{"name":"napari-bacseg","display_name":"BacSeg","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-bacseg.make_qwidget","title":"Make BacSeg QWidget","python_name":"napari_bacseg._widget:BacSeg","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-bacseg.make_qwidget","display_name":"BacSeg","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-bacseg","version":"1.0.18","dynamic":null,"platform":null,"supported_platform":null,"summary":"Bacterial segmentation and analysis platform than can inport/export files in multiple formats. Integrating many tools such as Cellpose, ColiCoords, Oufti/MicrobeTracker.","description":"# napari-BacSeg\n\n[![License BSD-3](https://img.shields.io/pypi/l/napari-bacseg.svg?color=green)](https://github.com/piedrro/napari-bacseg/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-bacseg.svg?color=green)](https://pypi.org/project/napari-bacseg)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-bacseg.svg?color=green)](https://python.org)\n[![tests](https://github.com/piedrro/napari-bacseg/workflows/tests/badge.svg)](https://github.com/piedrro/napari-bacseg/actions)\n[![codecov](https://codecov.io/gh/piedrro/napari-bacseg/branch/main/graph/badge.svg)](https://codecov.io/gh/piedrro/napari-bacseg)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-bacseg)](https://napari-hub.org/plugins/napari-bacseg)\n\nBacterial segmentation and analysis platform than can inport/export files in multiple formats. Integrating many tools such as Cellpose, ColiCoords, Oufti/MicrobeTracker.\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/stable/plugins/index.html\n-->\n\n## Installing BacSeg\n\nCreate a virtual environment and then activate it:\n\n    conda create –-name napari-bacseg python==3.9\n    conda activate napari-bacseg\n\nInstall `napari-bacseg` via [pip]:\n\n    pip install napari-bacseg\n\nLaunch Napari:\n\n    Napari\n\nSelect **napari-bacseg** from the **Plugins** dropdown menu\n\n\n## Installing BacSeg From GitHub\n\n    conda create –-name napari-bacseg python==3.9\n    conda activate napari-bacseg\n    conda install -c anaconda git\n    conda update --all\n\n    pip install napari[all]\n\n    pip install git+https://github.com/piedrro/napari-bacseg.git\n\n## Updating BacSeg From Github\nOnce you have installed the plugin, you can update the plugin by running the following commands:\n\n    pip install git+https://github.com/piedrro/napari-bacseg.git\n\n## GPU Installation\n Once you have installed the plugin, you can install the GPU version of the plugin by running the following commands:\n\n    pip uninstall torch torchvision torchaudio -y\n    pip3 install torch torchvision --index-url https://download.pytorch.org/whl/cu118\n\nIf the latest CUDA versions don't work, try an older version like cuda 11.3:\n\n    pip uninstall torch torchvision torchaudio -y\n    pip3 install torch torchvision --index-url https://download.pytorch.org/whl/cu113\n\n\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\"napari-bacseg\" 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/piedrro/napari-bacseg/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":null,"download_url":null,"author":null,"author_email":"Piers Turner <piers.turner@physics.ox.ac.uk>","maintainer":null,"maintainer_email":null,"license":null,"classifier":["Framework :: napari","Environment :: Plugins","License :: OSI Approved :: BSD License","Programming Language :: Python :: 3.9","Operating System :: OS Independent"],"requires_dist":["napari[all] >=0.4.19","torch","cellpose >=3.0.1","opencv-python","picassosr ==0.6.5","numpy","pyqt5","pyqt6","qtpy","scipy","natsort","tqdm","imagecodecs","tifffile","pandas","mat4py","glob2","matplotlib","scikit-image","roifile","openpyxl","shapely","colicoords","psutil","xmltodict","astropy","tiler","imageio-ffmpeg","aicspylibczi","czifile","omnipose","h5py","tox ; extra == 'testing'","pytest ; extra == 'testing'","pytest-cov ; extra == 'testing'","pytest-qt ; extra == 'testing'","napari ; extra == 'testing'","pyqt5 ; extra == 'testing'"],"requires_python":">=3.9","requires_external":null,"project_url":["Homepage, https://github.com/piedrro/napari-bacseg","Bug Tracker, https://github.com/piedrro/napari-bacseg/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}