Metadata-Version: 2.1
Name: CytoTable
Version: 0.0.2
Summary: Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.
Home-page: https://github.com/cytomining/CytoTable
License: BSD-3-Clause License
Keywords: python,cellprofiler,single-cell-analysis,way-lab
Author: Cytomining Community
Requires-Python: >=3.8,<3.13
Classifier: License :: Other/Proprietary License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Requires-Dist: cloudpathlib[all] (>=0.15.0,<0.16.0)
Requires-Dist: duckdb (>=0.8.0,<0.9.0)
Requires-Dist: parsl (>=2023.9.18)
Requires-Dist: pyarrow (>=13.0.0,<14.0.0)
Project-URL: Documentation, https://cytomining.github.io/CytoTable/
Project-URL: Repository, https://github.com/cytomining/CytoTable
Description-Content-Type: text/markdown

<img height="200" src="https://raw.githubusercontent.com/cytomining/cytotable/main/logo/with-text-for-light-bg.png?raw=true">

# CytoTable

![dataflow](docs/source/_static/dataflow.svg)
_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](https://github.com/cytomining/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 with the following command:

```shell
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](https://github.com/actions/runner-images#available-images).

Please see [contributing.md](docs/source/contributing.md) for more details on contributions, development, and testing.

## References

- [pycytominer](https://github.com/cytomining/pycytominer)
- [cytominer-database](https://github.com/cytomining/cytominer-database)
- [DeepProfiler](https://github.com/cytomining/DeepProfiler)
- [CellProfiler](https://github.com/CellProfiler/CellProfiler)
- [cytominer-eval](https://github.com/cytomining/cytominer-eval)

