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浙江大学学报（农业与生命科学版）
Journal of Zhejiang University (Agriculture and Life Sciences)  2022, Vol. 48 Issue (6): 797-806    DOI: 10.3785/j.issn.1008-9209.2022.07.181
Research articles     
Reconstruction of internal structures of Nilaparvata lugens using micro-computer tomography technology (Micro CT)
Runguo SHU1(),Hang ZHOU1,Zixiong CAO2,Kang HE1,Fei LI1()
1.Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
2.Object Research Systems (ORS) Inc. , Montr al (Qu bec) H3B 1A7, Canada
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Abstract  

The brown planthopper (Nilaparvata lugens) is an important rice pest. In this study, the tomographic images of adult brown planthopper were obtained by using micro-computer tomography technology (Micro CT). Three-dimensional models of internal tissues and organs of the brown planthopper were established by combining manual modeling and deep learning. Three-dimensional models of the central nervous system, muscle tissue, alimentary canal and reproductive system of the brown planthopper were obtained. These models preserved the original morphologies of these structures and accurately restored the spatial arrangement of all tissues and organs within the brown planthopper. Measurements of the internal organization of insects were analyzed using Dragonfly software. This study established and refined the three-dimensional reconstruction technique of insect tissues and organs, which can contribute to a more precise view of the internal organization structure of insects and can be used for phenotypic observation of insect morphology and organ development. It provides a new technique for insect development investigation and gene function analysis in entomology.

Key words： micro-computer tomography technology (Micro CT)      brown planthopper      internal structure      three-dimensional reconstruction      phenomics     
Received: 18 July 2022      Published: 27 December 2022
CLC:  Q 964  
Corresponding Authors: Fei LI     E-mail: runguoshu@zju.edu.cn;lifei18@zju.edu.cn
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Runguo SHU
Hang ZHOU
Zixiong CAO
Kang HE
Fei LI
Cite this article:

Runguo SHU,Hang ZHOU,Zixiong CAO,Kang HE,Fei LI. Reconstruction of internal structures of Nilaparvata lugens using micro-computer tomography technology (Micro CT). Journal of Zhejiang University (Agriculture and Life Sciences), 2022, 48(6): 797-806.

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https://www.zjujournals.com/agr/10.3785/j.issn.1008-9209.2022.07.181     OR     https://www.zjujournals.com/agr/Y2022/V48/I6/797


利用微计算机断层扫描技术重建褐飞虱内部结构

褐飞虱（Nilaparvata lugens）是一种重要的水稻害虫。本研究利用微计算机断层扫描技术（micro-computer tomography technology, Micro CT）获得了褐飞虱成虫的断层扫描图，通过人工建模和深度学习相结合的方式对褐飞虱内部组织和器官进行三维建模，获得了褐飞虱中枢神经系统、肌肉组织、消化道和生殖系统的三维模型，保留了这些结构的原始形态，准确地还原了褐飞虱体内各组织和器官的空间排布，并利用Dragonfly软件对昆虫的内部组织进行了空间体积的测量分析。本研究建立并完善了昆虫组织和器官的三维建模技术，有助于更为精准地观察昆虫的内部组织结构，可用于昆虫形态和器官发育的表型观察，为昆虫发育和基因功能研究提供了新技术和新方法。


关键词： 微计算机断层扫描技术,  褐飞虱,  内部结构,  三维重构,  表型组学 
项目 Item参数 Specification

X射线源

X-ray source

40～100 kV，10 W；点尺寸＜5 μm，4 W

X射线探测器

X-ray detector

1 600万像素sCMOS探测器

（4 096像素×4 096像素）

样品尺寸

Object size

最大直径75 mm，最大高度70 mm

仪器尺寸

Instrument dimension

宽×深×高为1 160 mm×520 mm×

330 mm（150 kg）

电源

Power supply

100～240 V 交流电，50～60 Hz，最大

电流3 A
Table 1 SkyScan 1272 CMOS specifications
Fig. 1 Internal and external structures of Micro CTA. Sampling device; B. SkyScan 1272 High Resolution 3D X-ray Microscope; C. Schematic diagram of the imaging path.
Fig. 2 3D reconstruction procedures of the original Micro CT images
Fig. 3 Micro CT images before sample position correction (A1-A3) and after sample position correction (B1-B3)X-Y, X-Z, and Y-Z represent three planes of Micro CT data.
Fig. 4 Gray density histograms before effective signal ampli-fication (A) and after effective signal amplification (B)
Fig. 5 Related position information of training data

体素

Voxel

样本1

Sample 1

样本2

Sample 2

样本3

Sample 3

样本4

Sample 4

样本5

Sample 5

总计

Total

总体素

Total voxels

51 06244 10046 23040 42044 100225 912

标记体素

Marked voxels

51 062（100.00%）44 100（100.00%）46 230（100.00%）40 420（100.00%）44 100（100.00%）225 912（100.00%）

目标区域

Target region

4 651（9.11%）3 362（7.62%）3 586（7.76%）1 049（2.60%）527（1.20%）13 175（5.83%）

背景区域

Background region

46 411（90.89%）40 738（92.38%）42 644（92.24%）39 371（97.40%）43 573（98.80%）212 737（94.17%）
Table 2 Voxel information related to training data
Patch大小 Patch size64
Patch移动步长 Patch stride ratio0.25
损失函数 Loss function

OrsDiceLoss

(1-DiceLoss)

优化算法 Optimization algorithmAdadelta

训练集Patch数

Patch count of training set

32

验证集Patch数

Patch count of validation set

7

数据增强设置

Data augmentation setting

20

训练集Patch数（增强）

Patch count of training set (augmentation)

6 321

验证集Patch数（增强）

Patch count of validation set (augmentation)

7
Table 3 Training parameters of deep learning model
Fig. 6 Loss function curve (A) and monitoring pictures (B) of deep learning model
Fig. 7 Muscle model output results from manual repair and stereological model optimizing stagesA. Muscle ROI segmented by deep learning model (green); B. Manually repaired ROI (purple); C. Smoothed ROI (orange); D. Final muscle mesh model (tawny).
Fig. 8 3D model of internal structures of BPH

组织和器官

Tissue and organ

体积

Volume/mm3

中枢神经系统 Central nervous system0.02
肌肉组织 Muscle tissue0.10
消化道 Alimentary canal0.01
生殖系统（雄性） Reproductive system (male)0.03
生殖系统（雌性） Reproductive system (female)0.04
Table 4 Volumes of structures of 3D model of BPH

基于Micro CT的褐飞虱三维重构系统

3D reconstruction system of BPH based on Micro CT

基于冷冻电镜的褐飞虱三维重构系统

3D reconstruction system of BPH based on Cryo-EM

项目

Item

费用

Cost/(104 CNY)

项目

Item

费用

Cost/(104 CNY)

Micro CT成像系统 Micro CT imaging system300冷冻电镜成像系统 Cryo-EM imaging system950
Dragonfly建模软件 Dragonfly modeling software25Amira建模软件 Amira modeling software70
图形工作站 Graphics workstation2图形工作站 Graphics workstation3
总计 Total327总计 Total1 023
最高成像精度 Maximum imaging accuracy/μm4.0最高成像精度 Maximum imaging accuracy/nm50
Table 5 Cost comparisons for using different 3D reconstruction systems
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