Drishti Paint 3.2: 一种开源的综合二维与三维分割的新工具

doi:10.19615/j.cnki.2096-9899.240619

古脊椎动物学报 ›› 2024, Vol. 62 ›› Issue (4): 313-320.DOI: 10.19615/j.cnki.2096-9899.240619CSTR: 32090.14.j.cnki.2096-9899.240619

• • 上一篇

Drishti Paint 3.2: 一种开源的综合二维与三维分割的新工具

王梦君¹^,², Ajay LIMAYE³, 卢静¹^,²^,^*()

1 中国科学院古脊椎动物与古人类研究所，中国科学院脊椎动物演化与人类起源重点实验室北京 100044
2 中国科学院大学北京 100049
3 澳大利亚国家计算中心，澳大利亚国立大学堪培拉 ACT 2601

收稿日期:2024-05-17 出版日期:2024-10-20 发布日期:2024-10-18
基金资助:
国家自然科学基金(42130209)

Drishti Paint 3.2: a new open-source tool for both 2D and 3D segmentation

WANG Meng-Jun¹^,², Ajay LIMAYE³, LU Jing¹^,²^,^*()

1 Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of VertebratePaleontology and Paleoanthropology, Chinese Academy of Sciences Beijing 100044
2 University of Chinese Academy of Sciences Beijing 100049
3 National Computational Infrastructure, Australian National University Canberra ACT 2601

Received:2024-05-17 Published:2024-10-20 Online:2024-10-18
Contact: *lujing@ivpp.ac.cn

1. supplementary materials advanced online.pdf(1398KB)

摘要/Abstract

摘要：

计算机断层扫描(CT)技术在近几十年来被广泛应用于古生物学相关研究领域。研究者借助CT扫描技术可以无损获得化石内部精细信息，进一步对材料进行深入研究。但是，如何对CT数据进行高效的三维分割与重建仍是研究者们在使用三维数据时面临的主要问题。大多数CT数据分割软件都采用二维分割的传统方法，难以直接对三维结果进行实时修正。介绍了三维可视化开源软件Drishti Paint 3.2版本中的曲线模式(Curves Mode)及其使用方法。该软件为研究者提供了同时在二维切片及三维窗口手动或半自动分割CT数据的新工具，为如何对古生物学研究中化石CT数据进行高效的三维分割与重建提供了新思路。

关键词: 计算机断层扫描(CT), 二维与三维分割, 三维重建, Drishti Paint

Abstract:

X-ray computed tomography (CT) has been an important technology in paleontology for several decades. It helps researchers to acquire detailed anatomical structures of fossils non-destructively. Despite its widespread application, developing an efficient and user-friendly method for segmenting CT data continues to be a formidable challenge in the field. Most CT data segmentation software operates on 2D interfaces, which limits flexibility for real-time adjustments in 3D segmentation. Here, we introduce Curves Mode in Drishti Paint 3.2, an open-source tool for CT data segmentation. Drishti Paint 3.2 allows users to manually or semi-automatically segment the CT data in both 2D and 3D environments, providing a novel solution for revisualizing CT data in paleontological studies.

Key words: X-ray computed tomography (CT), 2D and 3D segmentation, 3D reconstruction, Drishti Paint

中图分类号:

TP391.4

王梦君, Ajay LIMAYE, 卢静. Drishti Paint 3.2: 一种开源的综合二维与三维分割的新工具. 古脊椎动物学报, 2024, 62(4): 313-320.

WANG Meng-Jun, Ajay LIMAYE, LU Jing. Drishti Paint 3.2: a new open-source tool for both 2D and 3D segmentation. Vertebrata Palasiatica, 2024, 62(4): 313-320.

图/表 2

Fig. 1 General workflow of Drishti Paint 3.2 The core steps are shown here, more detailed procedures are displayed in the supplementary materials

Fig. 2 Segmentation of the right operculum of a bichir Erpetoichthys in Drishti Paint 3.2 A. original data of the whole specimen shown in Drishti Import 3.2; B. original 3D morphological data (right lateral view) shown in the 3D Viewer of Drishti Paint 3.2; C. extracted region of interest; D. working interface of Drishti Paint 3.2 under Curves Mode; E. segmented right operculum; i. 3D interface showing the right operculum to be segmented; ii. Z-axial view; iii. Y-axial view; iv. X-axial view

参考文献 15

[1]	Buzug T M, 2011. Computed tomography. In: Kramme R, Hoffmann K P, Pozos R S eds. Springer Handbook of Medical Technology. Berlin, Heidelberg: Springer Berlin Heidelberg. 311-342
[2]	Cunningham J A, Rahman I A, Lautenschlager S et al., 2014. A virtual world of paleontology. Trends Ecol Evol, 29: 347-357 DOI PMID
[3]	Du X K, Zhang F K, Lu J C et al., 1997. Computed tomography in research on paleontology. J Beijing Med Univ, 29: 46-47
[4]	Hu Y Z, Limaye A, Lu J, 2020. Three-dimensional segmentation of computed tomography data using Drishti Paint: new tools and developments. R Soc Open Sci, 7: 201033
[5]	Hu Y Z, Limaye A, Lu J, 2021. A 3D segmentation & reconstruction method in paleontology using Drishti. Bio-101: e1010668
[6]	Hu Y Z, Limaye A, Lu J, 2024. 3D revisualisation: a new method to revisit segmented data. R Soc Open Sci, 11: 240375
[7]	Kouraiss K, El Hariri K, El Albani A et al., 2019. Digitization of fossils from the Fezouata Biota (Lower Ordovician, Morocco): evaluating computed tomography and photogrammetry in collection enhancement. Geoheritage, 11: 1889-1901 DOI
[8]	Lakare S, Kaufman A, 2000. 3D segmentation techniques for medical volumes. Center for Visual Computing, Department of Computer Science, State University of New York, 2000: 59-68
[9]	Lautenschlager S, 2016. Reconstructing the past: methods and techniques for the digital restoration of fossils. R Soc Open Sci, 3: 160342
[10]	Lautenschlager S, Rücklin M, 2014. Beyond the print—virtual paleontology in science publishing, outreach, and education. J Paleontol, 88: 727-734 PMID
[11]	Limaye A, 2012. Drishti: a volume exploration and presentation tool. SPIE Proc, 8506: 191-199
[12]	Rahman I A, Smith S Y, 2015. Virtual paleontology: computer-aided analysis of fossil form and function. J Paleontol, 88: 633-635
[13]	Sutton M, Rahman I, Garwood R, 2014. Techniques for Virtual Palaeontology. New Jersey: John Wiley & Sons, Inc. 1-200
[14]	Sutton M, Rahman I, Garwood R, 2016. Virtual paleontology—an overview. Paleontol Soc Pap, 22: 1-20
[15]	Yin Z J, Lu J, 2019. Virtual palaeontology: when fossils illuminated by X-ray. Palaeoworld, 28: 425-428

Drishti Paint 3.2: 一种开源的综合二维与三维分割的新工具

Drishti Paint 3.2: a new open-source tool for both 2D and 3D segmentation

RichHTML

PDF

补充材料

可视化

摘要/Abstract

引用本文

使用本文

图/表 2

参考文献 15

相关文章 3

编辑推荐

Metrics

[1]	柯易晖, 裴睿, 徐星. 高分辨率 CT 扫描数据揭示晚侏罗世暴龙类五彩冠龙牙齿替换模式. 古脊椎动物学报, 2024, 62(3): 225-244.
[2]	朱幼安, 王雅婧, 瞿清明, 卢静, 朱敏. 基于CT数据的副云南鱼腰带部位形态再研究. 古脊椎动物学报, 2023, 61(2): 81-89.
[3]	崔心东, 李强, 乔妥, 朱敏. 云南曲靖下泥盆统洛霍考夫阶花鳞鱼类新材料. 古脊椎动物学报, 2020, 58(1): 1-15.