CytoTable
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, DuckDB, and Parsl 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
Pycytominerand AnnData workflows
View documentation → · View on GitHub →
Publication #
Patterns (Cell Press) · 2026
Scalable data harmonization for single-cell image-based profiling with CytoTable
Bunten, D. et al. Patterns 7, 101514 (2026).