{"name":"napari-phasors","display_name":"Napari Phasors","visibility":"public","icon":"","categories":["Annotation","Segmentation","Acquisition"],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-phasors.get_reader","title":"Open data with Napari Phasors","python_name":"napari_phasors._reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-phasors.convallaria_FLIM_sample_data","title":"Load convallaria FLIM sample data","python_name":"napari_phasors._sample_data:convallaria_FLIM_sample_data","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-phasors.embryo_FLIM_sample_data","title":"Load FLUTE's FLIM Embryo sample data","python_name":"napari_phasors._sample_data:embryo_FLIM_sample_data","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-phasors.paramecium_HSI_sample_data","title":"Load Paramecium Hyperspectral Image sample data","python_name":"napari_phasors._sample_data:paramecium_HSI_sample_data","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-phasors.plot_phasor","title":"Plot Phasor","python_name":"napari_phasors:PlotterWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-phasors.write_ome_tiff","title":"Write OME-TIFF","python_name":"napari_phasors:write_ome_tiff","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-phasors.PhasorTransform","title":"Phasor Custom Import","python_name":"napari_phasors:PhasorTransform","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-phasors.WriterWidget","title":"Export Phasor","python_name":"napari_phasors:WriterWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-phasors.get_reader","filename_patterns":["*.fbd","*.ptu","*.lsm","*.ome.tif","*.tif","*.ome.tiff","*.tiff","*.sdt","*.czi","*.flif","*.lif","*.json","*.b&h","*.bh","*.bhz","*.bin","*.ifli","*.ref","*.r64"],"accepts_directories":false}],"writers":[{"command":"napari-phasors.write_ome_tiff","layer_types":["image*","labels*"],"filename_extensions":[],"display_name":"Export Phasor to OME-TIFF"}],"widgets":[{"command":"napari-phasors.PhasorTransform","display_name":"Phasor Custom Import","autogenerate":false},{"command":"napari-phasors.plot_phasor","display_name":"Phasor Plot","autogenerate":false},{"command":"napari-phasors.WriterWidget","display_name":"Export Phasor","autogenerate":false}],"sample_data":[{"command":"napari-phasors.convallaria_FLIM_sample_data","key":"unique_id.1","display_name":"Convallaria FLIM"},{"command":"napari-phasors.embryo_FLIM_sample_data","key":"unique_id.2","display_name":"FLUTE's FLIM Embryo sample data FLIM"},{"command":"napari-phasors.paramecium_HSI_sample_data","key":"unique_id.3","display_name":"Paramecium Hyperspectral Image"}],"themes":null,"menus":{"napari/file/io_utilities":[{"when":null,"group":null,"submenu":"io_phasors_submenu"}],"napari/layers/visualize":[{"when":null,"group":null,"submenu":"phasor_plot_submenu"}],"napari/layers/data":[{"when":null,"group":null,"submenu":"io_phasors_submenu"}],"phasor_plot_submenu":[{"command":"napari-phasors.plot_phasor","when":null,"group":null,"alt":null}],"io_phasors_submenu":[{"command":"napari-phasors.PhasorTransform","when":null,"group":null,"alt":null},{"command":"napari-phasors.WriterWidget","when":null,"group":null,"alt":null}]},"submenus":[{"id":"phasor_plot_submenu","label":"Phasors","icon":null},{"id":"io_phasors_submenu","label":"Phasors","icon":null}],"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-phasors","version":"0.6.1","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"A simple plugin to use phasor analysis","description":"# napari-phasors\n\n[![License BSD-3](https://img.shields.io/pypi/l/napari-phasors.svg?color=green)](https://github.com/napari-phasors/napari-phasors/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-phasors.svg?color=green)](https://pypi.org/project/napari-phasors)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-phasors.svg?color=green)](https://python.org)\n[![tests](https://github.com/napari-phasors/napari-phasors/actions/workflows/run-tests.yml/badge.svg?branch=main)](https://github.com/napari-phasors/napari-phasors/actions/workflows/run-tests.yml)\n[![codecov](https://codecov.io/gh/napari-phasors/napari-phasors/branch/main/graph/badge.svg)](https://codecov.io/gh/napari-phasors/napari-phasors)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-phasors)](https://napari-hub.org/plugins/napari-phasors)\n[![Documentation Status](https://readthedocs.org/projects/napari-phasors/badge/?version=latest)](https://napari-phasors.readthedocs.io/en/latest/?badge=latest)\n[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.14647626-blue.svg)](https://doi.org/10.5281/zenodo.14647626)\n\nA comprehensive plugin for phasor analysis in napari. Based on the\n[phasorpy](https://www.phasorpy.org/) library.\n\n----------------------------------\n\n## Documentation\n\nFull documentation, including step-by-step guides and the API reference, is\navailable at **[https://napari-phasors.readthedocs.io](https://napari-phasors.readthedocs.io)**.\n\n## Features\n\n- **Reading** a wide range of FLIM and hyperspectral file formats:\n    - **Raw data formats:**\n        - `.ptu`, `.fbd`, `.sdt`, `.lsm`, `.tif`, `.tiff`, `.czi`, `.flif`, `.bh`, `.b&h`, `.bhz`, `.lif`, `.bin`, `.json`\n    - **Processed data formats:**\n        - `.ome.tif`, `.ome.tiff`, `.r64`, `.ref`, `.ifli`, `.lif`, `.json`\n- **Phasor analysis** on multiple layers simultaneously, including support for stacking multiple raw data files\n- **Calibration** using reference images with known lifetimes\n- **Filtering** with median, wavelet, and automatic thresholding (Otsu, Li, Yen)\n- **Component analysis** for multi-component systems\n- **Phasor Mapping** — colormap apparent/normal lifetime, phasor phase, and phasor modulation per pixel, with interactive 1D histograms, statistics tables, and arc overlay tools\n- **FRET analysis** with donor trajectory visualization and multi-layer donor/background source selection\n- **Selections** via manual drawing, circular/polar/elliptical cursors, and automatic clustering\n- **Exporting** results as OME-TIF or CSV (multiple layers simultaneously)\n\n## Installation\n\nYou can install `napari-phasors` via [pip]. Follow these steps from a\nterminal.\n\nWe recommend using `miniforge` whenever possible. Click\n[here](https://conda-forge.org/download/) to choose the right download option for your OS.\n**If you do not use `miniforge`, but rather Anaconda or Miniconda, replace\nthe `mamba` term whenever you see it below with `conda`.**\n\nCreate a conda environment with napari by typing :\n\n    mamba create -y -n napari-phasors-env napari pyqt6 python=3.14 # or 3.12 or 3.13\n\nActivate the environment :\n\n    mamba activate napari-phasors-env\n\nInstall `napari-phasors` via [pip] :\n\n    pip install napari-phasors\n\nAlternatively, install latest development version with :\n\n    pip install git+https://github.com/napari-phasors/napari-phasors.git\n\n## Contributing\n\nContributions are very welcome. Tests can be run with [tox], please ensure\nthe coverage at least stays the same before you submit a pull request.\n\n### Pre-commit Hooks\n\nThis project uses [pre-commit](https://pre-commit.com/) to run **black**,\n**isort**, and **ruff** automatically on every commit. To set it up:\n\n```bash\npip install pre-commit\npre-commit install\n```\n\nFrom now on, every `git commit` will auto-format and lint your code before\nthe commit goes through. You can also run the hooks manually on all files:\n\n```bash\npre-commit run --all-files\n```\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n\"napari-phasors\" is free and open source software.\n\nPlease cite doi: [https://doi.org/10.5281/zenodo.14647626](https://doi.org/10.5281/zenodo.14647626)\nif napari-phasors contributes to a project that leads to a publication.\n\n## Issues\n\nIf you encounter any problems, please [file an issue] along with a detailed\ndescription.\n\n[napari]: https://github.com/napari/napari\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\n[@napari]: https://github.com/napari\n[MIT]: http://opensource.org/licenses/MIT\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n\n[file an issue]: https://github.com/napari-phasors/napari-phasors/issues\n\n[napari]: https://github.com/napari/napari\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":null,"author_email":"Bruno Pannunzio <bpannunzio@pasteur.edu.uy>, Marcelo Leomil Zoccoler <marzoccoler@gmail.com>, Joaquín Rivero <jrivero94@outlook.com>, Bruno Schuty <schutyb@schutyb.com>, Leonel Malacrida <lmalacrida@pasteur.edu.uy>","maintainer":null,"maintainer_email":null,"license":"Copyright (c) 2026, Marcelo L. Zoccoler, Bruno Pannunzio, Joaquín Rivero, Bruno Schuty\nand Leonel Malacrida. All rights reserved.\n\nRedistribution and use in source and binary forms, with or without\nmodification, are permitted provided that the following conditions are met:\n\n* Redistributions of source code must retain the above copyright notice, this\n  list of conditions and the following disclaimer.\n\n* Redistributions in binary form must reproduce the above copyright notice,\n  this list of conditions and the following disclaimer in the documentation\n  and/or other materials provided with the distribution.\n\n* Neither the name of copyright holder nor the names of its\n  contributors may be used to endorse or promote products derived from\n  this software without specific prior written permission.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\nAND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\nIMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\nDISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE\nFOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL\nDAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR\nSERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER\nCAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\nOR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE\nOF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n","classifier":["Development Status :: 2 - Pre-Alpha","Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: BSD License","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.12","Programming Language :: Python :: 3.13","Programming Language :: Python :: 3.14","Topic :: Scientific/Engineering :: Image Processing","Topic :: Scientific/Engineering :: Visualization"],"requires_dist":["phasorpy>=0.8","qtpy","biaplotter>=0.4.2","fbdfile","sdtfile","ptufile","tifffile","pandas","pyqt6","pawflim","scipy","czifile","lfdfiles","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt; extra == \"testing\"","napari; extra == \"testing\"","qtpy; extra == \"testing\"","scikit-image; extra == \"testing\"","biaplotter>=0.4.2; extra == \"testing\"","pyqt6; extra == \"testing\"","pandas; extra == \"testing\"","black; extra == \"testing\"","isort; extra == \"testing\"","ruff; extra == \"testing\"","pre-commit; extra == \"testing\"","phasorpy>=0.8; extra == \"testing\"","tifffile; extra == \"testing\"","fbdfile; extra == \"testing\"","sdtfile; extra == \"testing\"","ptufile; extra == \"testing\"","pawflim; extra == \"testing\"","scipy; extra == \"testing\"","czifile; extra == \"testing\"","lfdfiles; extra == \"testing\""],"requires_python":">=3.12","requires_external":null,"project_url":["Homepage, https://github.com/napari-phasors/napari-phasors","Bug Tracker, https://github.com/napari-phasors/napari-phasors/issues","Documentation, https://github.com/napari-phasors/napari-phasors#README.md","Source Code, https://github.com/napari-phasors/napari-phasors","User Support, https://github.com/napari-phasors/napari-phasors/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}