cytodataframe 0.3.2__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- cytodataframe-0.3.2/.gitignore +150 -0
- cytodataframe-0.3.2/.pre-commit-config.yaml +82 -0
- cytodataframe-0.3.2/CITATION.cff +206 -0
- cytodataframe-0.3.2/CODE_OF_CONDUCT.md +3 -0
- cytodataframe-0.3.2/CONTRIBUTING.md +3 -0
- cytodataframe-0.3.2/LICENSE +28 -0
- cytodataframe-0.3.2/MANIFEST.in +22 -0
- cytodataframe-0.3.2/PKG-INFO +103 -0
- cytodataframe-0.3.2/README.md +71 -0
- cytodataframe-0.3.2/pyproject.toml +147 -0
- cytodataframe-0.3.2/setup.cfg +4 -0
- cytodataframe-0.3.2/src/cytodataframe/__init__.py +19 -0
- cytodataframe-0.3.2/src/cytodataframe/_version.py +24 -0
- cytodataframe-0.3.2/src/cytodataframe/frame.py +5415 -0
- cytodataframe-0.3.2/src/cytodataframe/image.py +472 -0
- cytodataframe-0.3.2/src/cytodataframe/volume.py +481 -0
- cytodataframe-0.3.2/src/cytodataframe.egg-info/PKG-INFO +103 -0
- cytodataframe-0.3.2/src/cytodataframe.egg-info/SOURCES.txt +22 -0
- cytodataframe-0.3.2/src/cytodataframe.egg-info/dependency_links.txt +1 -0
- cytodataframe-0.3.2/src/cytodataframe.egg-info/requires.txt +17 -0
- cytodataframe-0.3.2/src/cytodataframe.egg-info/scm_file_list.json +160 -0
- cytodataframe-0.3.2/src/cytodataframe.egg-info/scm_version.json +8 -0
- cytodataframe-0.3.2/src/cytodataframe.egg-info/top_level.txt +1 -0
- cytodataframe-0.3.2/uv.lock +4557 -0
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# This CITATION.cff file was generated with cffinit.
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# Visit https://bit.ly/cffinit to generate yours today!
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---
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cff-version: 1.2.0
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title: CytoDataFrame
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message: >-
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If you use this software, please cite it using the
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metadata from this file.
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type: software
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authors:
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- given-names: David
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family-names: Bunten
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orcid: 'https://orcid.org/0000-0001-6041-3665'
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- given-names: Jenna
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family-names: Tomkinson
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orcid: 'https://orcid.org/0000-0003-2676-5813'
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- given-names: Vincent
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family-names: Rubinetti
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orcid: 'https://orcid.org/0000-0002-4655-3773'
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- given-names: Gregory
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family-names: Way
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orcid: 'https://orcid.org/0000-0002-0503-9348'
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repository-code: 'https://github.com/cytomining/CytoDataFrame'
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identifiers:
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- description: Software DOI
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type: doi
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value: "10.5281/zenodo.14797074"
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abstract: >-
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An in-memory data analysis format for single-cell profiles alongside their corresponding images and segmentation masks.
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keywords:
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- python
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- single-cell-analysis
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- profiling
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- dataframes
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- data-analysis
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- way-lab
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license: BSD-3-Clause
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references:
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- authors:
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- name: "Way Lab CFReT_data Team"
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date-accessed: "2024-05-13"
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title: Way Lab CFReT_data CytoTable Data
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type: data
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repository-code: "https://github.com/WayScience/CFReT_data"
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url: "https://github.com/WayScience/CFReT_data/blob/main/3.process_cfret_features/data/converted_profiles/localhost231120090001_converted.parquet"
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scope: "localhost231120090001_converted.parquet"
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notes: >-
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Data from CFReT_data project is used to help validate
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expected results. Data is generated from CellProfiler
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and CytoTable.
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identifiers:
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- description: "Github Link with Contributors"
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type: url
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value: "https://github.com/WayScience/CFReT_data/graphs/contributors"
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- authors:
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- name: "Way Lab NF1_cellpainting_data Team"
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date-accessed: "2024-06-28"
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title: Way Lab NF1_cellpainting_data CytoTable Data
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type: data
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repository-code: "https://github.com/WayScience/nf1_cellpainting_data"
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notes: >-
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Data from NF1_cellpainting_data project is used to help validate
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expected results. Data is generated from CellProfiler
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and CytoTable. We use the following files from the repository:
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- "Plate_2_nf1_analysis.sqlite"
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- "Plate_2.parquet"
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type: url
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value: "https://github.com/WayScience/nf1_cellpainting_data/graphs/contributors"
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- title: >-
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Plate 2 (Cell Painting images from Plate 2 for NF1_cellpainting_data project)
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type: data
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url: https://figshare.com/articles/dataset/Plate_2/22233700
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notes: >-
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Image data for related NF1_cellpainting_data parquet sqlite.
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authors:
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- family-names: Tomkinson
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given-names: Jenna
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- family-names: Mattson-Hoss
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given-names: Michelle
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- family-names: Sarnoff
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given-names: Herb
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value: 10.6084/m9.figshare.22233700.v4
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- name: "Way Lab and Alexander Lab Nuclear Speckles Collaboration"
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Data from a collaborative project focusing on nuclear speckles
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Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations
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url: https://doi.org/10.1038/s41592-024-02241-6
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value: 10.1038/s41592-024-02241-6
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title: "Nessys: A new set of tools for the automated detection of nuclei within intact tissues and dense 3D cultures"
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journal: PLoS Biology
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dataset, available through the Image Data Resource (IDR) under accession
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number idr0062.
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title: "3D Noise Nuclei Segmentation Tutorial"
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url: "https://tutorials.cellprofiler.org/#3d-noise-nuclei-segmentation"
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This work uses data that were slightly modified from the
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CellProfiler 3D Noise Nuclei Segmentation tutorial.
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BSD 3-Clause License
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Copyright (c) 2024, Way Science
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modification, are permitted provided that the following conditions are met:
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list of conditions and the following disclaimer.
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this list of conditions and the following disclaimer in the documentation
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this software without specific prior written permission.
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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Name: cytodataframe
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Version: 0.3.2
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Summary: An in-memory data analysis format for single-cell profiles alongside their corresponding images and segmentation masks.
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Author: Way Science Community
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License-Expression: BSD-3-Clause
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# CytoDataFrame
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[](https://pypi.org/project/CytoDataFrame/)
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[](https://github.com/cytomining/CytoDataFrame/actions/workflows/run-tests.yml?query=branch%3Amain)
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[](https://github.com/astral-sh/ruff)
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[](https://github.com/astral-sh/uv)
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[](https://doi.org/10.5281/zenodo.14797074)
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_CytoDataFrame extends Pandas functionality to help display single-cell profile data alongside related images._
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CytoDataFrame is an advanced in-memory data analysis format designed for single-cell profiling, integrating not only the data profiles but also their corresponding microscopy images and segmentation masks.
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Traditional single-cell profiling often excludes the associated images from analysis, limiting the scope of research.
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CytoDataFrame bridges this gap, offering a purpose-built solution for comprehensive analysis that incorporates both the data and images, empowering more detailed and visual insights in single-cell research.
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CytoDataFrame is best suited for work within Jupyter notebooks.
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With CytoDataFrame you can:
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- Adjust image displays on-the-fly using interactive slider widgets.
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- Display image objects even when bounding box columns are missing, by cropping from compartment-center offsets or rendering whole fields of view.
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- Automatically detect 3D image volumes and render interactive [trame](https://github.com/Kitware/trame) views in notebooks when 3D dependencies are installed (with graceful fallback otherwise).
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- Disable automatic trame switching with `display_options={"auto_trame_for_3d": False}`.
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- Force trame layout regardless of auto-detection with `display_options={"view": "trame"}`.
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For images without bounding box columns (e.g. older CellProfiler outputs or image-level data):
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- Crop from compartment-center coordinates plus pixel offsets with `display_options={"offset_bounding_box": {"x_min": -20, "y_min": -20, "x_max": 20, "y_max": 20}}` (requires compartment center columns such as `Nuclei_Location_Center_X/Y`).
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- Render the full field of view without cropping with `display_options={"render_whole_image": True}` (works even with no bounding box and no center columns).
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For row display in notebook/widget tables:
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- When the table is larger than `display.max_rows`, the widget table inserts a midpoint ellipsis row (`…`) to indicate omitted rows.
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📓 ___Want to see CytoDataFrame in action?___ Check out our [example notebook](docs/src/examples/cytodataframe_at_a_glance.ipynb) for a quick tour of its key features.
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> ✨ CytoDataFrame development began within **[coSMicQC](https://github.com/cytomining/coSMicQC)** - a single-cell profile quality control package.
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> Please check out our work there as well!
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## Installation
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Install CytoDataFrame from source using the following:
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```shell
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# install from pypi
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pip install cytodataframe
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# or install directly from source
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pip install git+https://github.com/cytomining/CytoDataFrame.git
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```
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## Contributing, Development, and Testing
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Please see our [contributing](https://cytomining.github.io/CytoDataFrame/main/contributing) documentation for more details on contributions, development, and testing.
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## References
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|
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- [coSMicQC](https://github.com/cytomining/coSMicQC)
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- [pycytominer](https://github.com/cytomining/pycytominer)
|
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- [CellProfiler](https://github.com/CellProfiler/CellProfiler)
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- [CytoTable](https://github.com/cytomining/CytoTable)
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<img height="200" src="https://raw.githubusercontent.com/cytomining/cytodataframe/main/logo/with-text-for-light-bg.png?raw=true">
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|
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# CytoDataFrame
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[](https://pypi.org/project/CytoDataFrame/)
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[](https://github.com/cytomining/CytoDataFrame/actions/workflows/run-tests.yml?query=branch%3Amain)
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[](https://github.com/astral-sh/ruff)
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[](https://github.com/astral-sh/uv)
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[](https://doi.org/10.5281/zenodo.14797074)
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_CytoDataFrame extends Pandas functionality to help display single-cell profile data alongside related images._
|
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14
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+
|
|
15
|
+
CytoDataFrame is an advanced in-memory data analysis format designed for single-cell profiling, integrating not only the data profiles but also their corresponding microscopy images and segmentation masks.
|
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16
|
+
Traditional single-cell profiling often excludes the associated images from analysis, limiting the scope of research.
|
|
17
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CytoDataFrame bridges this gap, offering a purpose-built solution for comprehensive analysis that incorporates both the data and images, empowering more detailed and visual insights in single-cell research.
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CytoDataFrame is best suited for work within Jupyter notebooks.
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With CytoDataFrame you can:
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- View image objects alongside their feature data using a Pandas DataFrame-like interface.
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- Highlight image objects using mask or outline files to understand their segmentation.
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- Adjust image displays on-the-fly using interactive slider widgets.
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- Display image objects even when bounding box columns are missing, by cropping from compartment-center offsets or rendering whole fields of view.
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- Automatically detect 3D image volumes and render interactive [trame](https://github.com/Kitware/trame) views in notebooks when 3D dependencies are installed (with graceful fallback otherwise).
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For 3D notebook display behavior:
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- 3D-aware rendering is enabled by default (`display_options={"auto_trame_for_3d": True}`).
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- Disable automatic trame switching with `display_options={"auto_trame_for_3d": False}`.
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- Force trame layout regardless of auto-detection with `display_options={"view": "trame"}`.
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For images without bounding box columns (e.g. older CellProfiler outputs or image-level data):
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- Crop from compartment-center coordinates plus pixel offsets with `display_options={"offset_bounding_box": {"x_min": -20, "y_min": -20, "x_max": 20, "y_max": 20}}` (requires compartment center columns such as `Nuclei_Location_Center_X/Y`).
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- Render the full field of view without cropping with `display_options={"render_whole_image": True}` (works even with no bounding box and no center columns).
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For row display in notebook/widget tables:
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- CytoDataFrame respects pandas display settings (`display.max_rows`, `display.min_rows`).
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- When the table is larger than `display.max_rows`, the widget table inserts a midpoint ellipsis row (`…`) to indicate omitted rows.
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- You can control truncation behavior by changing pandas display options before rendering.
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📓 ___Want to see CytoDataFrame in action?___ Check out our [example notebook](docs/src/examples/cytodataframe_at_a_glance.ipynb) for a quick tour of its key features.
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> ✨ CytoDataFrame development began within **[coSMicQC](https://github.com/cytomining/coSMicQC)** - a single-cell profile quality control package.
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> Please check out our work there as well!
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## Installation
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Install CytoDataFrame from source using the following:
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```shell
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# install from pypi
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pip install cytodataframe
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# or install directly from source
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pip install git+https://github.com/cytomining/CytoDataFrame.git
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```
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## Contributing, Development, and Testing
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Please see our [contributing](https://cytomining.github.io/CytoDataFrame/main/contributing) documentation for more details on contributions, development, and testing.
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## References
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- [coSMicQC](https://github.com/cytomining/coSMicQC)
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69
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- [pycytominer](https://github.com/cytomining/pycytominer)
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70
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- [CellProfiler](https://github.com/CellProfiler/CellProfiler)
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- [CytoTable](https://github.com/cytomining/CytoTable)
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