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d33bs merged 2 commits into from
Sep 9, 2025
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Address readme typos and minor content changes #361

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address readme typos and content
d33bs Sep 8, 2025
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d33bs Sep 8, 2025
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2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
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Expand Up @@ -46,7 +46,7 @@ repos:
hooks:
- id: black
- repo: https://github.com/asottile/blacken-docs
rev: 1.19.1
rev: 1.20.0
hooks:
- id: blacken-docs
- repo: https://github.com/PyCQA/bandit
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12 changes: 6 additions & 6 deletions readme.md
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Expand Up @@ -13,17 +13,17 @@ _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 data output data at scale.
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).

> 📔 Check out our demonstration notebook for a one-stop reference of how to use CytoTable.
> 📔🧑‍🏫 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)
>
> 📓 Consider also checking out our demonstration notebook covering how to use cloud-based data sources with CytoTable.
> [CytoTable mise en place (general overview)](https://cytomining.github.io/CytoTable/examples/cytotable_from_the_cloud.html)
> 📓☁️ Consider also checking out our demonstration notebook covering how to use cloud-based data sources with CytoTable.
> [CytoTable from the cloud (cloud-based overview)](https://cytomining.github.io/CytoTable/examples/cytotable_from_the_cloud.html)

The name for the project is inspired from:
The name for the project is inspired by:

- __Cyto__: "1. (biology) cell." ([Wiktionary: Cyto-](https://en.wiktionary.org/wiki/cyto-))
- __Table__:
Expand Down Expand Up @@ -61,7 +61,7 @@ At scale, CytoTable transforms data into file formats which can be directly inte

## References

- [pycytominer](https://github.com/cytomining/pycytominer)
- [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)
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