An Open-Source Pipeline for Analyzing Changes In Microglial Morphology
An Open-Source Pipeline for Analyzing Changes In Microglial Morphology
复制标题
用于分析小胶质细胞形态变化的开源流程
DOI：
10.1101/2021.01.12.426422
复制
发表时间：
2021
期刊：
影响因子：
--
通讯作者：
Clarke D
中科院分区：
文献类型：
--
作者：
Clarke D
小胶质细胞形态的变化是大脑炎症状态的有力指标。在这里，我们提供了一个开源的小胶质细胞形态分析管道，首先清洗和注册小胶质细胞图像，然后提取描述小胶质细胞形态的62个参数。然后，它将对照和“炎症”训练数据进行比较，并使用降维来生成形态变化的单一度量（“炎症指数”）。我们通过研究短期高脂肪饮食对杂合子Cx3CR1-GFP小鼠的影响，发现饮食没有显著影响，因此可以计算该指数以评估炎症。我们的管道代表了第一个开源的小胶质细胞形态学管道，结合了半自动图像处理和降维。它使用免费软件（ImageJ和R），可以应用于各种各样的实验范例。我们预计它将使其他人能够更容易地利用小胶质细胞形态学分析提供的强大见解。
Changes in microglial morphology are powerful indicators of the inflammatory state of the brain. Here, we provide an open-source microglia morphology analysis pipeline that first cleans and registers images of microglia, before extracting 62 parameters describing microglial morphology. It then compares control and ‘inflammation’ training data and uses dimensionality reduction to generate a single metric of morphological change (an ‘inflammation index’). This index can then be calculated for test data to assess inflammation, as we demonstrate by investigating the effect of short-term high-fat diet consumption in heterozygous Cx3CR1-GFP mice, finding no significant effects of diet. Our pipeline represents the first open-source microglia morphology pipeline combining semi-automated image processing and dimensionality reduction. It uses free software (ImageJ and R) and can be applied to a wide variety of experimental paradigms. We anticipate it will enable others to more easily take advantage of the powerful insights microglial morphology analysis provides.