Medical image segmentation and creation of 3D models for embedding into 3D PDF files

doi:10.16098/j.issn.0529-1356.2016.06.024

Abstract

Abstract:

Objective To discuss how to convert medical images into a 3D model and embed them in a Portable Document Format (PDF) file. Methods Three opensource programs, 3D Slicer,MeshLab,TeXstudio, were used to volume clipping with ROI for segmentation models and embed them in 3D PDF. Results 3D Slicer used a variety of methods for model segmentation,Meshlab carried out model cleaning and segmentationand, generated TEX format files, exported U3D format files,and then generated 3D PDF files that were compiled by TeXstudio. Conclusion The method introduced in this paper is simple and easy to learn, and is helpful to promote the production and use of 3D PDF.

Key words: Inner ear, Magnetic resonance imaging, Three-Dimensional, Reconstruction, Software, Portable document format

YANG Xiao-kai WU Shu-zhi CHEN Xiao-su. Medical image segmentation and creation of 3D models for embedding into 3D PDF files[J]. Acta Anatomica Sinica, 2016, 47(6): 856-858.

References

［1］Prats-Galino A, Reina MA, Mavar Haramija M, et al. 3D interactive model of lumbar spinal structures of anesthetic interest ［J］. Clin Anat, 2015, 28 (2): 205-212.

［2］Newe A. Towards an easier creation of three-dimensional data for embedding into scholarly 3D PDF (Portable Document Format) files ［J］. Peer J, 2015, 3: e794.

［3］Shin DS, Chung MS, Park JS, et al. Portable document format file showing the surface models of cadaver whole body ［J］. J Korean Med Sci, 2012, 27(8):849-856.

［4］Ruthensteiner B, Hess M. Embedding 3D models of biological specimens in PDF publications ［J］. Microsc Res Tech, 2008, 71 (11):778-786.

［5］Kumar P, Ziegler A, Grahn A, et al. Leaving the structural ivory tower, assisted by interactive 3D PDF ［J］. Trends Biochem Sci, 2010, 35 (8): 419-422.

［6］Phelps A, Naeger DM, Marcovici P. Embedding 3D radiology models in portable document format ［J］. AJR Am J Roentgenol, 2012,199(6):1342-1344.

［7］Newe A, Ganslandt T. Simplified generation of biomedical 3D surface model data for embedding into 3D portable document format (PDF) files for publication and education ［J］. PLoS One, 2013,8(11):e79004.

［8］Yang XK, Zheng YY, WU SX. Study of BPPV precise manipulation treatment ［J］. Journal of Clinical Otorhinolaryngology Head and Neck Surgery, 2016, 30 (8): 623-626. (in Chinese)

杨晓凯, 郑炎焱, 吴森翔. 良性阵发性位置性眩晕精准手法复位探讨［J］. 临床耳鼻咽喉头颈外科杂志, 2016, 30 (8):623-626.

［9］Yang XK, Zheng YY, Wu ShZh, et al. Measurements of semicircular canal space direction based on 3D modeling of MRI data and clinical application ［J］. Acta Anatomica Sinica, 2016, 47 (2): 238-242. (in Chinese)

杨晓凯, 郑炎焱,吴曙智,等. 基于磁共振数据的三维半规管建模空间方向测量［J］. 解剖学报,2016,47(2):238-242.

[1]	YANG Yang SHI Jun LI Kun MA Yuan ZHANG Shao-jie HOU Er-fei WANG Chao-qun CHEN Jie WANG Xing LI Zhi-jun. Finite element analysis of cervical intervertebral discs after removing different ranges of uncinate processes [J]. Acta Anatomica Sinica, 2024, 55(1): 88-97.
[2]	YUAN Shuo ZHAO An-quan HUANG Qi-ri-mai-la-tu WU Hai-he XU Yong-sheng QI Yan-song BAO Hu-ri-cha. Association between posterior tibial slope and tibial torsion angle and recurrent patellar dislocation based on the full-length CT of the lower limbs [J]. Acta Anatomica Sinica, 2023, 54(6): 703-709.
[3]	SUN Juan CHEN Jing-wei YANG Yi LIN Tao MOU Ya-lin ZHAO Xiu-li ZENG Guo-xi ZHANG Yan . Effects of hypoxia preconditioning on hematology-related indexes through hypoxia inducible factor-1α/stromal cell-derived factor-1 pathway in rats [J]. Acta Anatomica Sinica, 2023, 54(5): 505-511.
[4]	Ling GU ZHANG Ping SONG KeXin Na Li Hong-yu Chen Zhang Jie CONG Jing ZHAI XiaoYue GU Ling ZHANG Ping SONG Ke-xin LI Na CHEN Hong-yu ZHANG Jie CONG -Jing ZHAI Xiao-yue . Morphometry of the ureteric bud branching in the developing mouse kidney [J]. Acta Anatomica Sinica, 2023, 54(5): 593-598.
[5]	BAI Peng LI Wei ZHONG Hua WANG Zhan-fei. Measurement of the magnetic resonance imaging of the area supratentorial and infratentorial mid-sagittal plane of the normal Tibetan adults [J]. Acta Anatomica Sinica, 2023, 54(5): 567-574.
[6]	MI Si-rong LIU Guang-xing ZHANG Zhen-wu YU Peng-hui JU Xiao-jun RAO Li-bing LI Li . Accuracy of 3D printing skull under different CT layer thickness [J]. Acta Anatomica Sinica, 2023, 54(5): 575-581.
[7]	ZHONG Hua WANG Ying FAN Ying-lei REN Hai-long PEMA Dor-ji TONG Qing-hua. Linear measurement of digital pelvic of normal Tibetan nationality female in Lhasa [J]. Acta Anatomica Sinica, 2023, 54(4): 460-464.
[8]	HU Ding-xiang ZHENG Rui-qing LI Chang-hui CHEN Liang HUANG He DENG Ten-xiao . Application value of 3D print navigation module in the precise placement of thoracic and lumbar vertebral arch screws [J]. Acta Anatomica Sinica, 2023, 54(3): 342-347.
[9]	GAO Ming-jie DAI Li-na XU Yang-yang SHA Li-rong ZHANG Yun-feng JIN Feng ZHANG Kai WANG Zhi-qiang LI Xiao-he WANG Hai-yan. Finite element analysis of 14-year-old adolescent after spinal foraminoplasty at L4-5 based on TESSYS technology [J]. Acta Anatomica Sinica, 2023, 54(3): 335-341.
[10]	GUO Lan-qian WANG Ding-xuan YI Gang LI Yan REN Jie-ying . Morphological classification and clinical significance of the coracoid process based on CT three-dimensional reconstruction [J]. Acta Anatomica Sinica, 2023, 54(1): 82-86.
[11]	DENG Si-qi GU Ling WANG Kai-yue CHEN Hong-yu LIU Yu-jie ZHANG Jie ZHAI Xiao-yue. Three-dimensional visualization on the relationship between tubules after macula densa and afferent arterioles in mouse kidney [J]. Acta Anatomica Sinica, 2023, 54(1): 87-91.
[12]	ZHANG Lei YANG Si-yi ZHANG Xiao-hong CAO Xing-wang XIA Zhang-rong ZHOU Xin. Anatomical characteristics and clinical significance of the syndesmosis based on MRI [J]. Acta Anatomica Sinica, 2022, 53(5): 628-632.
[13]	ZHANG Lei LI Zhi-qing TANG Xiao-gao ZHOU Xin LI Bing-kun FU Shi-jie. Anatomic classification of the sustentaculum tali and its characteristics analysis [J]. Acta Anatomica Sinica, 2022, 53(4): 515-519.
[14]	LI Ming-bo CHEN Xiao-ying ZHENG Hai-xia. Morphological analysis and measurement of spinoglenoid notch of scapula based on 3D reconstruction of CT [J]. Acta Anatomica Sinica, 2022, 53(3): 335-339.
[15]	ZHANG Tian-zhen ZHENG Xin-yu ZHANG Wei HE Zi-jing WANG Ling-zhi REN Da-peng YUAN Xiao. Cone-beam CT analysis of occlusal planes between different vertical skeletal types of adult class Ⅱ malocclusions in Shandong province [J]. Acta Anatomica Sinica, 2022, 53(2): 210-216.