{"id":13738013,"url":"https://github.com/ilastik/ilastik-napari","last_synced_at":"2025-04-30T21:04:27.503Z","repository":{"id":139653138,"uuid":"362848859","full_name":"ilastik/ilastik-napari","owner":"ilastik","description":"ilastik plugin for napari","archived":false,"fork":false,"pushed_at":"2024-04-17T11:28:37.000Z","size":2706,"stargazers_count":13,"open_issues_count":5,"forks_count":2,"subscribers_count":19,"default_branch":"main","last_synced_at":"2024-11-15T06:33:04.618Z","etag":null,"topics":["ilastik","napari-plugin"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ilastik.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-04-29T14:40:18.000Z","updated_at":"2024-08-02T13:25:03.000Z","dependencies_parsed_at":"2024-11-21T03:31:43.144Z","dependency_job_id":null,"html_url":"https://github.com/ilastik/ilastik-napari","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ilastik%2Filastik-napari","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ilastik%2Filastik-napari/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ilastik%2Filastik-napari/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ilastik%2Filastik-napari/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ilastik","download_url":"https://codeload.github.com/ilastik/ilastik-napari/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":227223709,"owners_count":17750386,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["ilastik","napari-plugin"],"created_at":"2024-08-03T03:02:08.904Z","updated_at":"2024-11-29T22:15:45.091Z","avatar_url":"https://github.com/ilastik.png","language":"Python","funding_links":[],"categories":["Python"],"sub_categories":[],"readme":"# ilastik-napari\n\n[Napari][napari] plugin for interactive pixel classification.\nDesigned to be similar to the pixel classification workflow in [classic ilastik][ilastik].\n\n## Installation\n\nThis plugin requires you to use a _conda_ environment. The environment manager conda comes in a few different forms.\nIf you haven't used conda before, you can find more information in the [conda user guide][conda-user-guide].\nYou can use whichever variant you prefer, as the resulting environment should be the same, but we recommend the [_mambaforge_][mambaforge] variant as it is usually the fastest.\nWhen using mambaforge, the `mamba` command usually replaces the `conda` command one would otherwise use.\n\nOnce you have installed mambaforge, set up a conda environment with napari and the _fastfilters_ package, and then use pip to install _ilastik-napari_:\n```shell\nmamba create -y -c ilastik-forge -c conda-forge -n my-napari-env napari fastfilters\nmamba activate my-napari-env\npip install ilastik-napari\n```\n\nFinally, run napari:\n```shell\nnapari\n```\nThat's it! You should be able to find the ilastik-napari plugin in the Plugins menu.\n\nIf you prefer to __install napari using pip__ instead of conda:\nMake sure to install `napari[all]`.\nUnless you want to [choose a PyQt implementation other than _PyQt5_][napari-pyqt], in which case you should leave out the `[all]` extra.\n\n## Usage\n\nAs a prerequisite, make sure you understand the [napari basics][napari-quickstart].\n\n1. Open your image, or use a sample in _File - Open Sample_.\n\n   ![Use a sample image](https://ilastik.org/assets/ilastik-napari/image-sample.png \"Use a sample image\")\n\n2. Activate the plugin in the _Plugins_ menu.\n\n   ![Activate the plugin](https://ilastik.org/assets/ilastik-napari/activation.png \"Activate the plugin\")\n\n3. In _layer list_, create a new _Labels_ layer.\n\n   ![Labels layer](https://ilastik.org/assets/ilastik-napari/labels-layer.png \"Labels layer\")\n\n4. In _layers control_, switch to the _paint_ action.\n\n   ![Paint action](https://ilastik.org/assets/ilastik-napari/paint-action.png \"Paint action\")\n\n5. Draw your background labels.\n\n   ![Paint the background](https://ilastik.org/assets/ilastik-napari/draw-background.png \"Paint the background\")\n\n6. Switch to a new label.\n\n   ![Switch label](https://ilastik.org/assets/ilastik-napari/new-label.png \"Switch label\")\n\n7. Draw your foreground labels.\n\n   ![Paint cells](https://ilastik.org/assets/ilastik-napari/draw-cells.png \"Paint cells\")\n\n8. Select output types you need, and click _Run_.\n\n   ![Plugin interface](https://ilastik.org/assets/ilastik-napari/interface.png \"Plugin interface\")\n\n9. The plugin will create one layer for each output type, which you save as normal napari layers.\n\n   ![Example output](https://ilastik.org/assets/ilastik-napari/example.png \"Example output\")\n\n## Development\n\nCreate a development environment:\n```\nmamba create -y -n ilastik-napari-dev -c ilastik-forge fastfilters setuptools-scm conda-build anaconda-client\nconda activate napari-ilastik-dev\npip install -e .\n```\n\nBuild conda package:\n```\nconda activate napari-ilastik-dev\nmamba build -c ilastik-forge conda-recipe\nanaconda upload /path/to/the/new/package.tar.bz2\n```\n\nBuild wheel and sdist packages:\n```\nconda activate napari-ilastik-dev\npip install build twine\npython -m build\npython -m twine upload --repository testpypi dist/*\n```\n\n[napari]: https://napari.org/\n[ilastik]: https://www.ilastik.org/\n[conda-user-guide]: https://docs.conda.io/projects/conda/en/latest/user-guide/index.html\n[miniconda]: https://docs.conda.io/en/latest/miniconda.html\n[mambaforge]: https://github.com/conda-forge/miniforge#mambaforge\n[napari-quickstart]: https://napari.org/tutorials/fundamentals/quick_start.html\n[napari-pyqt]: https://napari.org/stable/plugins/best_practices.html#don-t-include-pyside2-or-pyqt5-in-your-plugin-s-dependencies\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Filastik%2Filastik-napari","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Filastik%2Filastik-napari","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Filastik%2Filastik-napari/lists"}