Brain MRA 3D Skeleton Extraction Based on Normal Plane Centroid Algorithm

Authors

  • Guoying Feng College of Basic Medicine Binzhou Medical University, Yantai 264003, Shandong, China
  • Jie Zhu Center of Network Information Binzhou Medical University, Yantai 264003, Shandong, ChinaCenter of Network Information Binzhou Medical University, Yantai 264003, Shandong, China
  • Jun Li Department of Medical Imaging Yantai Affiliated Hospital Binzhou Medical University, Yantai 264100, Shandong, China

DOI:

https://doi.org/10.4108/eetpht.9.4450

Keywords:

MRA, average plane centroid algorithm, 3D reconstruction, skeleton extraction

Abstract

INTRODUCTION: Analysis of magnetic resonance angiography image data is crucial for early detection and prevention of stroke patients. Extracting the 3D Skeleton of cerebral vessels is the focus and difficulty of analysis.

OBJECTIVES: The objective is to remove other tissue components from the vascular tissue portion of the image with minimal loss by reading MRA image data and performing processing processes such as grayscale normalization, interpolation, breakpoint detection and repair, and image segmentation to facilitate 3D reconstruction of cerebral blood vessels and the reconstructed vascular tissues make extraction of the Skeleton easier.

METHODS: Considering that most of the existing techniques for extracting the 3D vascular Skeleton are corrosion algorithms, machine learning algorithms require high hardware resources, a large number of learning and test cases, and the accuracy needs to be confirmed, an average plane center of mass computation method is proposed, which improves the average plane algorithm by combining the standard plane algorithm and the center of mass algorithm.

RESULTS: Intersection points and skeleton breakpoints on the Skeleton are selected as critical points and manually labeled for experimental verification, and the algorithm has higher efficiency and accuracy than other algorithms in directly extracting the 3D Skeleton of blood vessels.

CONCLUSION: The method has low hardware requirements, accurate and reliable image data, can be automatically modeled and calculated by Python program, and meets the needs of clinical applications under information technology conditions.

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References

THOMAS KE, FOTAKI A, BOTNAR RM, FERREIRA VM. Imaging Methods: Magnetic Resonance Imaging[J]. Circ Cardiovasc Imaging. 2023;16(1):e014068. DOI: https://doi.org/10.1161/CIRCIMAGING.122.014068

THAYABARANATHAN T, KIM J, CADILHAC DA, et al. Global stroke statistics 2022[J]. International Journal of Stroke. SEP 2022; 17(9):946-956. DOI: https://doi.org/10.1177/17474930221123175

LIU L, CHEN W, ZHOU H, et al. Chinese Stroke Association guidelines for clinical management of cerebrovascular disorders: Executive summary and 2019 update of clinical management of ischaemic cerebrovascular diseases[J]. Stroke Vasc Neurol. 2020;5(2):159-176. DOI: https://doi.org/10.1136/svn-2020-000378

GBD 2016 Causes of Death Collaborators. Global, regional, and national age-sex specific mortality for 264 causes of death, 1980-2016: a systematic analysis for the Global Burden of Disease Study 2016 [published correction appears in Lancet. 2017 Oct 28;390(10106):e38]. Lancet. 2017;390(10100):1151-1210.

NIU J, RAN Y, CHEN R, et al. Use of PETRA-MRA to assess intracranial arterial stenosis: Comparison with TOF-MRA, CTA, and DSA. Front Neurol. 2023;13:1068132. DOI: https://doi.org/10.3389/fneur.2022.1068132

MASSEY RM, WARREN OJ, SZCZEKLIK M, et al. Skeletonization of radial and gastroepiploic conduits in coronary artery bypass surgery[J]. J Cardiothorac Surg. 2007;2:26. DOI: https://doi.org/10.1186/1749-8090-2-26

JIN D, IYER KS, CHEN C, et al. A Robust and Efficient Curve Skeletonization Algorithm for Tree-Like Objects Using Minimum Cost Paths.Pattern Recognit Lett. 2016;76:32-40. DOI: https://doi.org/10.1016/j.patrec.2015.04.002

WAGNER MG. Real-Time Thinning Algorithms for 2D and 3D Images using GPU processors. J Real-Time Image Process. 2020;17(5):1255-1266. DOI: https://doi.org/10.1007/s11554-019-00886-7

YANG H, ZHAO XY, WANG L. Review of Data Normalization Methods[J]. Computer Engineering and Applications, 2023,59(3):13-22. DOI: https://doi.org/10.54254/2755-2721/21/20231108

VAN DEN BERGE K, CHOU HJ, ROUX DE BÉZIEUX H, et al. The normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects[J]. Cell Rep Methods. 2022,2(11):100321. DOI: https://doi.org/10.1016/j.crmeth.2022.100321

ZHANG XJ. SPLINE INTERPOLATING OPERATORS AND THE BEST APPROXIMATION OF LINEAR FUNCTIONALS IN W2m SPACES[J]. MATHEMATICA NUMERICA SINICA, 2002,24(2):129-136.

ZHU J. Application of Convolutional Triple Interpolation Algorithm in Processing Medical Images[J]. China Computer & Communication, 2021,33(23):77-79+83.

TAVOOSI J, ZHANG C, MOHAMMADZADEH A, et al. Medical Image Interpolation Using Recurrent Type-2 Fuzzy Neural Network[J].Front Neuroinform. 2021;15:667375. DOI: https://doi.org/10.3389/fninf.2021.667375

ZUO C, QIAN J, FENG S, et al. Deep learning in optical metrology: a review [published correction appears in Light Sci Appl. 2022 Mar 27;11(1):74].Light Sci Appl. 2022;11(1):39. DOI: https://doi.org/10.1038/s41377-022-00757-0

XIAO C, LI F, ZHANG DY. Image Inpainting Detection Based on High-Pass Filter Attention Network[J]. Computer Systems Science and Engineering 2022, 43(3):1145-1154. DOI: https://doi.org/10.32604/csse.2022.027249

ZHANG F, XI QY, LI QX, et al. Feasibility of removing manual marks on ultrasonic images and repairing images based on double gradient combined with improved Criminisi algorithm[J]. Chin J Med Imaging Technol, 2023, 39(03):429-434.

SASMAL B, DHAL KG. A survey on utilizing Superpixel image for clustering-based image segmentation [published online ahead of print, 2023 Mar 8].Multimed Tools Appl. 2023;1-63. DOI: https://doi.org/10.1007/s11042-023-14861-9

KORNILOV A, SAFONOV I, YAKIMCHUK I. A Review of Watershed Implementations for Segmentation of Volumetric Images. J Imaging. 2022;8(5):127. DOI: https://doi.org/10.3390/jimaging8050127

KUBICEK J, VARYSOVA A, CERNY M, et al. Performance and Robustness of Regional Image Segmentation Driven by Selected Evolutionary and Genetic Algorithms: Study on MR Articular Cartilage Images[J]. Sensors (Basel). 2022;22(17):6335. DOI: https://doi.org/10.3390/s22176335

ZHANG W, WU Y, YANG B, et al. Overview of Multi-Modal Brain Tumor MR Image Segmentation. Healthcare (Basel). 2021;9(8):1051. DOI: https://doi.org/10.3390/healthcare9081051

KAR A, PETIT M, REFAHI Y, et al. Benchmarking of deep learning algorithms for 3D instance segmentation of confocal image datasets[J].PLoS Comput Biol. 2022; 18(4):e1009879. DOI: https://doi.org/10.1371/journal.pcbi.1009879

CHEN C, QIN C, QIU H, et al. Deep Learning for Cardiac Image Segmentation: A Review[J].Front Cardiovasc Med. 2020;7:25. Published 2020 Mar 5. doi:10.3389/ fcvm.2020.00025 DOI: https://doi.org/10.3389/fcvm.2020.00025

FU Y, LEI Y, WANG T, et al. A review of deep learning-based methods for medical image multi-organ segmentation[J].Phys Med. 2021;85:107-122. DOI: https://doi.org/10.1016/j.ejmp.2021.05.003

BRUNO A, ARDIZZONE E, VITABILE S, MIDIRI M. A Novel Solution Based on Scale Invariant Feature Transform Descriptors and Deep Learning for the Detection of Suspicious Regions in Mammogram Images. J Med Signals Sens. 2020;10(3):158-173.

BITTREMIEUX W, MEYSMAN P, NOBLE WS, LAUKENS K. Fast Open Modification Spectral Library Searching through Approximate Nearest Neighbor Indexing. J Proteome Res. 2018;17(10):3463-3474. DOI: https://doi.org/10.1021/acs.jproteome.8b00359

NIELSEN MS, NIKOLOV I, KRUSE EK, GARNÆS J, MADSEN CB. Quantifying the Influence of Surface Texture and Shape on Structure from Motion 3D Reconstructions. Sensors (Basel). 2022;23(1):178.

ZIEGLER JP, OYER SL. Prelaminated paramedian forehead flap for subtotal nasal reconstruction using three-dimensional printing[J]. BMJ Case Rep. 2021; 14(1):e238146. DOI: https://doi.org/10.1136/bcr-2020-238146

PENG W, PENG Z, TANG P, et al. Review of Plastic Surgery Biomaterials and Current Progress in Their 3D Manufacturing Technology. Materials (Basel). 2020;13(18):4108. DOI: https://doi.org/10.3390/ma13184108

TARASSOLI SP, SHIELD ME, ALLEN RS, et al. Facial Reconstruction: A Systematic Review of Current Image Acquisition and Processing Techniques. Front Surg. 2020;7:537616. DOI: https://doi.org/10.3389/fsurg.2020.537616

KANEDA A, NAKAGAWA T, TAMURA K, et al. A proposal of a new automated method for SfM/MVS 3D reconstruction through comparisons of 3D data by SfM/MVS and handheld laser scanners[J]. PLoS One. 2022;17(7):e0270660. DOI: https://doi.org/10.1371/journal.pone.0270660

GAO L, ZHAO Y, HAN J, et al. Research on Multi-View 3D Reconstruction Technology Based on SFM[J]. Sensors (Basel). 2022;22(12):4366. DOI: https://doi.org/10.3390/s22124366

NIELSEN MS, NIKOLOV I, KRUSE EK, et al. Quantifying the Influence of Surface Texture and Shape on Structure from Motion 3D Reconstructions[J]. Sensors (Basel). 2022;23(1):178. DOI: https://doi.org/10.3390/s23010178

ZHANG J, WU F, CHANG W, et al. Techniques and Algorithms for Hepatic Vessel Skeletonization in Medical Images: A Survey[J]. Entropy (Basel). 2022;24(4):465. DOI: https://doi.org/10.3390/e24040465

SILVERSMITH W, ZLATESKI A, BAE JA, et al. Igneous: Distributed dense 3D segmentation meshing, neuron skeletonization, and hierarchical downsampling[J]. Front Neural Circuits. 2022;16:977700. DOI: https://doi.org/10.3389/fncir.2022.977700

WU J, TURNER N, BAE JA, et al. RealNeuralNetworks.jl: An Integrated Julia Package for Skeletonization, Morphological Analysis, and Synaptic Connectivity Analysis of Terabyte-Scale 3D Neural Segmentations [J]. Front Neuroinform. 2022;16:828169. DOI: https://doi.org/10.3389/fninf.2022.828169

YUAN X, TRACHTENBERG JT, POTTER SM, et al. MDL-constrained 3-D grayscale skeletonization algorithm for automated extraction of dendrites and spines from fluorescence confocal images[J]. Neuroinformatics. 2009;7(4):213-232. DOI: https://doi.org/10.1007/s12021-009-9057-y

YU H, ZHANG X, WANG Z, et al. Research on the Pose Error Compensation Technology for the Mass and Centroid Measurement of Large-Sized Aircraft Based on Kinematics[J]. Sensors (Basel). 2023;23(2):701. DOI: https://doi.org/10.3390/s23020701

LUKIĆ T, BALÁZS P. Limited-view binary tomography reconstruction assisted by shape centroid[J]. Vis Comput. 2022;38(2):695-705. DOI: https://doi.org/10.1007/s00371-020-02044-8

Bitter I, Kaufman AE, Sato M. Penalized-distance volumetric skeleton algorithm. IEEE Trans Visualization Computer Graphics. 2001;7:195–206. DOI: https://doi.org/10.1109/2945.942688

LIN WH, GARDNER JL, WU SW. Context effects on probability estimation[J]. PLoS Biol. 2020;18(3):e3000 634. DOI: https://doi.org/10.1371/journal.pbio.3000634

YAMADA H, IMAIZUMI Y, MATSUMOTO M. Neural Population Dynamics Underlying Expected Value Computation[J]. J Neurosci. 2021;41(8):1684-1698. DOI: https://doi.org/10.1523/JNEUROSCI.1987-20.2020

LEBRE MA, VACANT A, GRAND-BROCHIER M, et al. Automatic 3-D skeleton-based segmentation of liver vessels from MRI and CT for Chouinard representation[C]// Proceedings of the 2018 25th IEEE International Conference on Image Processing (ICIP); Athens, Greece. 7–10 October 2018; pp. 3523–3527. DOI: https://doi.org/10.1109/ICIP.2018.8451310

MERVEILLE O, NAEGEL B, TALBOT H, et al. 2D filtering of curvilinear structures by ranking the orientation responses of path operators (RORPO)[J].Image Processing On Line, 2017, 7:246-261. DOI: https://doi.org/10.5201/ipol.2017.207

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Published

22-11-2023

How to Cite

1.
Feng G, Zhu J, Li J. Brain MRA 3D Skeleton Extraction Based on Normal Plane Centroid Algorithm. EAI Endorsed Trans Perv Health Tech [Internet]. 2023 Nov. 22 [cited 2024 Dec. 26];9. Available from: https://publications.eai.eu/index.php/phat/article/view/4450