diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4644c42..d16aedb 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -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: > diff --git a/readme.md b/readme.md index e3991fb..206c59d 100644 --- a/readme.md +++ b/readme.md @@ -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-)) @@ -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).