scmorph: a Python package for analysing single-cell morphological profiles

2025/08/22 by Jesko Wagner, Hugh Warden, Ava Khamseh +1 · 1 voice
Biochemistry, Genetics and Molecular Biology · #Single-cell and spatial transcriptomics #Cell Image Analysis Techniques #Advanced Fluorescence Microscopy Techniques

paper · pdf · doi:10.21105/joss.08324

openalex publication_date 2025/08/22 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/15

Abstract

scmorph is a Python package to analyse single-cell data from imaging data of cell populations, specifically morphological profiling experiments, which generate large tabular data.scmorph combines domain-specific methods such as single-cell hit calling and batch correction with the versatile and scalable scverse tools to offer feature selection, dimensionality reduction, and more.Overall, scmorph brings together a host of single-cell morphological profiling methods, making it applicable for a wide range of experimental designs and workflows.

Citations

• CellProfiler 4: improvements in speed, utility and usability
• ECOD: Unsupervised Outlier Detection Using Empirical Cumulative Distribution Functions
• On boosting the power of Chatterjee's rank correlation
• Use of Ranks in One-Criterion Variance Analysis

Discussions

• 100s of miRNAs changed cell morphology, 18 across multiple cell lines, e.g. miR-155-5p. Also, we needed to develop our own single-cell analysis framework: doi.org/10.21105/jos.... Great collaboration [bsky, 1 points, 0 comments]

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