IAMSAM: image-based analysis of molecular signatures using the Segment Anything Model

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2024-11-11 DOI:10.1186/s13059-024-03380-x

Dongjoo Lee, Jeongbin Park, Seungho Cook, Seongjin Yoo, Daeseung Lee, Hongyoon Choi

引用次数: 0

Abstract

Spatial transcriptomics is a cutting-edge technique that combines gene expression with spatial information, allowing researchers to study molecular patterns within tissue architecture. Here, we present IAMSAM, a user-friendly web-based tool for analyzing spatial transcriptomics data focusing on morphological features. IAMSAM accurately segments tissue images using the Segment Anything Model, allowing for the semi-automatic selection of regions of interest based on morphological signatures. Furthermore, IAMSAM provides downstream analysis, such as identifying differentially expressed genes, enrichment analysis, and cell type prediction within the selected regions. With its simple interface, IAMSAM empowers researchers to explore and interpret heterogeneous tissues in a streamlined manner.

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IAMSAM：基于图像的分子特征分析，使用分段 Anything 模型

空间转录组学是一种将基因表达与空间信息相结合的前沿技术，使研究人员能够研究组织结构中的分子模式。在这里，我们介绍 IAMSAM，这是一种基于网络的用户友好型工具，用于分析以形态特征为重点的空间转录组学数据。IAMSAM 利用 "任意分割模型"（Segment Anything Model）对组织图像进行精确分割，可根据形态特征半自动选择感兴趣的区域。此外，IAMSAM 还提供下游分析功能，如在选定区域内识别差异表达基因、富集分析和细胞类型预测。通过简单的界面，IAMSAM 使研究人员能够以简化的方式探索和解释异质组织。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.