CytoTable
Table of Contents
CytoTable harmonizes output from different high-content image analysis tools — including CellProfiler, DeepProfiler, and IN Carta — into a single, analysis-ready format. It scales to large datasets using Apache Parquet and DuckDB under the hood.
Key capabilities:
- Convert CellProfiler SQLite, CSV, and other formats into Parquet
- Harmonize schema differences across analysis tools
- Scale to datasets with millions of single cells
- Produce outputs compatible with pycytominer and AnnData workflows
Publication #
Patterns (Cell Press) · 2026
Scalable data harmonization for single-cell image-based profiling with CytoTable
Bunten D, Tomkinson J, Serrano E, Lippincott MJ, Brewer KI, et al.