{"name":"napari-k2-WaveBreaker","display_name":"K2 Wave Breaker","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-k2-WaveBreaker.AutocorrelationTool","title":"Initiate AutocorrelationTool","python_name":"napari_k2_wavebreaker._widget:AutocorrelationTool","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-k2-WaveBreaker.AutocorrelationTool","display_name":"napari-k2-WaveBreaker","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-k2-WaveBreaker","version":"0.2.5","dynamic":null,"platform":null,"supported_platform":null,"summary":"later","description":"# napari-k2-WaveBreaker\n\n[![License BSD-3](https://img.shields.io/pypi/l/napari-k2-WaveBreaker.svg?color=green)](https://github.com/SamKVs/napari-k2-WaveBreaker/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-k2-WaveBreaker.svg?color=green)](https://pypi.org/project/napari-k2-WaveBreaker)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-k2-WaveBreaker.svg?color=green)](https://python.org)\n[![tests](https://github.com/SamKVs/napari-k2-WaveBreaker/workflows/tests/badge.svg)](https://github.com/SamKVs/napari-k2-WaveBreaker/actions)\n[![codecov](https://codecov.io/gh/SamKVs/napari-k2-WaveBreaker/branch/main/graph/badge.svg)](https://codecov.io/gh/SamKVs/napari-k2-WaveBreaker)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-k2-WaveBreaker)](https://napari-hub.org/plugins/napari-k2-WaveBreaker)\n\n<div>\n    <img src=\"static/Logo.png\">\n</div>\n<h2>About this plugin</h2>\n\n\nThis Napari plugin was designed for the detection and quantification of periodic biological structures.\nAs this plugin has not been uploaded to napari-hub as of this moment it **cannot be installed on a pre-compiled, bundled \nversion of Napari**. Therefore Napari will need to be installed as a python package \n(<a href=\"https://napari.org/stable/tutorials/fundamentals/installation.html\">more info about Napari installation</a>). \nFurther information about the installation and licensing of the plugin can be found below. A detailed manual on the usage of the plugin can be found below as well. \n\n**If you have any questions or need help with the installation, please do hesitate to use the issues tab.**\n\n**In case you need a tutorial on how to use the plugin, please use the \"tutorial request\" label in the issues tab to reach out to me:**\n\n\n<h3>Guide</h3>\n\nActin is the most abundant protein in eukaryotic cells. As it is part of the cytoskeleton its function is essential for \nthe maintenance of the cell's morphological structure. In neurons, it was only recently that researchers started paying \nattention to the peculiar subcellular organization and localization of actin. First focussing on the dendritic spines, \nlater expanding to the axon.  \n\nThe axon initial segment (AIS) is defined as the most proximal 30-60 µm of the axon and is known for its sturdy \nactin-betaIV cytoskeletal structure which is known to facilitate the densely packed ion channels, regulatory and\nscaffolding proteins on the membrane. The recent popularity of superresolution microscopy techniques like STORM and STED\nhas made the study of the localization of these proteins relatively easy and straightforward.\n\n&nbsp;\n<p align=\"center\">\n    <img src=\"static/Figure 1.svg\" width=\"100%\">\n</p>\n&nbsp;\n\nBecause of this property of the AIS many ion channels are localized either perpendicular to the actin rings\nor attached to a scaffolding protein called Ankyrin G which is localized in between two actin rings. This results in ion \nchannels like the Kv 1.1 (displayed below) appearing similar to superresolution images of actin.\n\n&nbsp;\n<div align=\"center\">\n    <img src=\"static/AIS.png\" width=\"100%\" style=\"mix-blend-mode: screen\">\n    <i align=\"center\" style=\"font-size: 9px\"> Example image of a rat hippocampal neuron AIS immunostained for Kv1.1.\nImage made on a Zeiss AxioImager Z1 equipped with a STEDYCON scanhead detector for confocal and super-resolution imaging,\nfitted with 4 APDs. Post-acquisition, image was deconvolved using Huygens Deconvolution Software  </i>\n</div>\n\n&nbsp;\n\nThis plugin was designed to detect and quantify the distance and the goodness of periodicity between cellular periodic structures. \nAdditionally, it can be used to detect and quantify the periodicity shift between two periodic stuctures.\n\n&nbsp;\n\n\n\n<a href=\"static/WaveBreaker User Manual.pdf\">\n    <img src=\"static/UM BUT.svg\" width=\"50%\">  \n</a>\n\n<a href=\"static/TEMPLATE AUTOCORRELATION 0.17-0.21 (x10).xlsx\">\n    <img src=\"static/AC EX BUT.svg\" width=\"50%\">  \n</a>\n\n<a href=\"static/TEMPLATE CROSSCORRELATION (x15).xlsx\">\n    <img src=\"static/CC EX BUT.svg\" width=\"50%\">  \n</a>\n\n<a href=\"static/Post-processing.py\">\n    <img src=\"static/EX%20PY.svg\" width=\"50%\">\n</a>\n\n\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/index.html\n-->\n\n## Installation\n\nYou can install `napari-k2-WaveBreaker` via [pip]:\n\n    pip install napari-k2-WaveBreaker\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\"napari-k2-autocorrelation\" is free and open source software\n\n## Issues\n\nIf you encounter any problems, please file an issue along with a detailed description or reach out to me.\n\n[napari]: https://github.com/napari/napari\n\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\n\n[@napari]: https://github.com/napari\n\n[MIT]: http://opensource.org/licenses/MIT\n\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\n\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\n\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\n\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\n\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n\n[napari]: https://github.com/napari/napari\n\n[tox]: https://tox.readthedocs.io/en/latest/\n\n[pip]: https://pypi.org/project/pip/\n\n[PyPI]: https://pypi.org/\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":"Sam Kris Vanspauwen","author_email":"sam.vanspauwen.dk@gmail.com","maintainer":null,"maintainer_email":null,"license":"BSD-3-Clause","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 :: 3.8","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Topic :: Software Development :: Testing"],"requires_dist":["numpy","magicgui","qtpy","plotly","pandas","scikit-learn","opencv-python","matplotlib","pathvalidate","seaborn","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":null,"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}