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https://github.com/ilastik/ilastik-napari

ilastik plugin for napari
https://github.com/ilastik/ilastik-napari

ilastik napari-plugin

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ilastik plugin for napari

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README 

        
# ilastik-napari



[Napari][napari] plugin for interactive pixel classification.

Designed to be similar to the pixel classification workflow in [classic ilastik][ilastik].



## Installation



This plugin requires you to use a _conda_ environment. The environment manager conda comes in a few different forms.

If you haven't used conda before, you can find more information in the [conda user guide][conda-user-guide].

You 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.

When using mambaforge, the `mamba` command usually replaces the `conda` command one would otherwise use.



Once you have installed mambaforge, set up a conda environment with napari and the _fastfilters_ package, and then use pip to install _ilastik-napari_:

```shell

mamba create -y -c ilastik-forge -c conda-forge -n my-napari-env napari fastfilters

mamba activate my-napari-env

pip install ilastik-napari

```



Finally, run napari:

```shell

napari

```

That's it! You should be able to find the ilastik-napari plugin in the Plugins menu.



If you prefer to __install napari using pip__ instead of conda:

Make sure to install `napari[all]`.

Unless you want to [choose a PyQt implementation other than _PyQt5_][napari-pyqt], in which case you should leave out the `[all]` extra.



## Usage



As a prerequisite, make sure you understand the [napari basics][napari-quickstart].



1. Open your image, or use a sample in _File - Open Sample_.



   ![Use a sample image](https://ilastik.org/assets/ilastik-napari/image-sample.png "Use a sample image")



2. Activate the plugin in the _Plugins_ menu.



   ![Activate the plugin](https://ilastik.org/assets/ilastik-napari/activation.png "Activate the plugin")



3. In _layer list_, create a new _Labels_ layer.



   ![Labels layer](https://ilastik.org/assets/ilastik-napari/labels-layer.png "Labels layer")



4. In _layers control_, switch to the _paint_ action.



   ![Paint action](https://ilastik.org/assets/ilastik-napari/paint-action.png "Paint action")



5. Draw your background labels.



   ![Paint the background](https://ilastik.org/assets/ilastik-napari/draw-background.png "Paint the background")



6. Switch to a new label.



   ![Switch label](https://ilastik.org/assets/ilastik-napari/new-label.png "Switch label")



7. Draw your foreground labels.



   ![Paint cells](https://ilastik.org/assets/ilastik-napari/draw-cells.png "Paint cells")



8. Select output types you need, and click _Run_.



   ![Plugin interface](https://ilastik.org/assets/ilastik-napari/interface.png "Plugin interface")



9. The plugin will create one layer for each output type, which you save as normal napari layers.



   ![Example output](https://ilastik.org/assets/ilastik-napari/example.png "Example output")



## Development



Create a development environment:

```

mamba create -y -n ilastik-napari-dev -c ilastik-forge fastfilters setuptools-scm conda-build anaconda-client

conda activate napari-ilastik-dev

pip install -e .

```



Build conda package:

```

conda activate napari-ilastik-dev

mamba build -c ilastik-forge conda-recipe

anaconda upload /path/to/the/new/package.tar.bz2

```



Build wheel and sdist packages:

```

conda activate napari-ilastik-dev

pip install build twine

python -m build

python -m twine upload --repository testpypi dist/*

```



[napari]: https://napari.org/

[ilastik]: https://www.ilastik.org/

[conda-user-guide]: https://docs.conda.io/projects/conda/en/latest/user-guide/index.html

[miniconda]: https://docs.conda.io/en/latest/miniconda.html

[mambaforge]: https://github.com/conda-forge/miniforge#mambaforge

[napari-quickstart]: https://napari.org/tutorials/fundamentals/quick_start.html

[napari-pyqt]: https://napari.org/stable/plugins/best_practices.html#don-t-include-pyside2-or-pyqt5-in-your-plugin-s-dependencies