Orthanc for Whole-Slide Imaging
===============================


General Information
-------------------

This repository contains the source code of the official tools to
introduce support of whole-slide microscopic imaging (WSI) in
Orthanc. It is made of three separate components:

(a) A command-line tool called "Dicomizer" that converts whole-slide
    images to DICOM, according to Supplement 145. 

    The input images of the Dicomizer can be either formatted as
    standard hierarchical TIFF images, or as proprietary formats for
    digital pathology. In the latter case, OpenSlide is used to decode
    the input images.

(b) An Orthanc plugin that extends Orthanc Explorer with a Web viewer
    of whole-slide images.

(c) A command-line tool called "DicomToTiff" that converts some
    whole-slide image stored in an Orthanc server, into a standard
    hierarchical TIFF file. This tool can be used to export DICOM
    images to any post-processing framework.



Dependencies
------------

The whole-slide imaging framework is notably based upon the following
projects:

* Orthanc, a lightweight Vendor Neutral Archive (DICOM server):
  http://www.orthanc-server.com/

* OpenSlide, a simple interface to read whole-slide images encoded
  using proprietary file formats:
  http://openslide.org/

* OpenLayers, a framework to put a dynamic map in any web page:
  https://openlayers.org/

* OpenJPEG, an open-source JPEG 2000 codec:
  http://www.openjpeg.org/



Installation and usage
----------------------

Build instructions are similar to that of Orthanc:
https://orthanc.uclouvain.be/book/faq/compiling.html

Usage details are available as part of the Orthanc Book:
https://orthanc.uclouvain.be/book/plugins/wsi.html

The two command-line tools can be found in folder "Applications".
They come with an extensive "--help" option.

The Web viewer plugin can be found in folder "ViewerPlugin". It has no
specific option, so you just have to make your "Plugins" configuration
option of Orthanc point to the shared library containing the plugin:
https://orthanc.chu.ulg.ac.be/book/users/configuration.html



Contributing
------------

Instructions for contributing to the Orthanc project are included in
the Orthanc Book:
https://orthanc.uclouvain.be/book/developers/repositories.html



Licensing
---------

The WSI toolbox for Orthanc is licensed under the AGPL license.

We also kindly ask scientific works and clinical studies that make
use of Orthanc to cite Orthanc in their associated publications.
Similarly, we ask open-source and closed-source products that make
use of Orthanc to warn us about this use. You can cite our work
using the following BibTeX entry:

@Article{Jodogne2018,
  author="Jodogne, S{\'e}bastien",
  title="The {O}rthanc Ecosystem for Medical Imaging",
  journal="Journal of Digital Imaging",
  year="2018",
  month="May",
  day="03",
  issn="1618-727X",
  doi="10.1007/s10278-018-0082-y",
  url="https://doi.org/10.1007/s10278-018-0082-y"
}