From f2f7fb1d66b8f9387701cb073ca8da4d4abd2c44 Mon Sep 17 00:00:00 2001 From: d33bs Date: Thu, 11 Dec 2025 14:55:38 -0700 Subject: [PATCH 1/6] table of updates --- readme.md | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/readme.md b/readme.md index e3991fb5..bde0d1f0 100644 --- a/readme.md +++ b/readme.md @@ -20,11 +20,17 @@ 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) +Check out the following resources to get started! +We created tutorials which follow a narrative-driven approach. +There are also Jupyter notebooks for pragmatic, hand-on explanations of working with CytoTable. + +| 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) | The name for the project is inspired by: From c9a9a344a17f11123af9169606b8b92e4150f75d Mon Sep 17 00:00:00 2001 From: d33bs Date: Thu, 11 Dec 2025 14:57:32 -0700 Subject: [PATCH 2/6] move to own section --- readme.md | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/readme.md b/readme.md index bde0d1f0..83a1268a 100644 --- a/readme.md +++ b/readme.md @@ -20,18 +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 the following resources to get started! -We created tutorials which follow a narrative-driven approach. -There are also Jupyter notebooks for pragmatic, hand-on explanations of working with CytoTable. - -| 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) | - The name for the project is inspired by: - __Cyto__: "1. (biology) cell." ([Wiktionary: Cyto-](https://en.wiktionary.org/wiki/cyto-)) @@ -51,6 +39,20 @@ pip install cytotable pip install git+https://github.com/cytomining/CytoTable.git ``` +## Getting started + +Check out the following resources to get started! +We created tutorials which follow a narrative-driven approach. +There are also Jupyter notebooks for pragmatic, hand-on explanations of working with CytoTable. + +| 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). From b97c125369c2664239ef02927530a27af3456264 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci-lite[bot]" <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com> Date: Thu, 11 Dec 2025 22:00:11 +0000 Subject: [PATCH 3/6] [pre-commit.ci lite] apply automatic fixes --- readme.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/readme.md b/readme.md index 83a1268a..b3f5bdd2 100644 --- a/readme.md +++ b/readme.md @@ -45,13 +45,13 @@ Check out the following resources to get started! We created tutorials which follow a narrative-driven approach. There are also Jupyter notebooks for pragmatic, hand-on explanations of working with CytoTable. -| 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) | +| 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 From 36b29e4f1773d7161947156b6dffe585d5d77d6f Mon Sep 17 00:00:00 2001 From: d33bs Date: Thu, 11 Dec 2025 15:34:47 -0700 Subject: [PATCH 4/6] Update readme.md --- readme.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/readme.md b/readme.md index b3f5bdd2..7271d176 100644 --- a/readme.md +++ b/readme.md @@ -45,6 +45,8 @@ Check out the following resources to get started! We created tutorials which follow a narrative-driven approach. There are also Jupyter notebooks for pragmatic, hand-on explanations of working with CytoTable. +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) | From a1d790b6e0764d2f18174c40c38e02f957e50a06 Mon Sep 17 00:00:00 2001 From: Dave Bunten Date: Thu, 11 Dec 2025 17:09:00 -0700 Subject: [PATCH 5/6] Apply suggestions from code review Co-authored-by: Gregory Way --- readme.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/readme.md b/readme.md index 7271d176..206c59d5 100644 --- a/readme.md +++ b/readme.md @@ -41,9 +41,9 @@ pip install git+https://github.com/cytomining/CytoTable.git ## Getting started -Check out the following resources to get started! +Check out the following resources to get started with CytoTable! We created tutorials which follow a narrative-driven approach. -There are also Jupyter notebooks for pragmatic, hand-on explanations of working with CytoTable. +We also provide Jupyter notebooks for pragmatic, hands-on explanations. We suggest image analysts begin with the tutorials and explore the example notebooks afterwards. From 10e029592ff1b1e75a205e50b53f036e89678cc6 Mon Sep 17 00:00:00 2001 From: d33bs Date: Mon, 15 Dec 2025 09:48:55 -0700 Subject: [PATCH 6/6] Update .pre-commit-config.yaml --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4644c42e..d16aedb9 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: >