{"name":"napari-basicpy","display_name":"BaSiCpy shadow correction in napari","visibility":"public","icon":"","categories":[],"schema_version":"0.1.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-basicpy.shadow_correction","title":"Apply BaSiC Shadow Correction","python_name":"napari_basicpy._widget:BasicWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-basicpy.sample_data_random","title":"Provide artifical sample data","python_name":"napari_basicpy._sample_data:make_sample_data_random","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-basicpy.sample_data_cell_culture","title":"Provide artifical example","python_name":"napari_basicpy._sample_data:make_sample_data_cell_culture","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-basicpy.sample_data_timelapse_brightfield","title":"Provide artifical example","python_name":"napari_basicpy._sample_data:make_sample_data_timelapse_brightfield","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-basicpy.sample_data_timelapse_nanog","title":"Provide artifical example","python_name":"napari_basicpy._sample_data:make_sample_data_timelapse_nanog","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-basicpy.sample_data_timelapse_pu1","title":"Provide artifical example","python_name":"napari_basicpy._sample_data:make_sample_data_timelapse_pu1","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-basicpy.sample_data_wsi_brain","title":"Provide artifical example","python_name":"napari_basicpy._sample_data:make_sample_data_wsi_brain","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-basicpy.shadow_correction","display_name":"BaSiC Shadow Correction","autogenerate":false}],"sample_data":[{"command":"napari-basicpy.sample_data_random","key":"sample_data_random","display_name":"Random"},{"command":"napari-basicpy.sample_data_cell_culture","key":"sample_data_cell_culture","display_name":"Cell Culture"},{"command":"napari-basicpy.sample_data_timelapse_brightfield","key":"sample_data_timelapse_brightfield","display_name":"Timelapse Brightfield"},{"command":"napari-basicpy.sample_data_timelapse_nanog","key":"sample_data_timelapse_nanog","display_name":"Timelapse Nanog"},{"command":"napari-basicpy.sample_data_timelapse_pu1","key":"sample_data_timelapse_pu1","display_name":"Timelapse Pu1"},{"command":"napari-basicpy.sample_data_wsi_brain","key":"sample_data_wsi_brain","display_name":"WSI Brain"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-basicpy","version":"0.0.3","dynamic":null,"platform":null,"supported_platform":null,"summary":"BaSiCPy illumination correction for napari","description":"# napari-basicpy\n\n[![License](https://img.shields.io/pypi/l/napari-basicpy.svg?color=green)](https://github.com/tdmorello/napari-basicpy/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-basicpy.svg?color=green)](https://pypi.org/project/napari-basicpy)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-basicpy.svg?color=green)](https://python.org)\n[![tests](https://github.com/tdmorello/napari-basicpy/workflows/tests/badge.svg)](https://github.com/tdmorello/napari-basicpy/actions)\n[![codecov](https://codecov.io/gh/tdmorello/napari-basicpy/branch/main/graph/badge.svg)](https://codecov.io/gh/tdmorello/napari-basicpy)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-basicpy)](https://napari-hub.org/plugins/napari-basicpy)\n\nBaSiCPy illumination correction for [napari]\n\n## Example\n\n![example](resources/example.gif)\n\n----------------------------------\n\n## Installation\n\n### Recommended Installation Method\n\nWe highly recommend using a `conda` virtual environment to install and operate this plugin.\n\nTo use Python 3.9, for example:\n\n    conda create -n basicpy -c conda-forge python=3.9 napari pyqt && \\\n    conda activate basicpy && \\\n    pip install napari-basicpy\n\nFor further instructions on installing `napari`, visit their [install guide](https://napari.org/stable/tutorials/fundamentals/installation).\n\n---\n\n**IMPORTANT NOTE FOR APPLE SILICON AND WINDOWS USERS:**\n\nIf the above instructions fail with Apple silicon (e.g., M1/M2 chip) or Windows, you may need to install the `jax` and `jaxlib` following the instruction [here](https://github.com/peng-lab/BaSiCPy#installation).\n\n---\n\n### Other Installation Methods\n\nYou can also install `napari-basicpy` via [pip]:\n\n    pip install napari-basicpy\n\n\nTo install latest development version:\n\n    pip install git+https://github.com/peng-lab/napari-basicpy.git\n\nor\n\n    pip install git+https://github.com/tdmorello/napari-basicpy.git\n\n## Usage\n\n### General Usage\n\nThis plugin expects a stack of tiles as input. Mosaic images should be deconstructed into their tiled components before processing. Individual tiles should be two-dimensional.\n\nThere are many options to customize the performance of BaSiCPy. Please refer to the BaSiCPy documentation on parameters [here](https://basicpy.readthedocs.io/en/latest/api.html#basicpy.basicpy.BaSiC) for details.\n\n### Batch Processing\n\nComing soon...\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-basicpy\" is free and open source software\n\n## Issues\n\nIf you encounter any problems, please [file an issue](https://github.com/peng-lab/napari-basicpy/issues) along with a detailed description.\n\n[napari]: https://github.com/napari/napari\n[@napari]: https://github.com/napari\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n\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/tdmorello/napari-basicpy","download_url":null,"author":"Tim Morello","author_email":"tdmorello@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 :: Scientific/Engineering :: Image Processing"],"requires_dist":["basicpy >=1.2.0","numpy","qtpy","black ; extra == 'dev'","flake8 ; extra == 'dev'","flake8-black ; extra == 'dev'","flake8-docstrings ; extra == 'dev'","flake8-isort ; extra == 'dev'","isort ; extra == 'dev'","mypy ; extra == 'dev'","pre-commit ; extra == 'dev'","pydocstyle ; extra == 'dev'","pytest ; extra == 'dev'","pytest-qt ; extra == 'dev'","tox ; extra == 'testing'","pytest ; extra == 'testing'","pytest-cov ; extra == 'testing'","pytest-qt ; extra == 'testing'","napari ; extra == 'testing'","tox ; extra == 'tox-testing'","pytest ; extra == 'tox-testing'","pytest-cov ; extra == 'tox-testing'","pytest-qt ; extra == 'tox-testing'","napari ; extra == 'tox-testing'","pyqt5 ; extra == 'tox-testing'"],"requires_python":">=3.8","requires_external":null,"project_url":["Bug Tracker, https://github.com/peng-lab/napari-basicpy/issues","Documentation, https://github.com/peng-lab/napari-basicpy#README.md","Source Code, https://github.com/peng-lab/napari-basicpy","User Support, https://github.com/peng-lab/napari-basicpy/issues"],"provides_extra":["dev","testing","tox-testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}