Tools

Downstream evaluation — measures how reproducibly perturbation profiles retrieve their matched replicates, quantifying profile quality and similarity.

Quality control step — flags and removes low-quality cells before profile processing to prevent artifacts from propagating downstream.

Interactive exploration — view and inspect morphological profiles alongside their source cell images directly in Jupyter notebooks.

Upstream ingestion — converts raw CellProfiler, DeepProfiler, and IN Carta outputs into scalable, analysis-ready Parquet tables.

Alternative feature extraction — deep learning embeddings from raw microscopy images, bypassing classical segmentation-and-measurement pipelines.

Core processing pipeline — aggregates, normalizes, and feature-selects morphological profiles for downstream analysis.