臺灣博碩士論文加值系統

In this thesis, we build a web-based system for visualizing Drosophila's neuron, neuron groups, and neuropils. This system can help neuroscieance researchers know the relation between neuron and the behavior of Drosophila more directly. The data comes from a lot of states. First, researchers use X-ray to photograph the sinogram of Drosophila's brain. Then, use the technical of image reconstruction to build the 3D volume data. Thirdly, analyze the 3D data to recognize where the neurons are and build their geometry coordination. Professor Chiang's lab in NTHU has built 27K and 16K data in the database by using neuron tracking method. Finally, these neuron data can do the grouping by analyzing the similarity between each neuron's structure. In the previous work of our lab, we have built a database that contains about 2 thousand groups. The purposes of this visualizing system are: showing these neuron data clearly and efficiently, letting researchers operate and query the data conveniently, and building a security log-in system to protect the database. This system have gotten positive responses of neuroscience researchers.

In this thesis, we build a web-based system for visualizing Drosophila's neuron, neuron groups, and neuropils. This system can help neuroscieance researchers know the relation between neuron and the behavior of Drosophila more directly. The data comes from a lot of states. First, researchers use X-ray to photograph the sinogram of Drosophila's brain. Then, use the technical of image reconstruction to build the 3D volume data. Thirdly, analyze the 3D data to recognize where the neurons are and build their geometry coordination. Professor Chiang's lab in NTHU has built 27K and 16K data in the database by using neuron tracking method. Finally, these neuron data can do the grouping by analyzing the similarity between each neuron's structure. In the previous work of our lab, we have built a database that contains about 2 thousand groups. The purposes of this visualizing system are: showing these neuron data clearly and efficiently, letting researchers operate and query the data conveniently, and building a security log-in system to protect the database. This system have gotten positive responses of neuroscience researchers.

Chapter 1.Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1 Background and Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Purpose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Chapter 2.Relative work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.1 Fruit Fly Brain Observatory . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.2 Amira and Avizo 3D Software . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.3 Vaa3D . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Chapter 3.System overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
3.1 System introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
3.2 Control panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
3.2.1 Basic control page . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
3.2.2 Single neuron page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
3.2.3 Groups custom page . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
3.2.4 Neuropil page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
3.3 Action recording section . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
3.4 Main scene operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
3.4.1 Orbit camera controlling . . . . . . . . . . . . . . . . . . . . . . . . . 17
3.4.2 Neurons and groups visualizing . . . . . . . . . . . . . . . . . . . . . 17
3.4.3 Manipulate the neuron . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Chapter 4.Implementation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
4.1 System structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
4.2 Introduction of included modules . . . . . . . . . . . . . . . . . . . . . . . . . 20
4.2.1 Three.js . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
4.2.2 Node.js . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
4.2.3 MongoDB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
4.3 Basic scene settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
4.4 Scene rendering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
4.4.1 Material setting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
4.4.2 Render order and the Depth test setting . . . . . . . . . . . . . . . . . 24
4.4.3 Lights setting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
4.5 Details of the main shell and the neuropil shell settings . . . . . . . . . . . . . 26
4.5.1 Introduction of alpha blending . . . . . . . . . . . . . . . . . . . . . . 26
4.5.2 The material settings of the shells . . . . . . . . . . . . . . . . . . . . 27
4.6 Render a neuron . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
4.7 Line material . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
4.8 Enhancement line material . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
4.8.1 Normal map rendering . . . . . . . . . . . . . . . . . . . . . . . . . . 34
4.8.2 Group transparent rendering . . . . . . . . . . . . . . . . . . . . . . . 37
4.9 Point’s material . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
4.10 Ray casting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
4.11 Highlight the neuron . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
4.12 Camera movement and focusing . . . . . . . . . . . . . . . . . . . . . . . . . 40
4.13 Statement record . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
4.14 Screen shot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
4.15 Server setting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
4.15.1 Server’s structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
4.15.2 Routes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
4.15.3 Socket.IO . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Chapter 5.Result and Future work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
5.1 Result . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
5.1.1 Finding neural tracking errors . . . . . . . . . . . . . . . . . . . . . . 52
5.1.2 The render result of neurons . . . . . . . . . . . . . . . . . . . . . . . 53
5.1.3 Database query to search soma points . . . . . . . . . . . . . . . . . . 53
5.1.4 Recording user log . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
5.2 Future works . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

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