{"name":"arcosPx-napari","display_name":"arcosPx","visibility":"public","icon":"","categories":["Segmentation","Image Processing"],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"arcosPx-napari.remove_background","title":"Remove Background","python_name":"arcospx._widget:remove_background","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"arcosPx-napari.track_events","title":"Track Events","python_name":"arcospx._widget:track_events","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"arcosPx-napari.simple_thresholder","title":"Thresholding","python_name":"arcospx._widget:thresholder","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"arcosPx-napari.sample_data_circles","title":"Circles","python_name":"arcospx.cellular_automaton:sim_circles","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"arcosPx-napari.sample_data_target","title":"Target Pattern","python_name":"arcospx.cellular_automaton:sim_target_pattern","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"arcosPx-napari.sample_data_directional","title":"Directional Waves","python_name":"arcospx.cellular_automaton:sim_directional","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"arcosPx-napari.sample_data_chaotic","title":"Chaotic Waves","python_name":"arcospx.cellular_automaton:sim_chaotic","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"arcosPx-napari.remove_background","display_name":"Remove Background","autogenerate":false},{"command":"arcosPx-napari.simple_thresholder","display_name":"Thresholding","autogenerate":false},{"command":"arcosPx-napari.track_events","display_name":"Track Events","autogenerate":false}],"sample_data":[{"command":"arcosPx-napari.sample_data_circles","key":"circles","display_name":"Circles (can take a few seconds to load)"},{"command":"arcosPx-napari.sample_data_target","key":"target","display_name":"Target Pattern (can take a few seconds to load)"},{"command":"arcosPx-napari.sample_data_directional","key":"directional","display_name":"Directional Waves (can take a few seconds to load)"},{"command":"arcosPx-napari.sample_data_chaotic","key":"chaotic","display_name":"Chaotic Waves (can take a few seconds to load)"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"arcosPx-napari","version":"0.1.4","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"A plugin to track spatio-temporal correlations in images","description":"# arcosPx-napari\n\n[![License BSD-3](https://img.shields.io/pypi/l/arcosPx-napari.svg?color=green)](https://github.com/pertzlab/arcosPx-napari/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/arcosPx-napari.svg?color=green)](https://pypi.org/project/arcosPx-napari)\n[![Python Version](https://img.shields.io/pypi/pyversions/arcosPx-napari.svg?color=green)](https://python.org)\n[![tests](https://github.com/pertzlab/arcosPx-napari/workflows/tests/badge.svg)](https://github.com/pertzlab/arcosPx-napari/actions)\n[![codecov](https://codecov.io/gh/pertzlab/arcosPx-napari/branch/main/graph/badge.svg)](https://codecov.io/gh/pertzlab/arcosPx-napari)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/arcosPx-napari)](https://napari-hub.org/plugins/arcosPx-napari)\n\n\n## Introduction\n\nThis repository contains a dedicated ARCOS.px plugin for the [napari](https://napari.org/stable/) image viewer. It tracks spatio-temporal correlations in images as described in a publication of Grädel et al. _Tracking Coordinated Cellular Dynamics in Time-Lapse Microscopy with ARCOS.px_ ([link](https://doi.org/10.1101/2025.03.14.643386)).\n\n<p align=\"center\">\n  <img alt=\"ARCOS.px logo\" src=\"misc/ARCOS-px-logo.png\" width=\"45%\">\n&nbsp; &nbsp; &nbsp; &nbsp;\n  <img alt=\"CDL logo\" src=\"misc/cellular-dynamics-lab-logo2.png\" width=\"45%\"> \n</p>\n\nARCOS.px is a computational method to identify and track clusters of correlated cell signaling in time-lapse microscopy images. \nIt is the latest addition to the [ARCOS ecosystem](https://arcos.gitbook.io/home) developed in the [Cellular Dynamics Lab](https://www.pertzlab.net) at the University of Bern.\n\n![ARCOS.px napari plugin screenshot](misc/napari-plugin.png)\n\n\n<!--\nDon't miss the full getting started guide to set up your new package:\nhttps://github.com/napari/cookiecutter-napari-plugin#getting-started\n\nand review the napari docs for plugin developers:\nhttps://napari.org/stable/plugins/index.html\n-->\n\n## Example tracking\n\nActin polymerization waves in REF52 fibroblasts treated with 50 ng/mL PDGF, 24h before imaging.\n\n![Polymerisation wave in REF52 cells](misc/tracked_waves_rgb_wLabels_F1-181.gif)\n\n\n## Installation\n\nYou can install `arcosPx-napari` via [pip]:\n\n    pip install arcosPx-napari\n\n\n\nTo install latest development version :\n\n    pip install git+https://github.com/pertzlab/arcosPx-napari.git\n\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## License\n\nDistributed under the terms of the [BSD-3] license,\n\"arcosPx-napari\" 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[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/pertzlab/arcosPx-napari/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":"https://github.com/pertzlab/arcosPx-napari","download_url":null,"author":"Benjamin Grädel","author_email":"benjamin.graedel@unibe.ch","maintainer":null,"maintainer_email":null,"license":"BSD-3-Clause","classifier":["Development Status :: 2 - Pre-Alpha","Framework :: napari","Intended Audience :: Developers","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","magicgui","qtpy","arcos4py>=0.3.0","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt; extra == \"testing\"","napari; extra == \"testing\"","pyqt5; extra == \"testing\""],"requires_python":">=3.10","requires_external":null,"project_url":["Bug Tracker, https://github.com/pertzlab/arcosPx-napari/issues","Documentation, https://github.com/pertzlab/arcosPx-napari#README.md","Source Code, https://github.com/pertzlab/arcosPx-napari","User Support, https://github.com/pertzlab/arcosPx-napari/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}