CytoTable 0.0.3

Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.

CytoTable

Diagram showing data flow relative to this project.

Summary

CytoTable enables single-cell morphology data analysis by cleaning and transforming CellProfiler (.csv or .sqlite), cytominer-database (.sqlite), and DeepProfiler (.npz) output data at scale. CytoTable creates parquet files for both independent analysis and for input into Pycytominer. The Parquet files will have a unified and documented data model, including referenceable schema where appropriate (for validation within Pycytominer or other projects).

Installation

Install CytoTable from PyPI or from source:

# install from pypi
pip install cytotable

# install directly from source
pip install git+https://github.com/cytomining/CytoTable.git

Contributing, Development, and Testing

We test CytoTable using ubuntu-latest and macos-latest GitHub Actions runner images.

Please see contributing.md for more details on contributions, development, and testing.

References

• pycytominer
• cytominer-database
• DeepProfiler
• CellProfiler
• cytominer-eval