indicator that the method outperforms manual annotation. The method was also evaluated by using it for centerline refinement on 24 publicly available datasets of the Rotterdam Coronary Artery Evaluation Framework. Centerlines are extracted with an existing method and refined with the proposed method. This combination is currently ranked second out of 10 evaluated interactive centerline extraction methods. An additional qualitative expert evaluation in which 250 automatic segmentations were compared to manual segmentations showed that the automatically obtained contours were rated on average better than manual contours.
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Affiliation(s)
- Michiel Schaap
- Departments of Medical Informatics and Radiology, Erasmus MC—University Medical Center Rotterdam, The Netherlands.
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Spiegel M, Redel T, Struffert T, Hornegger J, Doerfler A. A 2D driven 3D vessel segmentation algorithm for 3D digital subtraction angiography data. Phys Med Biol 2011; 56:6401-19. [PMID: 21908904 DOI: 10.1088/0031-9155/56/19/015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Cerebrovascular disease is among the leading causes of death in western industrial nations. 3D rotational angiography delivers indispensable information on vessel morphology and pathology. Physicians make use of this to analyze vessel geometry in detail, i.e. vessel diameters, location and size of aneurysms, to come up with a clinical decision. 3D segmentation is a crucial step in this pipeline. Although a lot of different methods are available nowadays, all of them lack a method to validate the results for the individual patient. Therefore, we propose a novel 2D digital subtraction angiography (DSA)-driven 3D vessel segmentation and validation framework. 2D DSA projections are clinically considered as gold standard when it comes to measurements of vessel diameter or the neck size of aneurysms. An ellipsoid vessel model is applied to deliver the initial 3D segmentation. To assess the accuracy of the 3D vessel segmentation, its forward projections are iteratively overlaid with the corresponding 2D DSA projections. Local vessel discrepancies are modeled by a global 2D/3D optimization function to adjust the 3D vessel segmentation toward the 2D vessel contours. Our framework has been evaluated on phantom data as well as on ten patient datasets. Three 2D DSA projections from varying viewing angles have been used for each dataset. The novel 2D driven 3D vessel segmentation approach shows superior results against state-of-the-art segmentations like region growing, i.e. an improvement of 7.2% points in precision and 5.8% points for the Dice coefficient. This method opens up future clinical applications requiring the greatest vessel accuracy, e.g. computational fluid dynamic modeling.
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Affiliation(s)
- M Spiegel
- Pattern Recognition Lab, University Erlangen-Nuremberg, Erlangen, Germany.
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42
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Angiographic Image Analysis. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/978-1-4419-9779-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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43
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Farrar CT, Kamoun WS, Ley CD, Kim YR, Catana C, Kwon SJ, Rosen BR, Jain RK, Sorensen AG. Sensitivity of MRI tumor biomarkers to VEGFR inhibitor therapy in an orthotopic mouse glioma model. PLoS One 2011; 6:e17228. [PMID: 21390238 PMCID: PMC3048404 DOI: 10.1371/journal.pone.0017228] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 01/26/2011] [Indexed: 01/22/2023] Open
Abstract
MRI biomarkers of tumor edema, vascular permeability, blood volume, and average vessel caliber are increasingly being employed to assess the efficacy of tumor therapies. However, the dependence of these biomarkers on a number of physiological factors can compromise their sensitivity and complicate the assessment of therapeutic efficacy. Here we examine the response of these MRI tumor biomarkers to cediranib, a potent vascular endothelial growth factor receptor (VEGFR) inhibitor, in an orthotopic mouse glioma model. A significant increase in the tumor volume and relative vessel caliber index (rVCI) and a slight decrease in the water apparent diffusion coefficient (ADC) were observed for both control and cediranib treated animals. This contrasts with a clinical study that observed a significant decrease in tumor rVCI, ADC and volume with cediranib therapy. While the lack of a difference between control and cediranib treated animals in these biomarker responses might suggest that cediranib has no therapeutic benefit, cediranib treated mice had a significantly increased survival. The increased survival benefit of cediranib treated animals is consistent with the significant decrease observed for cediranib treated animals in the relative cerebral blood volume (rCBV), relative microvascular blood volume (rMBV), transverse relaxation time (T2), blood vessel permeability (Ktrans), and extravascular-extracellular space (νe). The differential response of pre-clinical and clinical tumors to cediranib therapy, along with the lack of a positive response for some biomarkers, indicates the importance of evaluating the whole spectrum of different tumor biomarkers to properly assess the therapeutic response and identify and interpret the therapy-induced changes in the tumor physiology.
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Affiliation(s)
- Christian T Farrar
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America.
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Popović Z, Liu W, Chauhan VP, Lee J, Wong C, Greytak AB, Insin N, Nocera DG, Fukumura D, Jain RK, Bawendi MG. A nanoparticle size series for in vivo fluorescence imaging. Angew Chem Int Ed Engl 2011; 49:8649-52. [PMID: 20886481 DOI: 10.1002/anie.201003142] [Citation(s) in RCA: 251] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Zoran Popović
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139-4307, USA
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Dalca A, Danagoulian G, Kikinis R, Schmidt E, Golland P. Segmentation of nerve bundles and ganglia in spine MRI using particle filters. MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION : MICCAI ... INTERNATIONAL CONFERENCE ON MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION 2011; 14:537-45. [PMID: 22003741 PMCID: PMC3232745 DOI: 10.1007/978-3-642-23626-6_66] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Automatic segmentation of spinal nerve bundles that originate within the dural sac and exit the spinal canal is important for diagnosis and surgical planning. The variability in intensity, contrast, shape and direction of nerves seen in high resolution myelographic MR images makes segmentation a challenging task. In this paper, we present an automatic tracking method for nerve segmentation based on particle filters. We develop a novel approach to particle representation and dynamics, based on Bézier splines. Moreover, we introduce a robust image likelihood model that enables delineation of nerve bundles and ganglia from the surrounding anatomical structures. We demonstrate accurate and fast nerve tracking and compare it to expert manual segmentation.
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Affiliation(s)
- Adrian Dalca
- MIT Computer Science and Artificial Inteligence, Cambridge, MA, USA
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46
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Worz S, von Tengg-Kobligk H, Henninger V, Rengier F, Schumacher H, Bockler D, Kauczor HU, Rohr K. 3-D Quantification of the Aortic Arch Morphology in 3-D CTA Data for Endovascular Aortic Repair. IEEE Trans Biomed Eng 2010; 57:2359-68. [DOI: 10.1109/tbme.2010.2053539] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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47
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Popović Z, Liu W, Chauhan VP, Lee J, Wong C, Greytak AB, Insin N, Nocera DG, Fukumura D, Jain RK, Bawendi MG. A Nanoparticle Size Series for In Vivo Fluorescence Imaging. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201003142] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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48
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Rittscher J. Characterization of Biological Processes through Automated Image Analysis. Annu Rev Biomed Eng 2010; 12:315-44. [DOI: 10.1146/annurev-bioeng-070909-105235] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jens Rittscher
- Visualization and Computer Vision Laboratory, GE Global Research, Niskayuna, New York, 12309;
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49
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Simultaneous measurement of RBC velocity, flux, hematocrit and shear rate in vascular networks. Nat Methods 2010; 7:655-60. [PMID: 20581828 PMCID: PMC2921873 DOI: 10.1038/nmeth.1475] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Accepted: 05/24/2010] [Indexed: 11/08/2022]
Abstract
Not all tumor vessels are equal. Tumor-associated vasculature includes immature vessels, regressing vessels, transport vessels undergoing arteriogenesis and peritumor vessels influenced by tumor growth factors. Current techniques for analyzing tumor blood flow do not discriminate between vessel subtypes and only measure average changes from a population of dissimilar vessels. We have developed methodologies for simultaneously quantifying blood flow (velocity, flux, hematocrit and shear rate) in extended networks at single capillary resolution in vivo. Our approach relies on deconvolution of signals produced by labeled red blood cells as they move relative to the scanning laser of a confocal or multiphoton microscope and provides fully-resolved three-dimensional flow profiles within vessel networks. Using this methodology, we show that blood velocity profiles are asymmetric near intussusceptive tissue structures in tumors in mice. Furthermore, we show that subpopulations of vessels, classified by functional parameters, exist in, around a tumor and in normal brain.
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Abstract
Most state-of-the-art algorithms for filament detection in 3-D image-stacks rely on computing the Hessian matrix around individual pixels and labeling these pixels according to its eigenvalues. This approach, while very effective for clean data in which linear structures are nearly cylindrical, loses its effectiveness in the presence of noisy data and irregular structures. In this paper, we show that using steerable filters to create rotationally invariant features that include higher-order derivatives and training a classifier based on these features lets us handle such irregular structures. This can be done reliably and at acceptable computational cost and yields better results than state-of-the-art methods.
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