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