美国Calico生命科学有限责任公司Austin E. Y. T. Lefebvre课题组报道了2D/3D活细胞显微镜中的自动细胞器分割、跟踪和分层特征提取。2025年2月27日出版的《自然—方法学》发表了这项成果。

在这里，研究人员介绍了Nellie，一个自动化的、无偏的管道，用于细胞内不同结构的分割、跟踪和特征提取。Nellie适应图像元数据，并采用分层分割来解决亚细胞器区域，而其辐射自适应模式匹配实现精确的运动跟踪。通过一个基于napari的热友好界面，Nellie无需编码专业知识即可进行全面的细胞器分析。研究小组通过从单通道数据中分离多个细胞器，通过图形自编码器量化线粒体对离子霉素的反应，以及跨细胞类型和时间点表征内质网网络，证明了Nellie的多功能性。该工具通过提供易于访问的细胞器动力学自动分析，解决了细胞生物学中的关键需求。

据了解，细胞器经历持续的形态变化和动态相互作用，是细胞稳态、应激反应和疾病进展的基础。尽管它们很重要，但由于其复杂的结构，快速的运动和现有分析工具的技术限制，量化细胞器形态和运动仍然具有挑战性。

附：英文原文

Title: Nellie: automated organelle segmentation, tracking and hierarchical feature extraction in 2D/3D live-cell microscopy

Author: Lefebvre, Austin E. Y. T., Sturm, Gabriel, Lin, Ting-Yu, Stoops, Emily, Lpez, Magdalena Preciado, Kaufmann-Malaga, Benjamin, Hake, Kayley

Issue&Volume: 2025-02-27

Abstract: Cellular organelles undergo constant morphological changes and dynamic interactions that are fundamental to cell homeostasis, stress responses and disease progression. Despite their importance, quantifying organelle morphology and motility remains challenging due to their complex architectures, rapid movements and the technical limitations of existing analysis tools. Here we introduce Nellie, an automated and unbiased pipeline for segmentation, tracking and feature extraction of diverse intracellular structures. Nellie adapts to image metadata and employs hierarchical segmentation to resolve sub-organellar regions, while its radius-adaptive pattern matching enables precise motion tracking. Through a user-friendly Napari-based interface, Nellie enables comprehensive organelle analysis without coding expertise. We demonstrate Nellie’s versatility by unmixing multiple organelles from single-channel data, quantifying mitochondrial responses to ionomycin via graph autoencoders and characterizing endoplasmic reticulum networks across cell types and time points. This tool addresses a critical need in cell biology by providing accessible, automated analysis of organelle dynamics.

DOI: 10.1038/s41592-025-02612-7

Source: https://www.nature.com/articles/s41592-025-02612-7