SpaFlow: a Nextflow pipeline for QC and clustering of MxIF datasets.

ABSTRACT:

Motivation

Multiplex immunofluorescence (MxIF) enables the quantification of multiple protein markers at a single-cell level while preserving spatial information, offering a powerful tool for studying tissue microenvironments. However, the flexibility in MxIF panel design poses challenges in standardizing cell phenotyping.

Results

We present SpaFlow, an efficient, customizable pipeline for unsupervised clustering and classification of MxIF data, implemented using Nextflow. SpaFlow performs quality control, clustering, and postclustering analysis on segmented and quantified MxIF data, facilitating reproducible and scalable analyses across various computing platforms. The SpaFlow pipeline integrates three clustering and classification packages-Seurat, SCIMAP, and CELESTA-each

SUBMITTER: Novotny BC 

PROVIDER: S-EPMC11879158 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature