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README.rst

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WSI Superpixel Guided Labeling
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WSI Superpixel Guided Labeling is a `Girder 3 <https://github.com/girder>`_ plugin designed to be used in conjunction with `HistomicsUI <https://github.com/DigitalSlideArchive/HistomicsUI>`_ and `HistomicsTK <https://github.com/DigitalSlideArchive/HistomicsTK>`_ to facilitate active learning on whole slide images.
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WSI Superpixel Guided Labeling is a `Girder 5 <https://github.com/girder>`_ plugin designed to be used in conjunction with `HistomicsUI <https://github.com/DigitalSlideArchive/HistomicsUI>`_ and `HistomicsTK <https://github.com/DigitalSlideArchive/HistomicsTK>`_ to facilitate active learning on whole slide images.
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This plugin leverages the output of certain HistomicsTK/SlicerCLI jobs to allow end users to label superpixel regions of whole slide images to be used as input for machine learning algorithms.
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Installation
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------------
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The recommended way to use this plugin is by adding it to the Digital Slide Archive's ``docker-compose`` deployment. First, check out both this repository and ``digital_slide_archive`` from Github, if you do not yet have a running instance of the Digital Slide Archive.
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The recommended way to use this plugin is by adding it to the Digital Slide Archive's ``docker-compose`` deployment. First, check out both this repository and `digital_slide_archive <https://github.com/DigitalSlideArchive/digital_slide_archive>`_ from Github, if you do not yet have a running instance of the Digital Slide Archive.
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If you don't already use a provisioning yaml file as part of your DSA deployment, you'll want to create one, e.g. ``provision.local.yaml``. Make sure this file contains the following: ::
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pip:
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- /opt/wsi-superpixel-guided-labeling
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rebuild-client: True
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- /opt/wsi-superpixel-guided-labeling
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shell:
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- cd /opt/wsi-superpixel-guided-labeling/wsi_superpixel_guided_labeling/web_client && npm install && npm run build
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resources:
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- model: collection
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name: Tasks

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