diff --git a/pyproject.toml b/pyproject.toml index c5c96cab..063df66f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,7 +33,8 @@ anndata = [ { version = "<0.12.2", python = "<3.11" }, { version = ">=0.12.2", python = ">=3.11" }, ] -# zarr is required by anndata <0.12.2 +# Explicit zarr dependency for +# anndata <0.12.2 and Python <3.11 zarr = [ { version = "<3.1.1", python = "<3.11" }, { version = ">=3.1.1", python = ">=3.11" }, diff --git a/readme.md b/readme.md index e7b4c914..dbf966e1 100644 --- a/readme.md +++ b/readme.md @@ -15,7 +15,7 @@ _Diagram showing data flow relative to this project._ 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 data 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). +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). The name for the project is inspired from: @@ -42,6 +42,17 @@ We test CytoTable using `ubuntu-latest` and `macos-latest` [GitHub Actions runne Please see [contributing.md](docs/source/contributing.md) for more details on contributions, development, and testing. +## Relationship to other projects + +CytoTable focuses on image-based profiling data harmonization and serialization. +At scale, CytoTable transforms data into file formats which can be directly integrated with: + +**Please let us know how you use CytoTable (we'd love to add your project to this list)**! + +- [Pycytominer](https://github.com/cytomining/pycytominer) for the bioinformatics pipeline for image-based profiling. +- [coSMicQC](https://github.com/cytomining/coSMicQC) for quality control. +- [CytoDataFrame](https://github.com/cytomining/CytoDataFrame) for interactive visualization of profiles with single cell images. + ## References - [pycytominer](https://github.com/cytomining/pycytominer)