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Merged
d33bs merged 6 commits into from
Oct 16, 2025
Merged

Enhance readme for clarity #381

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9e07e60
enhance readme for clarity
d33bs Oct 13, 2025
f9f9d0d
[pre-commit.ci lite] apply automatic fixes
pre-commit-ci-lite[bot] Oct 13, 2025
d62830d
linting
d33bs Oct 13, 2025
c63b565
Merge branch 'update-readme' of https://github.com/d33bs/CytoTable in…
d33bs Oct 13, 2025
6dcd6d5
Update .pre-commit-config.yaml
d33bs Oct 16, 2025
6803d45
Merge branch 'main' into update-readme
d33bs Oct 16, 2025
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4 changes: 2 additions & 2 deletions .pre-commit-config.yaml
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Expand Up @@ -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
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hooks:
- id: almanack-check
- repo: https://github.com/PyCQA/pylint
rev: v4.0.0
rev: v4.0.1
hooks:
- id: pylint
name: pylint
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9 changes: 6 additions & 3 deletions readme.md
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Expand Up @@ -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)
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