{"name":"napari-kics","display_name":"napari-kics","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-kics.KaryotypeWidget","title":"KaryotypeWidget","python_name":"napari_kics.widgets:KaryotypeWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-kics.load_sample_data","title":"load_sample_data","python_name":"napari_kics.widget_loader:load_sample_data","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-kics.KaryotypeWidget","display_name":"KaryotypeWidget","autogenerate":false}],"sample_data":[{"command":"napari-kics.load_sample_data","key":"sample","display_name":"sample"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-kics","version":"0.0.3rc6","dynamic":null,"platform":null,"supported_platform":null,"summary":"A plugin to estimate chromosome sizes from karyotype images.","description":"# napari-kics\n\n![napari-kics](https://github.com/mpicbg-csbd/napari-kics/raw/main/docs/banner.png?sanitize=true&raw=true)\n\n[![standard-readme compliant](https://img.shields.io/badge/readme%20style-standard-brightgreen.svg)](https://github.com/RichardLitt/standard-readme)\n[![License](https://img.shields.io/pypi/l/napari-kics.svg?color=green)](./LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-kics.svg?color=green)](https://pypi.org/project/napari-kics)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-kics.svg?color=green)](https://python.org)\n[![Python package](https://github.com/mpicbg-csbd/napari-kics/actions/workflows/python-package.yml/badge.svg)](https://github.com/mpicbg-csbd/napari-kics/actions/workflows/python-package.yml)\n\n\n> A plugin to estimate chromosome sizes from karyotype images.\n\n<small>*This [napari] plugin was generated with [Cookiecutter] using with [@napari]'s [cookiecutter-napari-plugin] template.*</small>\n\n\n## Table of Contents\n\n- Install\n- Usage\n- Example\n- Citation\n- Maintainer\n- Contributing\n- License\n\n\n## Install\n\nYou can install `napari-kics` via [pip]:\n\n```sh\npip install napari-kics\n```\n\nThis will install all required dependencies as well. We recommend installing it in a virtual environment, e.g. using [conda]:\n\n```sh\nconda create -n kics python\nconda activate kics\npip install napari-kics\n```\n\nWe recommend using [mamba] as a faster alternative to conda.\n\n\n## Usage\n\n1. Launch Napari via command line (`napari`).\n2. Activate the plugin via menu `Plugins -> napari-kics: Karyotype Widget`.\n3. Select file via `File -> Open File`.\n4. Follow instructions in the panel on the right.\n\nYou may use the interactive analysis plots directly via command line:\n\n```sh\nkaryotype-analysis-plots\n```\n\n\n## Example\n\n1. Launch Napari via command line (`napari`).\n2. Activate the plugin via menu `Plugins -> napari-kics: Karyotype Widget`.\n3. Select file via `File -> Open Sample -> napari-kics: sample`.\n4. Follow instructions in the panel on the right.\n\nTry out the interactive analysis plots directly via command line:\n\n```sh\nkaryotype-analysis-plots --example\n```\n\n\n## Citation\n\n> Arne Ludwig, Alexandr Dibrov, Gene Myers, Martin Pippel.\n> Estimating chromosome sizes from karyotype images enables validation of\n> *de novo* assemblies. To be published.\n\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n\"napari-kics\" is free and open source software\n\n\n## Issues\n\nIf you encounter any problems, please [file an issue] along with a detailed description.\n\n\n## Contributing\n\nContributions are very welcome. Please [file a pull request] with your\ncontribution.\n\nYou can setup a local development environment for `napari-kics` via [pip]:\n\n```sh\ngit clone https://github.com/mpicbg-csbd/napari-kics.git\ncd napari-kics\npip install -e .\n```\n\n\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n[@napari]: https://github.com/napari\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\n[napari]: https://github.com/napari/napari\n[tox]: https://tox.readthedocs.io/en/latest/\n[conda]: https://www.anaconda.com/products/distribution\n[mamba]: https://github.com/mamba-org/mamba\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n[file an issue]: https://github.com/mpicbg-csbd/napari-kics/issues\n[file a pull request]: https://github.com/mpicbg-csbd/napari-kics/pulls\n\n## Overview\nhttps://user-images.githubusercontent.com/17703905/139654249-685703b5-2196-4a73-a036-d40d578ebcdf.mp4\n\n\n\n\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":"Alexandr Dibrov","author_email":"dibrov@mpi-cbg.de","maintainer":null,"maintainer_email":null,"license":"BSD-3-Clause","classifier":["Development Status :: 2 - Pre-Alpha","Intended Audience :: Developers","Framework :: napari","Topic :: Scientific/Engineering :: Image Processing","Topic :: Scientific/Engineering :: Information Analysis","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3.7","Programming Language :: Python :: 3.8","Programming Language :: Python :: 3.9","Operating System :: OS Independent","License :: OSI Approved :: BSD License"],"requires_dist":["napari-plugin-engine (>=0.1.4)","numpy","napari[all]","scikit-image","pandas","pulp","pyqtgraph"],"requires_python":">=3.7","requires_external":null,"project_url":null,"provides_extra":null,"provides_dist":null,"obsoletes_dist":null},"npe1_shim":true}