EASI-ORC: A pipeline for the efficient analysis and segmentation of smFISH images for organelle-RNA colocalization measurements in yeast.

IF 5.1 1区生物学 Q1 BIOLOGY Communications Biology Pub Date : 2025-02-15 DOI:10.1038/s42003-025-07682-z

Shahar Garin, Liav Levavi, Jeffrey E Gerst

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Abstract

Analysis of single-molecule fluorescent in situ hybridization (smFISH) images is important to translate cellular image data into a quantifiable format. Although smFISH is the gold standard for RNA localization measurements, there are no freely available, user-friendly applications for assaying messenger RNA (mRNA) localization to organelles. EASI-ORC (Efficient Analysis and Segmentation of smFISH Images for Organelle-RNA Colocalization) is a novel pipeline for the automated analysis of multiple smFISH images of yeast cells. EASI-ORC automates the segmentation of cells and organelles, identifies bona fide smFISH signals, and measures mRNA-organelle colocalization. EASI-ORC is efficient, unbiased, and plots the colocalization data and statistical analyses. EASI-ORC utilizes existing ImageJ plugins and original scripts, thus allowing for free access and ease-of-use. To circumvent technical literacy issues, a step-by-step user guide is provided. EASI-ORC offers a robust solution to smFISH image analysis - one that saves time, effort and provides consistent measurements of mRNA-organelle colocalization in yeast.

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EASI-ORC：用于酵母细胞器- rna共定位测量的smFISH图像的高效分析和分割管道。

分析单分子荧光原位杂交（smFISH）图像对于将细胞图像数据转化为可量化的格式非常重要。虽然smFISH是RNA定位测量的金标准，但目前还没有免费的、用户友好的应用程序来测定信使RNA （mRNA）在细胞器上的定位。EASI-ORC （Efficient Analysis and Segmentation of smFISH Images for organille - rna Colocalization）是一种自动化分析酵母细胞多张smFISH图像的新方法。EASI-ORC可以自动分割细胞和细胞器，识别真正的smFISH信号，并测量mrna -细胞器共定位。EASI-ORC是高效的，无偏的，并绘制共定位数据和统计分析。EASI-ORC利用现有的ImageJ插件和原始脚本，从而允许免费访问和易于使用。为了避免技术知识问题，提供了一步一步的用户指南。EASI-ORC为smFISH图像分析提供了一个强大的解决方案，节省了时间和精力，并提供了酵母中mrna -细胞器共定位的一致测量。

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来源期刊

Communications Biology Medicine-Medicine (miscellaneous)

CiteScore

8.60

自引率

1.70%

发文量

1233

审稿时长

13 weeks

期刊介绍： Communications Biology is an open access journal from Nature Research publishing high-quality research, reviews and commentary in all areas of the biological sciences. Research papers published by the journal represent significant advances bringing new biological insight to a specialized area of research.