{"name":"napari-phasors","display_name":"Napari Phasors","visibility":"public","icon":null,"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.export_layer_as_csv","title":"Export Layer to CSV","python_name":"napari_phasors._writer:export_layer_as_csv","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-phasors.export_layer_as_image","title":"Export Layer as Image","python_name":"napari_phasors._writer:export_layer_as_image","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},{"id":"napari-phasors.BatchAnalysisWidget","title":"Batch Analysis","python_name":"napari_phasors:BatchAnalysisWidget","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":[".ome.tif"],"display_name":"Export Phasor to OME-TIFF"},{"command":"napari-phasors.export_layer_as_csv","layer_types":["image*","labels*"],"filename_extensions":[".csv"],"display_name":"Export Layer to CSV"},{"command":"napari-phasors.export_layer_as_image","layer_types":["image*","labels*"],"filename_extensions":[".png",".jpg",".jpeg",".tif"],"display_name":"Export Layer as Image"}],"widgets":[{"command":"napari-phasors.plot_phasor","display_name":"Phasor Plot","autogenerate":false},{"command":"napari-phasors.PhasorTransform","display_name":"Phasor Custom Import","autogenerate":false},{"command":"napari-phasors.WriterWidget","display_name":"Export Phasor","autogenerate":false},{"command":"napari-phasors.BatchAnalysisWidget","display_name":"Batch Analysis","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},{"command":"napari-phasors.BatchAnalysisWidget","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":"0.7.0","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"A plugin for performing phasor analysis of fluorescence microscopy data","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[![Conda Version](https://img.shields.io/conda/vn/conda-forge/napari-phasors.svg)](https://anaconda.org/conda-forge/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 (binlet pawFLIM), 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- **Batch Analysis** — apply the same reading and analysis pipeline (calibration, filtering, masking, component analysis, phasor mapping, FRET, selections) to every file in a folder and export the results headlessly\n\n## Installation\n\nThere are several ways to install napari-phasors:\n\n### Easiest: napari's plugin manager\n\nIf you already have [napari](https://napari.org) installed, go to\n**Plugins → Install/Uninstall Plugins...**, search for **napari-phasors**,\nand click **Install**.\n\n### Standalone installer (no Python required)\n\nPre-built installers for Windows (`.exe`), macOS\n(`.dmg`), and Linux (`.sh`) are available on the\n[latest release](https://github.com/napari-phasors/napari-phasors/releases/latest)\npage. Download and run — no Python installation\nneeded. Installers are ~350–470 MB and bundle\neverything required.\n\n### Using conda (conda-forge)\n\nnapari-phasors is available on the\n[conda-forge](https://anaconda.org/conda-forge/napari-phasors) channel,\nwhich installs napari, Qt, and every dependency in one step. We recommend\nusing [miniforge](https://conda-forge.org/download/). If you use Anaconda or\nMiniconda, replace `mamba` with `conda`.\n\n    mamba create -y -n napari-phasors-env -c conda-forge napari-phasors\n\nActivate the environment:\n\n    conda activate napari-phasors-env\n    napari\n\n### Using conda + pip\n\nAlternatively, create a plain conda environment and install napari-phasors\nfrom PyPI (useful to get a release before it lands on conda-forge):\n\n    mamba create -y -n napari-phasors-env napari pyqt6 python=3.14 # or 3.12, 3.13\n\nActivate the environment :\n\n    conda activate napari-phasors-env\n    pip install napari-phasors\n\n### Development version\n\n    pip install git+https://github.com/napari-phasors/napari-phasors.git\n\n## Contributing\n\nContributions are very welcome. See the [contributing\nguide](CONTRIBUTING.md) for how to set up a development environment, run\nthe tests, and submit a pull request.\n\nThis project adheres to a [Code of Conduct](CODE_OF_CONDUCT.md); by\nparticipating, you are expected to uphold it.\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, Bruno Pannunzio, Marcelo L. Zoccoler, 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>=0.10","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\"","pytest-xdist; extra == \"testing\"","pytest-timeout; 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>=0.10; 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}