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

IF 5.2 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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引用次数: 0

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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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.