Mercurial > hg > orthanc-book
changeset 797:4d431ad58521
cytomine
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Sun, 12 Dec 2021 15:25:43 +0100 |
parents | 7078e6e35580 |
children | 80b9ceeb4045 |
files | Sphinx/source/images/2021-12-12-Cytomine.png Sphinx/source/images/CytomineKeys.png Sphinx/source/plugins/wsi.rst |
diffstat | 3 files changed, 52 insertions(+), 1 deletions(-) [+] |
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--- a/Sphinx/source/plugins/wsi.rst Sat Dec 11 15:15:59 2021 +0100 +++ b/Sphinx/source/plugins/wsi.rst Sun Dec 12 15:25:43 2021 +0100 @@ -86,7 +86,7 @@ Usage of the plugin ------------------- -.. highlight:: json +.. highlight:: text You of course first have to :ref:`install Orthanc <compiling>`. Once Orthanc is installed, you must change the :ref:`configuration file @@ -294,6 +294,57 @@ parameters of your Orthanc server. +Interface with Cytomine +----------------------- + +`Cytomine <https://cytomine.be/>`__ is an "*open-source rich internet +application for collaborative analysis of multi-gigapixel images.*" +Starting with release 1.1 of the whole-slide imaging framework for +Orthanc, it is possible to exchange digital pathology images back and +forth between Orthanc and Cytomine according to the following +workflow: + +.. image:: ../images/2021-12-12-Cytomine.png + :align: center + :width: 500px + +| + +As can be seen, ``OrthancWSIDicomizer`` imports the source image from +Cytomine using its REST API, then puts the converted DICOM instances +onto Orthanc using its REST API. Here is a minimalist sample call to +the ``OrthancWSIDicomizer`` command-line tool to convert an image from +a Cytomine server onto an Orthanc server listening on +``localhost:8042`` with default parameters :: + + $ ./OrthancWSIDicomizer --cytomine-url=http://XXX --cytomine-image=325 \ + --cytomine-public-key=YYY --cytomine-private-key=ZZZ \ + --threads=4 --pyramid=1 --username=orthanc --password=orthanc --verbose + +The ``--cytomine-image`` parameter corresponds to the ID of the `Image +Instance <https://doc.uliege.cytomine.org/dev-guide/api/reference>`__ +of interest. This ID can easily be retrieved from the Web interface of +Cytomine: + +.. image:: ../images/Cytomine.png + :align: center + :width: 600px + +| + +The ``--cytomine-public-key`` and ``--cytomine-private-key`` +parameters grant access to the REST API of Cytomine, and can be found +in the parameters of your account using the Web interface of Cytomine: + +.. image:: ../images/CytomineKeys.png + :align: center + :width: 600px + +| + + + + REST API --------