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d33bs merged 5 commits into from
Aug 19, 2025
Merged

Documentation updates for clarifications #352

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96418f3
add more explicit note about zarr dependency
d33bs Aug 14, 2025
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add distinguishing notes about related projects
d33bs Aug 14, 2025
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linting
d33bs Aug 14, 2025
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d33bs Aug 18, 2025
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d33bs Aug 18, 2025
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3 changes: 2 additions & 1 deletion pyproject.toml
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Expand Up @@ -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" },
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13 changes: 12 additions & 1 deletion readme.md
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Expand Up @@ -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:

Expand All @@ -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)
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