绘制小胶质细胞参数软件（MMPS）：一款开源、用户友好的定量小胶质细胞形态分析工具
July 24th, 2026
微胶质细胞参数映射软件（MMPS）是一款用户友好的分析流程，无需编程专业知识，能够半自动化地从免疫荧光图像进行单细胞小胶质细胞形态学分析。MMPS在啮齿动物脂多糖诱导的神经炎症模型中得到验证，能够可复现地检测与激活相关的形态变化，并实现标准化、可扩展的小胶质表型分析。
小胶质细胞参数软件映射，或称MMPS，使我们能够研究缺氧性脑卒中后发铁死亡如何改变小胶质细胞亚群。MMPS解决了小胶质细胞分析领域的关键瓶颈，避免了繁琐的软件要求和必要的编码知识。首先，在计算机上打开GitHub存储库并下载Mapping Microglial Parameters Software或MMPS独立软件包。
在下载文件夹中，双击以启动存档实用程序以自动提取压缩文件夹。双击提取的MMPS应用程序图标以验证并打开MMPS软件包。单击选择图像文件夹选项并浏览计算机目录以找到项目文件。
授予文件夹访问权限并选择图像存储目录。接下来，单击选择输出文件夹，然后选择输出目录。选择要处理的图像，然后选择图像标记。
为图像分配动物标识符和处理组，并保存输入。要计算图像的像素大小，请从刻度尺选择校准。选择刻度尺的起始点和终点，并输入已知的刻度尺距离（以微米为单位），然后单击应用。
选择包含小胶质细胞信号的荧光通道。通过选中每个图像名称旁边的框来选择处理图像，如果图像之间的背景荧光不同，则单独处理它们。查看原始、预览、处理和掩模选项卡以比较图像处理阶段。
选择预览当前图像以调整其他处理设置。对于背景减除，将滚动球值设置在五到150像素之间。为减少光照伪影，使用三的去噪值，并将锐化值设置在一到二之间以改善边缘定义。
在优化图像处理设置后，单击处理选定图像。接下来，选择挑选体，所有图像。单击显示颜色C以查看RGB合成视图。
选择通道，如果图像颜色出现失真，则取消选择任何未使用的通道。单击显示调整以调整RGB视图中的通道亮度。选择显示DAPI和电离钙结合适配器分子一或IBA1共定位的小胶质细胞体。
使用退格或删除键删除错误选择的细胞体。按Enter或Return键继续下一张图像。在完成细胞体选择后，选择轮廓细胞体所有。
用至少八个轮廓点勾画每个选定的小胶质细胞的细胞体轮廓，不包括细胞突起。使用撤销最后一点、删除或退格键删除错误放置的轮廓点。按Enter、Return、双击或右键单击以完成每个细胞体的轮廓。
在完成细胞体轮廓后，单击生成所有掩模。在掩模生成设置中，调整最小强度以减少背景像素并平衡背景抑制和分支保留。选择QA所有掩模以开始掩模质量保证，并按从大到小的顺序查看所有呈现的掩模。
使用处理和掩模选项卡比较每个掩模与相应的小胶质细胞。要接受掩模，使用A键盘快捷键。要拒绝掩模，使用R键盘快捷键。
要撤销接受或拒绝，按B。使用键盘箭头键浏览掩模大小。选择最接近的掩模，准确捕获小胶质细胞分支而不包含邻近细胞、过多的背景、图像边缘或刻度尺。如果大多数不准确，请使用清除所有掩模选项以使用不同的阈值重新生成掩模。
接下来，选择计算简单特征以计算已接受掩模的各种参数，然后单击确定。对于其他分析，下载fractalanalysisimagej. py、sholl.
py，和skeletonanalysisimagej. py插件。对于分形和外壳分析，打开并运行fractalanalysisimagej。
py作为Fiji插件。然后输入输出目录位置。输入像素大小并选择仅分析每个细胞的最大掩模选项以分析每个细胞的最大接受掩模。
对于sholl分析，将sholl. py作为Fiji插件打开。输入输出目录位置、所需像素大小、步长大小。
选择使用细胞体半径作为起始半径，或输入固定的细胞体半径值（如果不使用MMPS得出的细胞体半径）。打开skeletonanalysisimagej. py作为Fiji插件进行骨骼分析。
在提示时，浏览并输入掩模目录、输出目录和像素大小的路径。完成后，将所有插件生成的结果导出为逗号分隔值文件到特定的输出目录中。使用脂多糖或LPS诱导的啮齿动物神经炎症模型对MMPS的验证研究表明，与车辆处理的对照组相比，LPS给药显著降低了平均质心距离和细胞周长。
在处理组之间，掩模面积、圆度或偏心率没有显著差异。与车辆对照组相比，LPS处理的动物的细胞体面积显著增加，这与胶质细胞的活化相关形态重塑一致。进一步下游，先进的形态分析表明，车辆处理的大鼠中微胶质细胞圆度和周长之间只有弱相关性，而LPS处理的大鼠之间有强相关性，这表明增加的微胶质细胞活化与减少的圆度和周长有关。
此外，掩模面积在车辆和LPS处理组中与平均质心距离呈现出强正相关，这与与微胶质细胞活化相关的分支变化一致。该协议使研究人员能够研究复杂的小胶质细胞分支、形态同质性和结构复杂性
Overview
This article introduces the Mapping Microglial Parameters Software (MMPS), an open-source platform designed for quantitative analysis of microglial morphology. MMPS addresses accessibility and usability challenges in current analysis tools by providing a user-friendly, Python-based solution compatible with immunofluorescence workflows. The software is validated using a rodent model of neuroinflammation, demonstrating its effectiveness in detecting morphological changes associated with microglial activation.
Key Study Components
Area of Science
- Neuroscience
- Immunology
- Image analysis
Background
- Microglia are central nervous system immune cells involved in tissue degradation and remodeling after neurological injury.
- Quantitative morphology analysis can distinguish microglial subpopulations and preserve in situ information.
- Existing analysis platforms often require specialized expertise or are not publicly accessible.
- There is a need for standardized, accessible tools for microglial morphology analysis.
Purpose of Study
- To develop an open-source, user-friendly software for microglial morphology analysis.
- To enable semi-automated, single-cell analysis without coding expertise.
- To validate the software using a rodent neuroinflammation model.
Methods Used
- Development of MMPS using Python 3.11.
- Integration with immunofluorescence-based imaging workflows.
- Implementation of a graphical user interface for accessible operation.
- Validation using a rodent lipopolysaccharide (LPS)-induced neuroinflammation model.
Main Results
- MMPS enables semi-automated, quantitative analysis of microglial morphology at the single-cell level.
- Microglia from LPS-treated animals showed significantly increased soma area (p < 0.01).
- Microglia from LPS-treated animals exhibited reduced cell perimeter (p < 0.05) compared to controls.
- These morphological changes are consistent with microglial activation and neuroinflammation.
Conclusions
- MMPS provides a standardized and reproducible platform for microglial morphology analysis.
- The software is accessible to users without coding expertise.
- MMPS facilitates cross-laboratory comparison and reproducibility in microglial research.
Frequently Asked Questions
Executive Industry Relevance
Quantitative microglial morphology analysis is critical for de-risking neuroinflammation targets and advancing CNS drug discovery. The Mapping Microglial Parameters Software (MMPS) enables standardized, reproducible measurement of microglial activation states, supporting predictive confidence in early discovery and translational research. Its accessibility and cross-laboratory compatibility address key bottlenecks in neuroimmune target validation and portfolio triage.
Strategic Applications in Biopharma R&D
Early Discovery & Target Validation
- Enables quantitative interrogation of microglial activation in disease-relevant models.
- Supports functional target validation by distinguishing subtle morphological phenotypes.
- Facilitates mechanistic de-risking of neuroimmune pathways in CNS disorders.
- Improves predictive confidence for advancing neuroinflammation targets.
Screening & Assay Development
- Standardizes image-based microglial morphology assays for reproducible outputs.
- Prepares validated biological systems for compound screening and phenotypic profiling.
- Enables scalable, semi-automated analysis compatible with immunofluorescence workflows.
- Supports reliable quantitative evaluation of compound effects on microglial states.
Translational & Preclinical Research
- Aligns morphological readouts with translational biomarkers of neuroinflammation.
- Ensures continuity from discovery through preclinical validation in rodent models.
- Reduces risk in advancing neuroimmune assets by providing robust, quantitative endpoints.
- Supports cross-study and cross-laboratory reproducibility for regulatory submissions.
Pipeline & Workflow Integration
MMPS integrates into the discovery-to-preclinical continuum by enabling standardized, quantitative analysis of microglial morphology in immunofluorescence-based workflows.
- Discovery Biology: Provides hypothesis-driven quantification of microglial activation and morphological phenotypes.
- Screening: Delivers reproducible, quantitative outputs for assay development and compound evaluation.
- Analytics: Generates statistical measurements (e.g., soma area, cell perimeter) for condition comparison and decision-making.
- Translational Research: Aligns with preclinical neuroinflammation models for biomarker continuity.
- Enterprise Reuse: Offers an open-source, user-friendly platform adaptable across CNS research programs.
Operational & Enterprise Impact
- Scientific Value: Increases predictive confidence and reduces mechanistic ambiguity in neuroimmune target validation.
- Operational Value: Standardizes and semi-automates morphology analysis, improving reproducibility and scalability.
- Strategic Value: Enables informed go/no-go decisions and capital-efficient advancement of CNS assets.
- Portfolio Impact: Supports risk-adjusted prioritization of neuroinflammation programs with robust quantitative endpoints.
Implementation Considerations
- Requires expertise in immunofluorescence imaging and neurobiology for optimal use.
- Needs compatible imaging instrumentation and computational infrastructure for image processing.
- Demands cross-team standardization of imaging and analysis protocols for reproducibility.
- Adaptable to various rodent neuroinflammation models and potentially other CNS disease systems.
- Dependent on image quality and parameter selection for accurate morphological quantification.