开源软件贡献
我们开发了多个开源算法和软件工具，已在医学影像社区广泛采用。我的贡献包括：
- Grow From Seed交互式分割算法：成为全球最大的开源医学图像计算平台3D Slicer的核心模块
- Robust Statistics Segmenter：集成到3D Slicer中
- 球面小波ITK滤波器：包含在InsightToolkit (ITK)中
- 共形球映射ITK滤波器：包含在InsightToolkit (ITK)中
- 统计形状分析 (SPoM)：定量形状分析框架，提供Docker镜像
- 多尺度形状表示：基于小波的三维形状分解
Statistical shape analysis --- A quantitatively validated approach Source code
In our project:
``Gao Y, Bouix S. Statistical Shape Analysis using 3D Poisson Equation---A Quantitatively Validated Approach. Medical Image Analysis. , vol. 30, pp. 72-84, 2016.''
- We proposed a new statistical shape analysis/morphometry technique based on the 3D Poisson Equation.
- In addition, we proposed a quantitative evaluation framework for morphometry/shape analysis methods.
- To the best of our knowledge, this is the first quantitative morphometry evaluation framework and the proposed method is the morphometry technique that is systematically and quantitatively validated and evaluated.
- The source code is hosted on github at here.
多尺度形状分解与重建，三维小波变换（ITK格式）源代码下载
In our project:
``Y. Gao, B. Corn, D. Schifter, and A. Tannenbaum, Multiscale 3D shape representation and segmentation with applications to hippocampal/caudate extraction from brain MRI, Medical Image Analysis, vol. 16, no. 2, pp. 374-385, 2012''
we proposed a multi-scale shape decomosition and reconstruction for 3D shapes of arbitrary topology. As a bi-product, we release the code for performing 2D and 3D wavelet transformation on ITK images. The source code is hosted on github at here.
曲面共形映射至球面（VTK、ITK格式） Source code
Given a genus-0 surface, that is, a closed surface with no holes and no handles, this filter maps the surface to a sphere. The angle will be preserved during the mapping. It's based on the paper On the Laplace-Beltrami operator and brain surface flattening by Angenent, Haker, Tannenbaum and Kikinis, published on IEEE TMI. The implementation is now shipped with the InsightToolkit. The implementation and the usage is detailed in the
Gao Y, Melonakos J, Tannenbaum AR. Conformal Flattening ITK Filter. MICCAI, Open Science Workshop/Insight Journal, 2006
For example, the surface below on the left will be mapped to the sphere on the right.
The sources code here, however, is a further improvement over the previous publication: First, after we submitted it to the Insight Journal, thanks to the contribution of Dr. Alexandre Gouaillard and the open science philosophy of the journal, the code has been improved to be more coherent with the ITK framework. Later, we utilized the preconditioned conjugate gradient solver in the computation which significantly accelerated the algorithm. The last improvement was a to make sure that the points on the final sphere is more evenly distributed.
Comparing with the code now in ITK 3.20, the code here has tighter convergence criteria and therefore gives better result. These changes will be adopted in ITKv4.
Grow From Seed：基于局部统计信息的交互式三维分割软件 源代码
这是一个面向最终用户的交互式三维图像分割工具，完全集成在3D Slicer软件中。自2014年以来，它已成为3D Slicer（全球最大的开源医学图像计算软件平台）的核心交互式分割组件。
``Gao Y*, Chen X, Yang Q, Lasso A, Kolesov I, Pieper S, Kikinis R, Tannenbaum A, Zhu L*. An effective and open source interactive 3D medical image segmentation solution. Scientific Reports. 2024; 14:29878.''
主要特性：
- 用户友好的交互式分割，只需少量用户输入（几个笔画）
- 实时三维分割反馈
- 作为核心模块集成到3D Slicer中
- 被多个国家的研究人员用于研究和临床实验
- 支持多种医学成像模态（MRI、CT、超声）
影响：该算法已在医学影像研究社区广泛采用，并在全球临床研究应用中使用。3D Slicer由美国、德国、英国、日本、加拿大等多国大学研究院连续十年联合开发，其中美国卫生署NIH资助经费超过三千万美元。
源代码可在GitHub上获取：Grow From Seed 代码库
球面上的小波变换
- How to do wavelet analysis on a 2-sphere?
- How that can be applied to localized analysis of a shape?
TODO: I'll add code here soon.