{"name":"napari-ndev","display_name":"nDev","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-ndev.get_reader","title":"Get BioIO Reader","python_name":"napari_ndev._napari_reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-ndev.make_ndev_container","title":"Make nDev App","python_name":"napari_ndev.widgets._ndev_container:nDevContainer","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-ndev.make_utilities_container","title":"Make Image Utilities","python_name":"napari_ndev.widgets._utilities_container:UtilitiesContainer","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-ndev.make_workflow_container","title":"Make Batch 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napari-ndev\n\n[](https://github.com/TimMonko/napari-ndev/raw/main/LICENSE)\n[](https://pypi.org/project/napari-ndev)\n[](https://pypistats.org/packages/napari-ndev)\n[](https://python.org)\n[](https://github.com/TimMonko/napari-ndev/actions)\n[](https://codecov.io/gh/TimMonko/napari-ndev)\n[](https://napari-hub.org/plugins/napari-ndev)\n\n[](https://doi.org/10.5281/zenodo.14787853)\n\n![\"logo\"](\"./resources/nDev-logo-large.png\")
\n\nA collection of widgets intended to serve any person seeking to process microscopy images from start to finish, *with no coding necessary*. `napari-ndev` was designed to address the **gap between the napari viewer and batch python scripting**.\n\n* Accepts **diverse image formats**, dimensionality, file size, and maintains key metadata.\n* Allows **advanced, arbitrary image processing** workflows to be used by novices.\n* **User-friendly** sparse annotation and batch training of **machine learning classifiers**.\n* Flexible label measurements, parsing of metadata, and summarization for **easily readable datasets**.\n* Designed for ease of use, modification, and reproducibility.\n\n## [Check out the Docs to learn more!](https://ndev-kit.github.io)\n\n### See the [poster presented at BINA 2024](https://ndev-kit.github.io/BINA_poster/) for an overview of the plugins in action\n\n### Try out the [Virtual I2K 2024 Workshop](https://ndev-kit.github.io/tutorial/00_setup/) for an interactive tutorial\n\n## Installation\n\n**napari-ndev** is a pure Python package, and can be installed with [pip]:\n\n```bash\npip install napari-ndev\n```\n\nIf napari is currently not installed in your environment, you will also need to include a QtPy backend:\n\n```bash\npip install napari-ndev[qtpy-backend]\n```\n\nThe easiest way to get started with **napari-ndev** is to install all the optional dependencies (see note below) with:\n\n```bash\npip install napari-ndev[all]\n```\n\n----------------------------------\n\n### Optional Libraries\n\n**napari-ndev** is most useful when interacting with some other napari plugins (e.g. napari-assistant) and can read additional filetypes. A few extra BSD3 compatible napari-plugins may be installed with [pip]:\n\n```bash\npip install napari-ndev[extras]\n```\n\n**napari-ndev** can optionally use GPL-3 licensed libraries to enhance its functionality, but are not required. If you choose to install and use these optional dependencies, you must comply with the GPL-3 license terms. The main functional improvement is from some `bioio` libraries to support extra image formats, including `czi` and `lif` files. These libraries can be installed with [pip]:\n\n```bash\npip install napari-ndev[gpl-extras]\n```\n\nIn addition, you may need to install specific [`bioio` readers](https://github.com/bioio-devs/bioio) to support your specific image, such as `bioio-czi` and `bioio-lif` (included in `[gpl-extras]`) or `bioio-bioformats`.\n\n### Development Libraries\n\nFor development use the `[dev]` optional libraries to verify your changes, which includes the `[docs]` and `[testing]` optional groups. However, the Github-CI will test pull requests with `[testing]` only.\n\n----------------------------------\n\nThe wide breadth of this plugin's scope is only made possible by the amazing libraries and plugins from the python and napari community, especially [Robert Haase](https://github.com/haesleinhuepf).\n\nThis [napari] plugin was generated with [Cookiecutter] using [napari]'s [cookiecutter-napari-plugin] template.\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-ndev\" is free and open source software.\n\nSome optional libraries can be installed to add functionality to `napari-ndev`, including some that may be more restrictive than this package's BSD-3-Clause.\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\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":null,"author_email":"Tim Monko ","maintainer":null,"maintainer_email":null,"license":"BSD-3-Clause","classifier":["Development Status :: 3 - Alpha","Framework :: napari","Intended Audience :: Education","Intended Audience :: Science/Research","License :: OSI Approved :: BSD License","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Topic :: Scientific/Engineering :: Image Processing","Topic :: Scientific/Engineering :: Visualization","Topic :: Software Development :: User Interfaces","Topic :: Software Development :: Libraries :: Python Modules","Topic :: Utilities"],"requires_dist":["numpy<2.0,>=1.26","siphash24>=1.6","magicgui>=0.8.3","magic-class","napari[optional]>=0.4.19","apoc","pyclesperanto-prototype","pyclesperanto","dask","napari-workflows","napari-pyclesperanto-assistant","napari-segment-blobs-and-things-with-membranes","natsort","seaborn","stackview","tifffile<2025.2.18,>=2023.3.15","scikit-image>=0.18.0","ngff-zarr>0.10.0","zarr<3","bioio>=1.1.0","bioio-base==1.0.4","bioio-imageio>=1","bioio-tifffile>=1","bioio-ome-tiff>=1","bioio-ome-zarr>=1","bioio-nd2>=1","matplotlib-scalebar>=0.8.1","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","tox; extra == \"testing\"","tox-uv; extra == \"testing\"","pytest-qt; extra == \"testing\"","napari[all]; extra == \"testing\"","pyqt5; extra == \"testing\"","bioio-czi>=1.0.1; extra == \"testing\"","napari-ndev[extras]; extra == \"testing\"","mkdocs; extra == \"docs\"","mkdocs-autorefs; extra == \"docs\"","mkdocs-material; extra == \"docs\"","mkdocstrings; extra == \"docs\"","mkdocstrings-python; extra == \"docs\"","mkdocs-jupyter; extra == \"docs\"","mkdocs-pdf; extra == \"docs\"","mkdocs-spellcheck[all]; extra == \"docs\"","mkdocs-literate-nav; extra == \"docs\"","mkdocs-table-reader-plugin; extra == \"docs\"","black; extra == \"docs\"","ruff; extra == \"dev\"","pre-commit; extra == \"dev\"","napari-ndev[testing]; extra == \"dev\"","napari-ndev[docs]; extra == \"dev\"","napari-ndev[pyqt6]; extra == \"qtpy-backend\"","napari[pyqt6]; extra == \"pyqt6\"","napari[pyqt5]; extra == \"pyqt5\"","napari[pyside]; extra == \"pyside\"","napari-simpleitk-image-processing; extra == \"extras\"","bioio-czi>=1.0.1; extra == \"gpl-extras\"","bioio-lif>=1; extra == \"gpl-extras\"","napari-ndev[qtpy-backend]; extra == \"all\"","napari-ndev[extras]; extra == \"all\"","napari-ndev[gpl_extras]; extra == \"all\""],"requires_python":">=3.9","requires_external":null,"project_url":["Bug Tracker, https://github.com/TimMonko/napari-ndev/issues","Documentation, https://ndev-kit.github.io/","Source Code, https://github.com/TimMonko/napari-ndev"],"provides_extra":["testing","docs","dev","qtpy-backend","pyqt6","pyqt5","pyside","extras","gpl-extras","all"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}