Vispro改进了Visium空间转录组学的成像分析

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2025-06-18 DOI:10.1186/s13059-025-03648-w

Huifang Ma, Xingyuan Zhang, Yilong Qu, Anru R. Zhang, Zhicheng Ji

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引用次数: 0

摘要

空间转录组学使空间分辨的基因表达分析成为可能，但伴随的组织学图像往往被基准标记和背景区域退化，阻碍了解释。为了解决这个问题，我们推出了Vispro，这是一款针对10x Visium数据进行优化的端到端自动图像处理工具。Vispro包括用于基准标记检测、图像恢复、组织区域检测和断开组织区域分割的模块。通过提高图像质量，Vispro提高了下游分析的准确性和性能，包括组织和细胞分割、图像配准、由组织学背景引导的基因表达植入和空间域检测。

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Vispro improves imaging analysis for Visium spatial transcriptomics

Spatial transcriptomics enables spatially resolved gene expression analysis, but accompanying histology images are often degraded by fiducial markers and background regions, hindering interpretation. To address this, we introduce Vispro, an end-to-end automated image processing tool optimized for 10× Visium data. Vispro includes modules for fiducial marker detection, image restoration, tissue region detection, and segmentation of disconnected tissue areas. By enhancing image quality, Vispro improves the accuracy and performance of downstream analyses, including tissue and cell segmentation, image registration, gene expression imputation guided by histological context, and spatial domain detection.

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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.