Metadata-Version: 2.4 Name: RosettaX Version: 0.1.0 Summary: Interactive fluorescence and scattering calibration workflows for flow cytometry. Author-email: Martin Poinsinet de Sivry-Houle License-Expression: AGPL-3.0-or-later Project-URL: Homepage, https://github.com/MartinPdeS/RosettaX Project-URL: Documentation, https://martinpdes.github.io/RosettaX/ Project-URL: Repository, https://github.com/MartinPdeS/RosettaX.git Keywords: flow-cytometry,calibration,scattering,fluorescence,data-analysis Classifier: Programming Language :: Python Classifier: Programming Language :: Python :: 3 Classifier: Programming Language :: Python :: 3.13 Classifier: Programming Language :: Python :: Implementation :: CPython Classifier: Development Status :: 3 - Alpha Classifier: Topic :: Scientific/Engineering :: Physics Classifier: Intended Audience :: Science/Research Requires-Python: >=3.10 Description-Content-Type: text/x-rst License-File: LICENSE Requires-Dist: PyMieSim==5.1.2 Requires-Dist: numpy>=2.2.6 Requires-Dist: dash>=4.1.0 Requires-Dist: dash-bootstrap-components>=2.0.4 Requires-Dist: plotly>=6.7.0 Requires-Dist: gunicorn>=23.0.0 Provides-Extra: testing Requires-Dist: pytest<10.0,>=7.4; extra == "testing" Requires-Dist: pytest-cov<8,>=2; extra == "testing" Requires-Dist: pytest-json-report~=1.5; extra == "testing" Requires-Dist: coverage~=7.6; extra == "testing" Provides-Extra: documentation Requires-Dist: numpydoc~=1.8; extra == "documentation" Requires-Dist: sphinx>=6; extra == "documentation" Requires-Dist: sphinx-gallery~=0.17; extra == "documentation" Requires-Dist: sphinx-rtd-theme~=3.0; extra == "documentation" Requires-Dist: pydata-sphinx-theme~=0.15; extra == "documentation" Provides-Extra: dev Requires-Dist: flake8==7.3.0; extra == "dev" Provides-Extra: bundling Requires-Dist: pyinstaller<7,>=6.14; extra == "bundling" Dynamic: license-file RosettaX ======== .. image:: https://raw.githubusercontent.com/MartinPdeS/RosettaX/master/RosettaX/assets/logo_light.svg :alt: RosettaX logo .. list-table:: :widths: 10 25 25 25 :header-rows: 0 * - Meta - |python| - |docs| - |zenodo| * - Testing - |ci/cd| - |coverage| - * - PyPI - |PyPi| - |PyPi_download| - * - Anaconda - |anaconda| - |anaconda_download| - RosettaX is an interactive calibration application for flow cytometry. It provides local graphical workflows for fluorescence and scattering calibration, combining FCS data loading, histogram inspection, peak identification, calibration fitting, runtime profile management, and reusable calibration export in a single interface. The goal of RosettaX is to make calibration workflows explicit, inspectable, repeatable, and easier to maintain across experiments. The application is designed as a practical bridge between experimental cytometry data, optical modeling, detector settings, calibration references, and downstream analysis. Overview ******** Flow cytometry calibration is often distributed across several disconnected tools: instrument software, notebooks, scripts, spreadsheets, manually selected peaks, copied constants, and exported configuration files. This fragmentation makes calibration procedures difficult to audit, reproduce, compare, and reuse. RosettaX brings these steps into a structured application. A calibration session can be configured, inspected, fitted, saved, and reused without separating the scientific model from the practical workflow. This is particularly useful when calibration results need to remain traceable across instruments, detector settings, reference materials, and analysis pipelines. RosettaX currently focuses on two main calibration workflows: * fluorescence calibration * scattering calibration The fluorescence workflow supports calibration from reference intensity data. The scattering workflow connects measured cytometry signals with optical parameters such as particle size, refractive index, detector configuration, and scattering intensity. Features ******** RosettaX currently provides: * fluorescence calibration workflows * scattering calibration workflows * FCS data loading * interactive histogram inspection * peak identification and peak finding * calibration fitting * reusable calibration export * runtime profile management * detector and optical parameter presets * support for default and custom parameter configurations * local graphical application behavior suitable for repeated calibration work Why RosettaX ************ RosettaX is intended to reduce the amount of manual and implicit work involved in flow cytometry calibration. Typical calibration workflows often require users to move between acquisition software, custom scripts, spreadsheets, and manually recorded parameters. This can make it difficult to know exactly which data, peaks, settings, assumptions, and fitted models produced a given calibration result. RosettaX addresses this by keeping the workflow organized around explicit steps: * load the relevant cytometry data * select or define the calibration context * inspect the signal distributions * identify the calibration peaks * fit the calibration relation * review the result * export a reusable calibration file This makes the calibration process easier to document, compare, repeat, and adapt to new experiments. Typical Workflow **************** A typical RosettaX session follows these steps: #. launch the local application #. load or select a runtime profile #. import the relevant FCS data #. choose the fluorescence or scattering calibration workflow #. configure the detector, optical, and calibration parameters #. inspect histograms and identify calibration peaks #. fit the calibration model #. review the calibration result #. save the calibration for later reuse The exact procedure depends on the selected workflow, but the application is organized so that each step remains visible and traceable. Scientific Scope **************** RosettaX is intended for research and development workflows involving flow cytometry calibration. It focuses on calibration analysis and calibration file generation rather than instrument control. The application is especially relevant when experimental cytometry data, reference materials, optical parameters, detector settings, and reusable analysis profiles need to be managed together in a structured workflow. For scattering calibration, RosettaX is designed to connect measured cytometry signals with optical modeling concepts, including particle size, refractive index, collection geometry, detector configuration, and scattering intensity. This makes it suitable for workflows where optical interpretation and instrument calibration need to remain linked. Data Handling ************* RosettaX runs locally. The application does not upload FCS files, calibration profiles, calibration results, or generated configuration files to a remote service. Data remain on the machine running the software unless the user explicitly moves, uploads, or shares them outside the application. Project Status ************** RosettaX is currently in alpha development. The application is usable for development, testing, and iterative calibration workflow design. However, the public API, internal organization, and graphical workflows may still change. New users should expect active development and occasional breaking changes. Current development priorities include: * improving workflow robustness * expanding automated tests * improving documentation * adding reproducible examples * strengthening calibration validation * refining the graphical interface * improving packaging and release workflows Installation ************ PyPI ==== .. code-block:: bash pip install RosettaX Anaconda ======== .. code-block:: bash conda install -c martinpdes rosettax From Source =========== .. code-block:: bash git clone https://github.com/MartinPdeS/RosettaX.git cd RosettaX pip install -e . Usage ***** After installation, launch RosettaX with: .. code-block:: bash rosettax This starts the local graphical calibration application. Common CLI options: .. code-block:: bash rosettax --host 0.0.0.0 --port 8050 rosettax --no-browser rosettax --fcs-file-path /path/to/sample.fcs rosettax --version The application opens a browser based interface served from the local machine. It is intended for local calibration workflows and does not require a remote server. Documentation ************* The documentation is available here: `RosettaX documentation `_ The documentation is expected to evolve with the application. At this stage, the README provides the high level overview, while the full documentation contains more detailed usage information. Development *********** Install the project in editable mode with development dependencies: .. code-block:: bash pip install -e ".[dev,testing,documentation]" Build a local PyInstaller bundle with: .. code-block:: bash pip install -e ".[bundling]" pyinstaller rosettax.spec --clean This creates a standalone bundle under ``dist/rosettax`` for the current operating system. Cross platform bundles must still be built natively on each target operating system. Run the test suite with: .. code-block:: bash pytest Run tests with coverage using: .. code-block:: bash pytest --cov=RosettaX The repository includes configuration for testing, coverage, documentation, and continuous integration. These tools are intended to support reproducible development as the project matures. Contributing ************ Contributions are welcome. Useful contributions include: * bug reports * workflow suggestions * documentation improvements * test cases * calibration examples * user interface improvements * support for additional calibration workflows For substantial changes, please open an issue first so that the intended direction can be discussed before implementation. Citation ******** If you use RosettaX in scientific work, please cite the repository and the archived Zenodo release: .. code-block:: text Martin Poinsinet de Sivry-Houle. (2026). MartinPdeS/RosettaX: Pre-release (v0.0.10). Zenodo. https://doi.org/10.5281/zenodo.19846630 A formal citation file may be added in a future release. Contact ******* RosettaX is developed by `Martin Poinsinet de Sivry Houle `_. For collaboration, questions, or feedback: `martin.poinsinet.de.sivry@gmail.com `_ License ******* RosettaX is distributed under the GNU Affero General Public License v3.0 or later. See the repository ``LICENSE`` file for the full license text. Commercial licensing, support, validation, or custom deployment agreements may be discussed with the author. .. |zenodo| image:: https://zenodo.org/badge/1087203577.svg :target: https://doi.org/10.5281/zenodo.19846629 .. |python| image:: https://img.shields.io/pypi/pyversions/rosettax.svg :alt: Python :target: https://www.python.org/ .. |docs| image:: https://github.com/martinpdes/rosettax/actions/workflows/deploy_documentation.yml/badge.svg :target: https://martinpdes.github.io/RosettaX/ :alt: Documentation Status .. |PyPi| image:: https://badge.fury.io/py/RosettaX.svg :alt: PyPI version :target: https://pypi.org/project/RosettaX/ .. |PyPi_download| image:: https://img.shields.io/pypi/dm/rosettax.svg :alt: PyPI downloads :target: https://pypistats.org/packages/rosettax .. |ci/cd| image:: https://github.com/martinpdes/rosettax/actions/workflows/deploy_coverage.yml/badge.svg :target: https://martinpdes.github.io/RosettaX/actions :alt: Test Status .. |anaconda_download| image:: https://anaconda.org/martinpdes/rosettax/badges/downloads.svg :alt: Anaconda downloads :target: https://anaconda.org/martinpdes/rosettax .. |anaconda| image:: https://anaconda.org/martinpdes/rosettax/badges/version.svg :alt: Anaconda version :target: https://anaconda.org/martinpdes/rosettax .. |coverage| image:: https://raw.githubusercontent.com/MartinPdeS/RosettaX/python-coverage-comment-action-data/badge.svg :alt: Test coverage :target: https://htmlpreview.github.io/?https://github.com/MartinPdeS/RosettaX/blob/python-coverage-comment-action-data/htmlcov/index.html