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Mateos MJ, Bribiesca E, Guzmán-Arenas A, Aguilar W, Marquez-Flores JA. 3D Tortuosity computation as a shape descriptor and its application to brain structure analysis. BMC Med Imaging 2024; 24:130. [PMID: 38834987 DOI: 10.1186/s12880-024-01312-6] [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: 02/14/2023] [Accepted: 05/27/2024] [Indexed: 06/06/2024] Open
Abstract
In this study, we propose a novel method for quantifying tortuosity in 3D voxelized objects. As a shape characteristic, tortuosity has been widely recognized as a valuable feature in image analysis, particularly in the field of medical imaging. Our proposed method extends the two-dimensional approach of the Slope Chain Code (SCC) which creates a one-dimensional representation of curves. The utility of 3D tortuosity ( τ 3 D ) as a shape descriptor was investigated by characterizing brain structures. The results of the τ 3 D computation on the central sulcus and the main lobes revealed significant differences between Alzheimer's disease (AD) patients and control subjects, suggesting its potential as a biomarker for AD. We found a p < 0.05 for the left central sulcus and the four brain lobes.
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Affiliation(s)
- Maria-Julieta Mateos
- Graduate Program in Computer Science and Engineering, Universidad Nacional Autónoma de México, Mexico City, México.
| | - Ernesto Bribiesca
- Institute of Research in Applied Mathematics and Systems (IIMAS), Universidad Nacional Autónoma de México, Circuito Escolar 3000, Ciudad Universitaria, 04510, Coyoacán, Mexico City, México
| | - Adolfo Guzmán-Arenas
- Centro de Investigación en Computación, Instituto Politécnico Nacional, Mexico City, México
| | - Wendy Aguilar
- Institute of Research in Applied Mathematics and Systems (IIMAS), Universidad Nacional Autónoma de México, Circuito Escolar 3000, Ciudad Universitaria, 04510, Coyoacán, Mexico City, México
| | - Jorge A Marquez-Flores
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, 04510, Mexico City, México
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Freitas-Andrade M, Comin CH, da Silva MV, Costa LDF, Lacoste B. Unbiased analysis of mouse brain endothelial networks from two- or three-dimensional fluorescence images. NEUROPHOTONICS 2022; 9:031916. [PMID: 35620183 PMCID: PMC9125696 DOI: 10.1117/1.nph.9.3.031916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
Significance: A growing body of research supports the significant role of cerebrovascular abnormalities in neurological disorders. As these insights develop, standardized tools for unbiased and high-throughput quantification of cerebrovascular structure are needed. Aim: We provide a detailed protocol for performing immunofluorescent labeling of mouse brain vessels, using thin ( 25 μ m ) or thick (50 to 150 μ m ) tissue sections, followed respectively by two- or three-dimensional (2D or 3D) unbiased quantification of vessel density, branching, and tortuosity using digital image processing algorithms. Approach: Mouse brain sections were immunofluorescently labeled using a highly selective antibody raised against mouse Cluster of Differentiation-31 (CD31), and 2D or 3D microscopy images of the mouse brain vasculature were obtained using optical sectioning. An open-source toolbox, called Pyvane, was developed for analyzing the imaged vascular networks. The toolbox can be used to identify the vasculature, generate the medial axes of blood vessels, represent the vascular network as a graph, and calculate relevant measurements regarding vascular morphology. Results: Using Pyvane, vascular parameters such as endothelial network density, number of branching points, and tortuosity are quantified from 2D and 3D immunofluorescence micrographs. Conclusions: The steps described in this protocol are simple to follow and allow for reproducible and unbiased analysis of mouse brain vascular structure. Such a procedure can be applied to the broader field of vascular biology.
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Affiliation(s)
| | - Cesar H. Comin
- Federal University of São Carlos, Department of Computer Science, São Carlos, Brazil
| | | | - Luciano da F. Costa
- University of São Paulo, São Carlos Institute of Physics, FCM-USP, São Paulo, Brazil
| | - Baptiste Lacoste
- The Ottawa Hospital Research Institute, Neuroscience Program, Ottawa, Ontario, Canada
- University of Ottawa, Faculty of Medicine, Department of Cellular and Molecular Medicine, Ottawa, Ontario, Canada
- University of Ottawa Brain and Mind Research Institute, Ottawa, Ontario, Canada
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Song Y, Zhou Z, Liu H, Du R, Zhou Y, Zhu S, Chen S. Tortuosity of branch retinal artery is more associated with the genesis and progress of diabetic retinopathy. Front Endocrinol (Lausanne) 2022; 13:972339. [PMID: 36277715 PMCID: PMC9582450 DOI: 10.3389/fendo.2022.972339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE The purpose of this study is to investigate the potential of using the tortuosity of branch retinal artery as a more promising indicator for early detection and accurate assessment of diabetic retinopathy (DR). DESIGN AND METHOD The diagnoses, consisting of whether DR or not as well as DR severity, were given by ophthalmologists upon the assessment of those fundus images from 495 diabetic patients. Meanwhile, benefiting from those good contrast and high optical resolution fundus images taken by confocal scanning laser ophthalmoscope, the branch arteries, branch veins, main arteries and main veins in retina can be segmented independently, and the tortuosity values of them were further extracted to investigate their potential correlations with DR genesis and progress based on one-way ANOVA test. RESULTS For both two comparisons, i.e., between non-DR group and DR group as well as among groups with different DR severity levels, larger tortuosity increments were always observed in retinal arteries and the increments in branch retinal vessels were even larger. Furthermore, it was newly found that branch arterial tortuosity was significantly associated with both DR genesis (p=0.030) and DR progress (p<0.001). CONCLUSION Based on this cohort study of 495 diabetic patients without DR and with different DR severity, the branch arterial tortuosity has been found to be more closely associated with DR genesis as well as DR progress. Therefore, the branch arterial tortuosity is expected to be a more direct and specific indicator for early detection of DR as well as accurate assessment of DR severity, which can further guide timely and rational management of DR to prevent from visual impairment or even blindness resulting from DR.
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Affiliation(s)
- Yunfeng Song
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, China
| | - Zheng Zhou
- School of Innovation and Entrepreneurship, Liaoning Institute of Science and Technology, Benxi, China
| | - Henan Liu
- Department of Ophthalmology, Shengjing Hospital, China Medical University, Shenyang, China
| | - Runyu Du
- Department of Endocrinology, Shengjing Hospital, China Medical University, Shenyang, China
| | - Yaoyao Zhou
- School of Innovation and Entrepreneurship, Liaoning Institute of Science and Technology, Benxi, China
| | - Shanshan Zhu
- Research Institute for Medical and Biological Engineering, Ningbo University, Ningbo, China
- *Correspondence: Shanshan Zhu, ; Shuo Chen,
| | - Shuo Chen
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, China
- Key Laboratory of Intelligent Computing in Medical Image, Ministry of Education, Shenyang, China
- *Correspondence: Shanshan Zhu, ; Shuo Chen,
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Ocular Fluid Mechanics and Drug Delivery: A Review of Mathematical and Computational Models. Pharm Res 2021; 38:2003-2033. [PMID: 34936067 DOI: 10.1007/s11095-021-03141-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/10/2021] [Indexed: 10/19/2022]
Abstract
The human eye is a complex biomechanical structure with a range of biomechanical processes involved in various physiological as well as pathological conditions. Fluid flow inside different domains of the eye is one of the most significant biomechanical processes that tend to perform a wide variety of functions and when combined with other biophysical processes play a crucial role in ocular drug delivery. However, it is quite difficult to comprehend the effect of these processes on drug transport and associated treatment experimentally because of ethical constraints and economic feasibility. Computational modeling on the other hand is an excellent means to understand the associated complexity between these aforementioned processes and drug delivery. A wide range of computational models specific to different types of fluids present in different domains of the eye as well as varying drug delivery modes has been established to understand the fluid flow behavior and drug transport phenomenon in an insilico manner. These computational models have been used as a non-invasive tool to aid ophthalmologists in identifying the challenges associated with a particular drug delivery mode while treating particular eye diseases and to advance the understanding of the biomechanical behavior of the eye. In this regard, the author attempts to summarize the existing computational and mathematical approaches proposed in the last two decades for understanding the fluid mechanics and drug transport associated with different domains of the eye, together with their application to modify the existing treatment processes.
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Fasaeiyan N, Soltani M, Moradi Kashkooli F, Taatizadeh E, Rahmim A. Computational modeling of PET tracer distribution in solid tumors integrating microvasculature. BMC Biotechnol 2021; 21:67. [PMID: 34823506 PMCID: PMC8620574 DOI: 10.1186/s12896-021-00725-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 11/05/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND We present computational modeling of positron emission tomography radiotracer uptake with consideration of blood flow and interstitial fluid flow, performing spatiotemporally-coupled modeling of uptake and integrating the microvasculature. In our mathematical modeling, the uptake of fluorodeoxyglucose F-18 (FDG) was simulated based on the Convection-Diffusion-Reaction equation given its high accuracy and reliability in modeling of transport phenomena. In the proposed model, blood flow and interstitial flow are solved simultaneously to calculate interstitial pressure and velocity distribution inside cancer and normal tissues. As a result, the spatiotemporal distribution of the FDG tracer is calculated based on velocity and pressure distributions in both kinds of tissues. RESULTS Interstitial pressure has maximum value in the tumor region compared to surrounding tissue. In addition, interstitial fluid velocity is extremely low in the entire computational domain indicating that convection can be neglected without effecting results noticeably. Furthermore, our results illustrate that the total concentration of FDG in the tumor region is an order of magnitude larger than in surrounding normal tissue, due to lack of functional lymphatic drainage system and also highly-permeable microvessels in tumors. The magnitude of the free tracer and metabolized (phosphorylated) radiotracer concentrations followed very different trends over the entire time period, regardless of tissue type (tumor vs. normal). CONCLUSION Our spatiotemporally-coupled modeling provides helpful tools towards improved understanding and quantification of in vivo preclinical and clinical studies.
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Affiliation(s)
- Niloofar Fasaeiyan
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, Tehran Province, Iran
- Department of Civil Engineering, Polytechnique University, Montreal, QC, Canada
| | - M Soltani
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, Tehran Province, Iran.
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON, Canada.
- Centre for Biotechnology and Bioengineering (CBB), University of Waterloo, Waterloo, ON, Canada.
- Advanced Bioengineering Initiative Center, Computational Medicine Center, K. N. Toosi University of Technology, Tehran, Tehran Province, Iran.
| | - Farshad Moradi Kashkooli
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, Tehran Province, Iran
| | - Erfan Taatizadeh
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, Tehran Province, Iran
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Arman Rahmim
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
- Departments of Radiology and Physics, University of British Columbia, Vancouver, BC, Canada
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
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Abstract
Advances in retinal imaging are enabling researchers and clinicians to make precise noninvasive measurements of the retinal vasculature in vivo. This includes measurements of capillary blood flow, the regulation of blood flow, and the delivery of oxygen, as well as mapping of perfused blood vessels. These advances promise to revolutionize our understanding of vascular regulation, as well as the management of retinal vascular diseases. This review provides an overview of imaging and optical measurements of the function and structure of the ocular vasculature. We include general characteristics of vascular systems with an emphasis on the eye and its unique status. The functions of vascular systems are discussed, along with physical principles governing flow and its regulation. Vascular measurement techniques based on reflectance and absorption are briefly introduced, emphasizing ways of generating contrast. One of the prime ways to enhance contrast within vessels is to use techniques sensitive to the motion of cells, allowing precise measurements of perfusion and blood velocity. Finally, we provide a brief introduction to retinal vascular diseases.
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Affiliation(s)
- Stephen A Burns
- Indiana University School of Optometry, Bloomington, Indiana 47405, USA; , ,
| | - Ann E Elsner
- Indiana University School of Optometry, Bloomington, Indiana 47405, USA; , ,
| | - Thomas J Gast
- Indiana University School of Optometry, Bloomington, Indiana 47405, USA; , ,
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Vilela MA, Amaral CE, Ferreira MAT. Retinal vascular tortuosity: Mechanisms and measurements. Eur J Ophthalmol 2020; 31:1497-1506. [PMID: 33307777 DOI: 10.1177/1120672120979907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Retinal vessel tortuosity has been used in the diagnosis and management of different clinical situations. Notwithstanding, basic concepts, standards and tools of measurement, reliable normative data and clinical applications have many gaps or points of divergence. In this review we discuss triggering causes of retinal vessel tortuosity and resources used to assess and quantify it, as well as current limitations.
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Affiliation(s)
- Manuel Ap Vilela
- Federal University of Health Sciences of Porto Alegre, Porto Alegre, Brazil
| | - Carlos Ev Amaral
- Federal University of Health Sciences of Porto Alegre, Porto Alegre, Brazil
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Moradi Kashkooli F, Soltani M, Rezaeian M, Taatizadeh E, Hamedi MH. Image-based spatio-temporal model of drug delivery in a heterogeneous vasculature of a solid tumor - Computational approach. Microvasc Res 2019; 123:111-124. [PMID: 30711547 DOI: 10.1016/j.mvr.2019.01.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/29/2019] [Accepted: 01/29/2019] [Indexed: 12/31/2022]
Abstract
The solute transport distribution in a tumor is an important criterion in the evaluation of the cancer treatment efficacy. The fraction of killed cells after each treatment can quantify the therapeutic effect and plays as a helpful tool to evaluate the chemotherapy treatment schedules. In the present study, an image-based spatio-temporal computational model of a solid tumor is provided for calculation of interstitial fluid flow and solute transport. Current model incorporates heterogeneous microvasculature for angiogenesis instead of synthetic mathematical modeling. In this modeling process, a comprehensive model according to Convection-Diffusion-Reaction (CDR) equations is employed due to its high accuracy for simulating the binding and the uptake of the drug by tumor cells. Based on the velocity and the pressure distribution, transient distribution of the different drug concentrations (free, bound, and internalized) is calculated. Then, the fraction of killed cells is obtained according to the internalized concentration. Results indicate the dependence of the drug distribution on both time and space, as well as the microvasculature density. Free and bound drug concentration have the same trend over time, whereas, internalized and total drug concentration increases over time and reaches a constant value. The highest amount of concentration occurred in the tumor region due to the higher permeability of the blood vessels. Moreover, the fraction of killed cells is approximately 78.87% and 24.94% after treatment with doxorubicin for cancerous and normal tissues, respectively. In general, the presented methodology may be applied in the field of personalized medicine to optimize patient-specific treatments. Also, such image-based modeling of solid tumors can be used in laboratories that working on drug delivery and evaluating new drugs before using them for any in vivo or clinical studies.
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Affiliation(s)
| | - M Soltani
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, Iran; Advanced Bioengineering Initiative Center, Computational Medicine Center, K. N. Toosi University of Technology, Tehran, Iran; Department of Electrical and Computer Engineering, University of Waterloo, ON, Canada; Centre for Biotechnology and Bioengineering (CBB), University of Waterloo, Waterloo, Ontario, Canada; Cancer Biology Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mohsen Rezaeian
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, Iran
| | - Erfan Taatizadeh
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, Iran
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Predicting retinal tissue oxygenation using an image-based theoretical model. Math Biosci 2018; 305:1-9. [DOI: 10.1016/j.mbs.2018.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 08/03/2018] [Accepted: 08/09/2018] [Indexed: 02/02/2023]
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10
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Kumari N, Cher J, Chua E, Hamzah H, Wong TY, Cheung CY. Association of serum lutein and zeaxanthin with quantitative measures of retinal vascular parameters. PLoS One 2018; 13:e0203868. [PMID: 30260964 PMCID: PMC6160008 DOI: 10.1371/journal.pone.0203868] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 08/29/2018] [Indexed: 12/12/2022] Open
Abstract
To evaluate the association between serum carotenoids and quantitative measures of retinal vasculature in elderly Singapore Chinese subjects. The following details were collected in 128 healthy subjects: sociodemographics, lifestyle information, medical and drug history, and anthropometric measurements. Serum concentrations of carotenoids were estimated in fasting venous blood using high performance liquid chromatography. Retinal vascular parameters were quantitatively measured from retinal photographs using a computer-assisted program (Singapore I Vessel Assessment). The mean age of the population was 54.1 years (range 40 to 81 years). In multiple linear regression analysis, per SD decrease in retinal arteriolar caliber [β = 0.045 (0.003 to 0.086), p = 0.036], per SD increase in retinal venular caliber [β = -0.045 (-0.086 to -0.003), p = 0.036] and per SD increase in arteriolar branching angle [β = -0.039 (-0.072 to -0.006), p = 0.021] were associated with decreased serum lutein. Per SD increase in retinal venular tortuosity [β = -0.0075 (-0.0145 to -0.0004), p = 0.039] and per SD increase in arteriolar branching angle (β = -0.0073 [-0.0142 to -0.0059], p = 0.041) were associated with decreased serum zeaxanthin. None of the other carotenoids demonstrated meaningful relationship with quantitative measures of retinal vasculature. Lower levels of lutein and zeaxanthin demonstrated significant relationship with adverse quantitative measures of retinal vasculature in elderly healthy subjects.
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Affiliation(s)
- Neelam Kumari
- Department of Ophthalmology and Visual Sciences, Khoo Teck Puat Hospital, Singapore, Republic of Singapore
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Republic of Singapore
- * E-mail:
| | - Joanna Cher
- Department of Ophthalmology and Visual Sciences, Khoo Teck Puat Hospital, Singapore, Republic of Singapore
| | - Edwin Chua
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Republic of Singapore
| | - Haslina Hamzah
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Republic of Singapore
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Republic of Singapore
- Ophthalmology and Visual Sciences Academic Clinical Programme, Duke-NUS Graduate Medical School, National University of Singapore, Singapore, Republic of Singapore
| | - Carol Y. Cheung
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Republic of Singapore
- Department of Ophthalmology and Visual Sciences, the Chinese University of Hong Kong, Shatin, Hong Kong, The People’s Republic of China
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Noise-estimation-based anisotropic diffusion approach for retinal blood vessel segmentation. Neural Comput Appl 2017. [DOI: 10.1007/s00521-016-2811-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Ben Abdallah M, Malek J, Azar AT, Belmabrouk H, Esclarín Monreal J, Krissian K. Adaptive noise-reducing anisotropic diffusion filter. Neural Comput Appl 2015. [DOI: 10.1007/s00521-015-1933-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Automatic extraction of blood vessels in the retinal vascular tree using multiscale medialness. Int J Biomed Imaging 2015; 2015:519024. [PMID: 25977682 PMCID: PMC4421077 DOI: 10.1155/2015/519024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 11/12/2014] [Indexed: 11/30/2022] Open
Abstract
We propose an algorithm for vessel extraction in retinal images. The first step consists of applying anisotropic diffusion filtering in the initial vessel network in order to restore disconnected vessel lines and eliminate noisy lines. In the second step, a multiscale line-tracking procedure allows detecting all vessels having similar dimensions at a chosen scale. Computing the individual image maps requires different steps. First, a number of points are preselected using the eigenvalues of the Hessian matrix. These points are expected to be near to a vessel axis. Then, for each preselected point, the response map is computed from gradient information of the image at the current scale. Finally, the multiscale image map is derived after combining the individual image maps at different scales (sizes). Two publicly available datasets have been used to test the performance of the suggested method. The main dataset is the STARE project's dataset and the second one is the DRIVE dataset. The experimental results, applied on the STARE dataset, show a maximum accuracy average of around 94.02%. Also, when performed on the DRIVE database, the maximum accuracy average reaches 91.55%.
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