Software

Python package for reproducible processing of image-based profiling data, published in Nature Methods (2025).

Python package for harmonizing and converting large-scale single-cell microscopy data into analysis-ready formats. Published in Patterns (2026).

Python package for single-cell quality control

Compresses gene expression data across latent space dimensionalities to learn complementary biological representations

Version-controlled Cell Painting profiles from >10,000 compound perturbations (Broad Institute resource)