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ilastik plugin for napari

Project description


Napari plugin for interactive pixel classification. Designed to be similar to the pixel classification workflow in classic ilastik.


Currently, this plugin requires you to use a conda environment. If you haven't used conda before, please read conda user guide.

Instad of the default miniconda installation, we highly recommend to use mambaforge. It has better default settings, and the mamba command, which is an (almost) drop-in replacement for conda.

After installing mambaforge, create a new environment with this plugin installed:

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

Finally, launch napari in the new environment.

conda activate my-napari-env

Napari Hub and pip

You can also install this plugin via Napari Hub or pip. However, in this case you must do that inside a conda environment with the fastfilters package installed:

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


As a prerequisite, make sure you understand the napari basics.

  1. Open your image, or use a sample in File - Open Sample.

    Use a sample image

  2. Activate the plugin in the Plugins menu.

    Activate the plugin

  3. In layer list, create a new Labels layer.

    Labels layer

  4. In layers control, switch to the paint action.

    Paint action

  5. Draw your background labels.

    Paint the background

  6. Switch to a new label.

    Switch label

  7. Draw your foreground labels.

    Paint cells

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

    Plugin interface

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

    Example output


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/*

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