{"name":"napari-relax","display_name":"ReLAX","visibility":"public","icon":null,"categories":[],"schema_version":"0.3.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-relax.get_reader","title":"LineageTree reader","python_name":"napari_relax._reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-relax.get_writer","title":"LineageTree writer","python_name":"napari_relax._writer:write_single_image","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-relax.lineage_tree_analysis","title":"Lineage tree analysis","python_name":"napari_relax._widgets:LineageTreeAnalysisWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-relax.cross_embryo_comparison","title":"Cross Lineagetree comparison","python_name":"napari_relax._widgets:CrossEmbryoComparisonWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-relax.load_demo","title":"Load data","python_name":"napari_relax.demo_data:load_demo","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-relax.load_celegans","title":"Load C. elegans","python_name":"napari_relax.demo_data:load_celegans","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-relax.get_reader","filename_patterns":["*.lT","*.lt","*.LT","*.mastodon","*.xml","*.bmf"],"accepts_directories":false}],"writers":[{"command":"napari-relax.get_writer","layer_types":["points"],"filename_extensions":[".lt",".lT",".LT"],"display_name":""}],"widgets":[{"command":"napari-relax.lineage_tree_analysis","display_name":"Lineage tree analysis","autogenerate":false},{"command":"napari-relax.cross_embryo_comparison","display_name":"Cross Lineagetree comparison","autogenerate":false}],"sample_data":[{"command":"napari-relax.load_demo","key":"unique_id.6","display_name":"demo lineageTree dataset"},{"command":"napari-relax.load_celegans","key":"unique_id.7","display_name":"C. elegans dataset"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configurations":{"progeny_canvas":{"title":"Attributes of canvas","properties":{"node_size":{"schema_":"https://json-schema.org/draft/2020-12/schema","title":"Size of Nodes","type":"number","default":1,"description":null,"enum":null,"minimum":null,"maximum":null,"exclusive_maximum":null,"exclusive_minimum":null,"multiple_of":null,"max_length":null,"min_length":0},"edge_size":{"schema_":"https://json-schema.org/draft/2020-12/schema","title":"Size of Edges","type":"number","default":1,"description":null,"enum":null,"minimum":null,"maximum":null,"exclusive_maximum":null,"exclusive_minimum":null,"multiple_of":null,"max_length":null,"min_length":0},"font_size":{"schema_":"https://json-schema.org/draft/2020-12/schema","title":"Font size","type":"integer","default":8,"description":null,"enum":null,"minimum":null,"maximum":null,"exclusive_maximum":null,"exclusive_minimum":null,"multiple_of":null,"max_length":null,"min_length":0}}}}},"package_metadata":{"metadata_version":"2.4","name":"napari-relax","version":"0.1.0","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"A plugin to visualise and manipulate cell lineage trees","description":"# napari-relax\n\n[![License BSD-3](https://img.shields.io/pypi/l/napari-relax.svg?color=green)](https://github.com/guignardlab/napari-relax/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-relax.svg?color=green)](https://pypi.org/project/napari-relax)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-relax.svg?color=green)](https://python.org)\n[![tests](https://github.com/guignardlab/napari-relax/workflows/tests/badge.svg)](https://github.com/guignardlab/napari-relax/actions)\n[![codecov](https://codecov.io/gh/guignardlab/napari-relax/branch/main/graph/badge.svg)](https://codecov.io/gh/guignardlab/napari-relax)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-relax)](https://napari-hub.org/plugins/napari-relax)\n[![npe2](https://img.shields.io/badge/plugin-npe2-blue?link=https://napari.org/stable/plugins/index.html)](https://napari.org/stable/plugins/index.html)\n[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border-purple.json)](https://github.com/copier-org/copier)\n\n**ReLAX** (Reconstructed Lineage Analysis & eXploration) is a [napari] plugin to visualise and compare cell lineage trees. It gives [LineageTree] datasets a graphical interface, so no programming is needed.\n\n**Documentation: [guignardlab.github.io/napari-relax](https://guignardlab.github.io/napari-relax/)**\n\n## Features\n\n- **Explore** tracking datasets in the napari viewer and in an interactive Lineage Viewer, side by side.\n- **Relabel** lineages and save them as `.lT` files.\n- **Recolor** cells by clone or by any numeric attribute of the dataset.\n- **Compare** lineages and sublineages with unordered tree edit distances, shown as an interactive clustermap.\n- **Compare across datasets**, even with different time resolutions.\n\nReLAX opens `.lT`, MaMuT and ASTEC `.xml`, Mastodon and `.bmf` files, and comes with two demo datasets under **File > Open Sample > ReLAX**.\n\n## Installation\n\nReLAX requires Python 3.10 or newer and napari 0.9 or newer. You can install `napari-relax` via [pip]:\n\n```\npip install napari-relax\n```\n\nIf napari is not already installed, you can install `napari-relax` with napari and Qt via:\n\n```\npip install \"napari-relax[all]\"\n```\n\nTo install the latest development version:\n\n```\npip install git+https://github.com/guignardlab/napari-relax.git\n```\n\nThen open **Plugins > Lineage tree analysis** or **Plugins > Cross Lineagetree comparison** in napari. The [Quick Start](https://guignardlab.github.io/napari-relax/quick_start/q_start/) walks through a first session.\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\nThe documentation is built with [MkDocs] from the `docs/` folder and published automatically when `main` changes. To preview it locally:\n\n```\npip install -e \".[docs]\"\nmkdocs serve\n```\n\nSee the [developer documentation](https://guignardlab.github.io/napari-relax/developer/architecture/) for an overview of the code.\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n\"napari-relax\" is free and open source software\n\n## Issues\n\nIf you encounter any problems, please [file an issue] along with a detailed description.\n\n----------------------------------\n\nThis [napari] plugin was generated with [copier] using the [napari-plugin-template].\n\n[napari]: https://github.com/napari/napari\n[LineageTree]: https://guignardlab.github.io/LineageTree/\n[copier]: https://copier.readthedocs.io/en/stable/\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[napari-plugin-template]: https://github.com/napari/napari-plugin-template\n[MkDocs]: https://www.mkdocs.org/\n[file an issue]: https://github.com/guignardlab/napari-relax/issues\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":"Giannis Liaskas, Jules Vanaret","author_email":"Léo Guignard <leo.guignard@univ-amu.fr>","maintainer":null,"maintainer_email":null,"license":"Copyright (c) 2025, Léo Guignard\nAll 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 :: 3.10","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Programming Language :: Python :: 3.13","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy","matplotlib","lineagetree<=4.0.0","napari[all]; extra == \"all\"","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt; extra == \"testing\"","napari[qt]; extra == \"testing\"","mkdocs<2,>=1.6; extra == \"docs\"","mkdocs-material<10,>=9.7; extra == \"docs\"","mkdocstrings[python]>=1.0; extra == \"docs\""],"requires_python":">=3.10","requires_external":null,"project_url":["Bug Tracker, https://github.com/guignardlab/napari-relax/issues","Documentation, https://guignardlab.github.io/napari-relax/","Source Code, https://github.com/guignardlab/napari-relax","User Support, https://github.com/guignardlab/napari-relax/issues"],"provides_extra":["all","testing","docs"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}