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JoVE Journal
Biology
使用 Cell-ACDC 分析多维显微镜数据
使用 Cell-ACDC 分析多维显微镜数据
JoVE Journal
Biology
This content is Free Access.
JoVE Journal Biology
Analysis of Multidimensional Microscopy Data Using Cell-ACDC

使用 Cell-ACDC 分析多维显微镜数据

Full Text
570 Views
06:17 min
November 7, 2025

DOI: 10.3791/68954-v

Francesco Padovani*1, Timon Stegmaier*1, Benedikt Mairhörmann1,2,3, Kurt M. Schmoller1

1Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center,Helmholtz Zentrum München, 2Institute of Network Biology, Molecular Targets and Therapeutics Center,Helmholtz Zentrum München, 3Institute of AI for Health, Computational Health Center,Helmholtz Zentrum München

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Please note that some of the translations on this page are AI generated. Click here for the English version.

Overview

This research addresses the challenges in the analysis of multidimensional microscopy data, specifically in tracking cell division cycles. The study introduces Cell-ACDC, an open-source software that integrates AI-driven models to enhance segmentation, tracking, and quantification of microscopy datasets.

Key Study Components

Research Area

  • Cell biology
  • Microscopy data analysis
  • Bioinformatics

Background

  • Current AI models are complex and often inaccessible for biological workflows.
  • Manual correction of segmentation data is tedious without proper tools.
  • The need for an efficient and user-friendly software solution is critical to expedite biological discoveries.

Methods Used

  • Cell-ACDC software for analyzing cell division cycles.
  • Utilizes multifaceted segmentation and tracking algorithms.
  • Advanced visualization techniques for user-driven corrections.

Main Results

  • Demonstrated effective segmentation and tracking of cell cycles.
  • Improved accuracy in annotation of cell division events.
  • Facilitated integration of new methods into existing workflows.

Conclusions

  • Cell-ACDC offers enhanced access to AI models for bioimage analysis.
  • This study paves the way for more efficient automated solutions in microscopy research.

Frequently Asked Questions

What is Cell-ACDC?
Cell-ACDC is an open-source software designed to analyze cell division cycles through advanced AI-driven models.
How does Cell-ACDC improve segmentation?
It offers semi-automated tools for correcting segmentation masks, enhancing data accuracy.
Is Cell-ACDC user-friendly?
Yes, it features a graphical user interface that simplifies the process of selecting data and applying corrections.
Can new methods be integrated into Cell-ACDC?
Absolutely, the software supports community-driven additions, allowing for easy integration of new techniques.
What biological systems can be analyzed with Cell-ACDC?
Cell-ACDC can be used for various biological systems, including yeast and mouse embryonic stem cells.
What are the key benefits of using Cell-ACDC?
Its benefits include improved segmentation accuracy, user-friendly interfaces, and enhanced accessibility to AI models.

准确分析多维显微镜数据需要复杂的工作流程。本文演示如何使用 Cell-ACDC 软件。它利用最先进的人工智能驱动模型进行显微镜数据的分割、跟踪、细胞谱系分析和量化。至关重要的是,它通过一个创新框架来补充这些模型,用于对模型输出进行半自动校正。

我们正在通过开发一款名为Cell-ACDC的细胞分裂周期分析软件,改进多维显微镜数据的分析,以克服快速生物发现的瓶颈。现有的AI模型往往难以访问。此外,可视化和人工校正是实现高质量结果的必要条件。

然而,没有合适的工具,这些任务可能会变得非常繁琐。要开始,请在可视化和正确模块的主窗口中点击“启动图形界面”。点击新窗口工具栏中的文件夹图标,选择包含数据的文件夹。

然后点击选择文件夹确认选择。使用下拉菜单选择通道相位对比预处理,然后按确定确认。选择分段掩码名称,然后点击加载已选中,加载上一步创建的分段文件。

点击确定确认已加载位置,确认图片属性。提示时,选择“否”以防止加载额外的荧光数据。使用模式选择器选择分段和跟踪模式。

在菜单栏中,进入追踪,然后选择选择实时追踪算法,并根据生物体选择所需的实时追踪器。用左右方向键在画面间切换。导航到第10帧。

按S键激活手动花苞分离工具,右键点击即可自动拆分细胞一的分段掩码。现在,导航到第14帧。按B键激活画笔工具,用鼠标左键绘制花蕾缺失的分段遮罩。

继续进行后续帧,同时使用现有工具纠正分割和追踪错误。至少纠正到第42帧。使用模式选择器启动细胞周期分析。

提示时,选择“是”进入第一帧。用左右方向键在画面间切换。点击确定,在提示时接受细胞周期注释表的初始化,并导航到第41帧。

右键点击单元一或其芽,分离连接并注释细胞分裂事件。继续查看所有相关帧,并使用现有工具纠正自动母芽分配中的错误。要将芽分配到母芽,请按A键激活分配芽到母机工具。按住并长按芽上的右键,拖到对应的母细胞,然后松开鼠标键。

要重新初始化单元周期注释,请从工具栏中选择相应选项。要切断或重新绑定母芽关联,确保不选择任何工具。右键点击现有的母芽组合以断开关联,或再次右键点击以重新建立连接。

使用模式选择器激活普通师系谱系树。提示时,选择“是”进入第一帧,并用左右方向键在画面间导航。使用编辑工具栏中的工具纠正自动母子分配中的错误。

当提示时,点击“传播”以应用更改。要将母亲分配到新的细胞ID,请按F激活“寻找新细胞ID的母亲”工具。右键点击新细胞以循环切换候选母亲。肿瘤球体的核分片揭示了核体积分布广泛,大量物体体积较小,少数物体体积极大。

肿瘤类器官的三维视图显示了许多带有标识的分段细胞核,Z切片显示每个细胞核上涂有红色分段轮廓。在出芽酵母中,H2B蛋白含量在芽出时急剧增加,并在核分裂前趋于平稳。酵母数据集中核分裂时,细胞核数量突然增加。

在小鼠胚胎干细胞中,细胞面积逐渐增加直到达到最大值,随后在细胞分裂时减少,后来在子细胞中又开始上升。因此,Cell-ACDC是一个开源软件框架,能够轻松访问AI模型进行生物图像分析,并确保显微镜数据的高可共享性。Cell-ACDC 的一个重要方面是社区可以轻松地将新方法集成到带有标准化数据结构的现有工作流程中。

利用Cell-ACDC的校正数据对最先进方法进行微调,可以为全自动生物图像分析奠定基础。

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