Metadata-Version: 2.1
Name: histomicsui
Version: 1.0.1.dev6
Summary: Organize, visualize, and analyze histology images.
Home-page: https://github.com/DigitalSlideArchive/histomicsui
Author: Kitware, Inc.
Author-email: kitware@kitware.com
License: Apache Software License 2.0
Description: =======================================
        HistomicsUI |build-status| |codecov-io|
        =======================================
        
        Organize, visualize, and analyze histology images.
        
        `HistomicsUI`_ organizes and manages whole slide image (WSI) files using Girder_.  It has a dedicated interface to select WSI, add annotations manually, and to run analysis and algorithms on all or parts of images.
        
        Girder provides authentication, access control, and diverse storage options, including using local file systems and Amazon S2.  WSI images are read and displayed via the large_image_ module.  Algorithms are containerized using Docker_ and are run using the slicer_cli_web_ Girder plugin.  These can be run on multiple worker machines via `Girder Worker`_ and celery_.
        
        A set of common algorithms are provided by HistomicsTK_.
        
        Installation
        ------------
        
        Linux
        =====
        
        In linux with Python 3.6 or newer:
        
        Prerequisites:
        
        - MongoDB must be installed and running.
        - An appropriate version of Python must be installed.
        
        .. code-block:: bash
        
          pip install histomicsui --find-links https://girder.github.io/large_image_wheels
          girder build
          girder serve
        
        To use Girder Worker:
        
        .. code-block:: bash
        
          pip install girder_slicer_cli_web[worker]
          GW_DIRECT_PATHS=true girder_worker -l info -Ofair --prefetch-multiplier=1
        
        The first time you start HistomicsUI, you'll also need to configure Girder with at least one user and one assetstore (see the Girder_ documentation).  Additionally, it is recommended that you install the HistomicsTK_ algorithms.  This can be done going to the Admin Console, Plugins, Slicer CLI Web settings.  Set a default task upload folder, then import the `dsarchive/histomicstk:latest` docker image.
        
        Reference Deployment
        ====================
        
        The standard deployment of HistomicsUI is the `Digital Slide Archive`_.  The associated repository has tools for readily installing via Docker, VirtualBox, or shell scripts on Ubuntu.
        
        Development
        ===========
        
        The most convenient way to develop on HistomicsUI is to use the `devops scripts from the Digial Slide Archive <https://github.com/DigitalSlideArchive/digital_slide_archive/tree/master/devops>`_. 
        
        Funding
        -------
        This work is funded in part by the NIH grant U24-CA194362-01_.
        
        .. _HistomicsUI: https://github.com/DigitalSlideArchive/HistomicsUI
        .. _Docker: https://www.docker.com/
        .. _Kitware: https://www.kitware.com/
        .. _U24-CA194362-01: http://grantome.com/grant/NIH/U24-CA194362-01
        
        .. _Girder: http://girder.readthedocs.io/en/latest/
        .. _Girder Worker: https://girder-worker.readthedocs.io/en/latest/
        .. _large_image: https://github.com/girder/large_image
        .. _slicer_cli_web: https://github.com/girder/slicer_cli_web
        .. _slicer execution model: https://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation
        .. _Discourse forum: https://discourse.girder.org/c/histomicstk
        .. _Gitter Chatroom: https://gitter.im/DigitalSlideArchive/HistomicsTK?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
        .. _celery: http://www.celeryproject.org/
        .. _HistomicsTK: https://github.com/DigitalSlideArchive/HistomicsTK
        .. _Digital Slide Archive: https://github.com/DigitalSlideArchive/digital_slide_archive
        
        .. |build-status| image:: https://circleci.com/gh/DigitalSlideArchive/HistomicsUI.svg?style=svg
            :target: https://circleci.com/gh/DigitalSlideArchive/HistomicsUI
            :alt: Build Status
        
        .. |codecov-io| image:: https://codecov.io/github/DigitalSlideArchive/HistomicsUI/coverage.svg?branch=master
            :target: https://codecov.io/github/DigitalSlideArchive/HistomicsUI?branch=master
            :alt: codecov.io
        
        
        
Keywords: girder-plugin,histomicsui
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Python: >=3.6
Description-Content-Type: text/x-rst
