Skip to content
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -63,7 +63,7 @@ repos:
hooks:
- id: vulture
- repo: https://github.com/pre-commit/mirrors-mypy
rev: v1.19.0
rev: v1.19.1
hooks:
- id: mypy
exclude: >
Expand Down
22 changes: 16 additions & 6 deletions readme.md
Original file line number Diff line number Diff line change
Expand Up @@ -20,12 +20,6 @@ This helps biologists by lowering the barrier between image acquisition and data
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)
>
> 📓☁️ 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 by:

- __Cyto__: "1. (biology) cell." ([Wiktionary: Cyto-](https://en.wiktionary.org/wiki/cyto-))
Expand All @@ -45,6 +39,22 @@ pip install cytotable
pip install git+https://github.com/cytomining/CytoTable.git
```

## Getting started

Check out the following resources to get started with CytoTable!
We created tutorials which follow a narrative-driven approach.
We also provide Jupyter notebooks for pragmatic, hands-on explanations.

We suggest image analysts begin with the tutorials and explore the example notebooks afterwards.

| Resource | What it covers | Link |
| ---------------- | ----------------------------------------------- | -------------------------------------------------------------------------------------------------------------- |
| Tutorial | CellProfiler SQLite or CSV to Parquet | [Open tutorial](https://cytomining.github.io/CytoTable/tutorials/cellprofiler_to_parquet.html) |
| Tutorial | NPZ embeddings to Parquet | [Open tutorial](https://cytomining.github.io/CytoTable/tutorials/npz_embeddings_to_parquet.html) |
| Tutorial | Multi-plate merge with tablenumber | [Open tutorial](https://cytomining.github.io/CytoTable/tutorials/multi_plate_merge_tablenumber.html) |
| Example notebook | CytoTable mise en place (general overview) | [Open notebook](https://cytomining.github.io/CytoTable/examples/cytotable_mise_en_place_general_overview.html) |
| Example notebook | CytoTable from the cloud (cloud-based overview) | [Open notebook](https://cytomining.github.io/CytoTable/examples/cytotable_from_the_cloud.html) |

## Contributing, Development, and Testing

We test CytoTable using `ubuntu-latest` and `macos-latest` [GitHub Actions runner images](https://github.com/actions/runner-images#available-images).
Expand Down