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SpaFlow:用于QC和MxIF数据集集群集的Nextflow管道

Brenna C Novotny¹, Raymond Moore¹, Lynn Langit¹

¹Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, United States.

Bioinformatics advances

|March 5, 2025

概括

SpaFlow是分析多重免疫光 (MxIF) 数据的新管道,可实现标准化的细胞表型和在复杂组织微环境中有效识别细胞群.

科学领域:

生物医学成像技术生物医学成像技术
计算生物学计算生物学
免疫学免疫学免疫学

背景情况:

多复合免疫光学 (MxIF) 允许单细胞蛋白质的量化和组织微环境的空间分析.
由于面板设计灵活性,在MxIF数据中标准化细胞表型是具有挑战性的.

研究的目的:

开发一个高效和可定制的管道,用于无监督的集群和MxIF数据的分类.
为了使MxIF数据在不同平台上进行可复制和可扩展的分析.
在大型数据集中简化细胞类型识别.

主要方法:

使用Nextflow进行质量控制,集群和后集群分析,实施SpaFlow管道.
基于表型标记的细胞类型识别的Seurat,SCIMAP和CELESTA的整合.
开发一种元集群方法,在多个感兴趣的区域中凝聚集群.
包括强大的质量控制步骤,如信号总和和细胞密度过.

主要成果:

在对297个卵巢瘤核的案例研究中,SpaFlow成功地确定了具有生物意义的细胞群,包括瘤透性淋巴细胞.
该管道在分析大型数据集方面表现出了效率和速度.
使用连续桃体切片验证了可复制性,证实了细胞群的一致识别.

结论:

SpaFlow为细胞表型和分析MxIF数据提供了标准化和高效的解决方案.
该管道为组织微环境研究的可复制和可扩展研究提供了便利.
SpaFlow是研究人员使用高维成像数据研究复杂的生物系统的一个有价值的工具.

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相关概念视频

Flow Cytometry

Flow Cytometry

The development of flow cytometry techniques began in 1934 with initial attempts by Andrew Moldavan, a bacteriologist who counted the cells in a flowing capillary system. Moldavan pumped cells through a capillary tube focused under a microscope for visualization. The invention of photometry allowed the measurement of differentially-stained cells, and Louis Kamentsky developed the first multiparameter flow cytometer in 1965 to identify and count the cancer cells in cervical tissue specimens.
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