diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 3324d3e2..411d71fb 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -16,7 +16,7 @@ repos: hooks: - id: poetry-check - repo: https://github.com/tox-dev/pyproject-fmt - rev: "v2.10.0" + rev: "v2.11.0" hooks: - id: pyproject-fmt - repo: https://github.com/codespell-project/codespell @@ -82,7 +82,7 @@ repos: hooks: - id: almanack-check - repo: https://github.com/PyCQA/pylint - rev: v4.0.0 + rev: v4.0.1 hooks: - id: pylint name: pylint diff --git a/readme.md b/readme.md index 2bf512d8..e3991fb5 100644 --- a/readme.md +++ b/readme.md @@ -13,9 +13,12 @@ _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`), and other sources such as IN Carta output data at scale. -CytoTable creates parquet files for both independent analysis and for input into [Pycytominer](https://github.com/cytomining/pycytominer). -The output files (such as [Parquet](https://parquet.apache.org/) and [anndata](https://github.com/scverse/anndata) file formats) have a documented data model, including referenceable schema where appropriate (for validation within Pycytominer or other image-based profiling projects). +Image-based profiling often entails preparing data for analysis by transforming the outputs of image analysis tools into a consistent, analysis-ready format. +CytoTable streamlines analyses by harmonizing CellProfiler (`.csv` or `.sqlite`), cytominer-database (`.sqlite`), DeepProfiler (`.npz`), or other sources such as IN Carta output data at scale. +This helps biologists by lowering the barrier between image acquisition and data interpretation, enabling them to focus on biological insights rather than file formats or data wrangling. + +CytoTable creates Parquet or AnnData files for both independent analysis and for input into [Pycytominer](https://github.com/cytomining/pycytominer). +The output files (such as [Parquet](https://parquet.apache.org/) and [AnnData](https://github.com/scverse/anndata) file formats) have a documented data model, including referenceable schema where appropriate (for validation within Pycytominer or other image-based profiling projects). > 📔🧑‍🏫 Check out our demonstration notebook for a one-stop reference of how to use CytoTable. > [CytoTable mise en place (general overview)](https://cytomining.github.io/CytoTable/examples/cytotable_mise_en_place_general_overview.html)