Topic
QC thresholds
What mitochondrial and count cutoffs should I use, and which cells am I throwing away?
Fixed cutoffs copied from a vignette remove real biology: tumor cells and cardiomyocytes have high mitochondrial fractions, and plasma cells or neutrophils have low counts. Thresholds should be per sample, data-driven (MAD-based) and inspected against what got removed.
- How to Choose Cell QC Thresholds in Spatial Transcriptomics
Copying the 10% mito cutoff from a PBMC tutorial into your tumor Visium slide will quietly delete every high-mitochondrial tumor spot you came to study.