{"name":"napari-bleach-correct","display_name":"Bleaching Correction","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-bleach-correct.make_sample_data","title":"Load sample data from napari Bleach Correction","python_name":"napari_bleach_correct._sample_data:make_sample_data","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-bleach-correct.main_widget","title":"Bleaching Correction","python_name":"napari_bleach_correct._dock_widget:MainWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-bleach-correct.main_widget","display_name":"Bleaching Correction","autogenerate":false}],"sample_data":[{"command":"napari-bleach-correct.make_sample_data","key":"unique_id.1","display_name":"Bleaching Mito"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-bleach-correct","version":"0.0.1","dynamic":null,"platform":null,"supported_platform":null,"summary":"A napari plugin to correct time-lapse images for photobleaching.","description":"# napari-bleach-correct\n\n[![License](https://img.shields.io/github/license/marx-alex/napari-bleach-correct)](https://github.com/marx-alex/napari-bleach-correct)\n[![PyPI](https://img.shields.io/pypi/v/napari-bleach-correct.svg?color=green)](https://pypi.org/project/napari-bleach-correct)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-bleach-correct.svg?color=green)](https://python.org)\n[![tests](https://github.com/marx-alex/napari-bleach-correct/workflows/tests/badge.svg)](https://github.com/marx-alex/napari-bleach-correct/actions)\n[![codecov](https://codecov.io/gh/marx-alex/napari-bleach-correct/branch/main/graph/badge.svg)](https://codecov.io/gh/marx-alex/napari-bleach-correct)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-bleach-correct)](https://napari-hub.org/plugins/napari-bleach-correct)\n\n## Bleach correction for napari\n\nThis plugin is a python implementation of three different algorithms for bleach correction and can be used \nto correct time-lapse images that lose intensity due to photobleaching. The implementation is based on the ImageJ \nplugin Bleach Corrector by Miura et al. All methods work with 2D and 3D time series.\n\nNapari Bleach correction is easy to use:\n\n![Demo](./data/demo.gif)\n\n### Ratio Method\n\nThis is the simplest method. Every pixel in a frame is multiplied by the ratio from the mean intensity of the \nfirst frame to that of the *i-th* frame.\n\nAssumptions:\n* the mean intensity is constant through the time-lapse\n* the background fluorescence is the same for every pixel and frame\n\nParameters:\n* Background Intensity: Must be estimated\n\n### Exponential Curve Fitting\n\nDrift estimation of fluorescence signal by fitting the mean intensity to an exponential curve.\nThe image is corrected by the decay in the normalized exponential function.\n\nAssumptions:\n* time intervals between frames are equal\n\nParameters:\n* Exponential Curve: Bleaching can be modelled as a mono- or bi-exponential curve\n\n### Histogram Matching\n\nBleaching correction by matching histograms to a reference image.\nThe correct pixel values can be calculated by the cumulative distribution function\nof a frame and its reference frame. This method introduced by Miura et al.\n\nParameters:\n* Reference Frame: Match the frame's histogram with the first our neighbor frame \n\n**The Histogram Matching method using the neighbor frame as reference is a good start to correct bleaching.**\nAll methods are described in detail in Miura et al.\n\n## References\n\n* Miura K. [Bleach correction ImageJ plugin for compensating the photobleaching of time-lapse sequences.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7871415/) F1000Res. 2020 Dec 21;9:1494. doi: 10.12688/f1000research.27171.1\n* [Documentation of the ImageJ plugin](https://wiki.cmci.info/downloads/bleach_corrector)\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\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/plugins/stable/index.html\n-->\n\n## Installation\n\nYou can install `napari-bleach-correct` via [pip]:\n\n    pip install napari-bleach-correct\n\n\n\nTo install latest development version :\n\n    pip install git+https://github.com/marx-alex/napari-bleach-correct.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 [MIT] license,\n\"napari-bleach-correct\" 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/marx-alex/napari-bleach-correct/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/marx-alex/napari-bleach-correct","download_url":null,"author":"Alexander Marx","author_email":"a.marx95@gmx.de","maintainer":null,"maintainer_email":null,"license":"MIT","classifier":["Development Status :: 2 - Pre-Alpha","Intended Audience :: Developers","Framework :: napari","Topic :: Software Development :: Testing","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3.8","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Operating System :: OS Independent","License :: OSI Approved :: MIT License"],"requires_dist":["numpy","magicgui","qtpy","scikit-image","scipy","pyqtgraph","tox ; extra == 'testing'","pytest ; extra == 'testing'","pytest-cov ; extra == 'testing'","pytest-qt ; extra == 'testing'","napari ; extra == 'testing'","pyqt5 ; extra == 'testing'"],"requires_python":">=3.8","requires_external":null,"project_url":["Bug Tracker, https://github.com/marx-alex/napari-bleach-correct/issues","Documentation, https://github.com/marx-alex/napari-bleach-correct#README.md","Source Code, https://github.com/marx-alex/napari-bleach-correct","User Support, https://github.com/marx-alex/napari-bleach-correct/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}