DeepAD: An automated and interpretable machine learning pipeline for image analyses of biomarkers in Alzheimer's disease

DeepAD：一种自动化且可解释的机器学习管道，用于阿尔茨海默病生物标志物的图像分析

• 批准号: 22K15658
• 负责人: Poon CharissaTingAmanda
• 金额: $ 2.83万
• 依托单位: Institute of Physical and Chemical Research
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Early-Career Scientists
• 财政年份: 2022
• 资助国家: 日本
• 起止时间: 2022-04-01 至 2026-03-31
• 项目状态: 未结题
• 来源: https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-22K15658/
• 关键词: alzheimer's disease; amyloid; deep learning; image processing; microscopy; 画像情報処理・画像認識; 分子・細胞・神経生物学; 認知症疾患; グリア細胞; コンピュータビジョン

研究の目的 To goal of the project is to develop an image processing pipeline that uses computational tools, including deep learning, to automate image analyses of Alzheimer's disease microscopy images.研究実施計画 For FY2022 and FY2023, the 2 goals are to use computational tools to automatically preprocess microscopy images of AD mouse brain, and to segment, quantify, and conduct morphological feature analysis of Ab plaques. I have developed image preprocessing pipelines to preprocess 2D AD images from the original collaborator, as well as 3D images from a new collaborator. I developed an automated workflow for processing gene expression images, which was accepted as a peer-reviewed conference paper; the computational tools developed for this work can be applied to the 若手 project. In collaboration with other lab members, we developed novel methods to conduct instant segmentation of sparse, punctate objects; this work was submitted as for peer-review at 2 other conferences.

该项目目标的研究目标是开发图像处理管道，该管道使用包括深度学习在内的计算工具来自动化阿尔茨海默氏病显微镜图像的图像分析。针对2022财年和2023财年的研究实施计划，这两个目标是使用计算工具自动预处理显微镜图像，以分割，量化，量化和进行AB斑块的形态特征分析。我已经开发了图像预处理管道，以从原始合作者和新合作者的3D图像中进行预处理2D AD图像。我开发了一个自动化工作流以处理基因表达图像，该图像被接受为同行评审的会议论文。为这项工作开发的计算工具可以应用于年轻项目。与其他实验室成员合作，我们开发了新颖的方法来进行稀疏，点状对象的即时分割。这项工作是在其他两个会议上提交的同行评审。

项目成果

An automated pipeline to create an atlas of in situ hybridization gene expression data in the adult marmoset brain

用于创建成年狨猴大脑中原位杂交基因表达数据图谱的自动化管道

• 发表时间: 2023
• 期刊: International Symposium on Biomedical Imaging
• 作者: Poon;Charissa; Rachmadi;Muhammad Febrian; Byra;Michal; Schlachter;Matthias; Xu;Binbin; Shimogori;Tomomi; Skibbe;Henrik
• 通讯作者: Henrik

Semi-supervised semantic segmentation of in situ hybridization gene expression in the marmoset brain

狨猴大脑原位杂交基因表达的半监督语义分割

• 发表时间: 2022
• 作者: Poon;Charissa; Rachmadi;Muhammad Febrian; Byra;Michal; Shimogori;Tomomi; Skibbe;Henrik
• 通讯作者: Henrik

Improving Segmentation of Objects with Varying Sizes in Biomedical Images using Instance-wise and Center-of-Instance Segmentation Loss Function

使用实例级和实例中心分割损失函数改进生物医学图像中不同尺寸对象的分割

• 发表时间: 2023
• 期刊: Proceedings of Machine Learning Research
• 作者: Rachmadi;Muhammad Febrian; Poon;Charissa; Skibbe;Henrik
• 通讯作者: Henrik