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cytomine
author Sebastien Jodogne <s.jodogne@gmail.com>
date Sun, 12 Dec 2021 15:25:43 +0100
parents 525d59a7c198
children 02121f3c7e65
comparison
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796:7078e6e35580 797:4d431ad58521
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86 Usage of the plugin 86 Usage of the plugin
87 ------------------- 87 -------------------
88 88
89 .. highlight:: json 89 .. highlight:: text
90 90
91 You of course first have to :ref:`install Orthanc <compiling>`. Once 91 You of course first have to :ref:`install Orthanc <compiling>`. Once
92 Orthanc is installed, you must change the :ref:`configuration file 92 Orthanc is installed, you must change the :ref:`configuration file
93 <configuration>` to tell Orthanc where it can find the plugin: This is 93 <configuration>` to tell Orthanc where it can find the plugin: This is
94 done by properly modifying the ``Plugins`` configuration option. You 94 done by properly modifying the ``Plugins`` configuration option. You
290 path to the target TIFF file. 290 path to the target TIFF file.
291 291
292 Similarly to the DICOM-izer, the command-line options ``--orthanc``, 292 Similarly to the DICOM-izer, the command-line options ``--orthanc``,
293 ``--username`` and ``--password`` can be used to specify the 293 ``--username`` and ``--password`` can be used to specify the
294 parameters of your Orthanc server. 294 parameters of your Orthanc server.
295
296
297 Interface with Cytomine
298 -----------------------
299
300 `Cytomine <https://cytomine.be/>`__ is an "*open-source rich internet
301 application for collaborative analysis of multi-gigapixel images.*"
302 Starting with release 1.1 of the whole-slide imaging framework for
303 Orthanc, it is possible to exchange digital pathology images back and
304 forth between Orthanc and Cytomine according to the following
305 workflow:
306
307 .. image:: ../images/2021-12-12-Cytomine.png
308 :align: center
309 :width: 500px
310
311 |
312
313 As can be seen, ``OrthancWSIDicomizer`` imports the source image from
314 Cytomine using its REST API, then puts the converted DICOM instances
315 onto Orthanc using its REST API. Here is a minimalist sample call to
316 the ``OrthancWSIDicomizer`` command-line tool to convert an image from
317 a Cytomine server onto an Orthanc server listening on
318 ``localhost:8042`` with default parameters ::
319
320 $ ./OrthancWSIDicomizer --cytomine-url=http://XXX --cytomine-image=325 \
321 --cytomine-public-key=YYY --cytomine-private-key=ZZZ \
322 --threads=4 --pyramid=1 --username=orthanc --password=orthanc --verbose
323
324 The ``--cytomine-image`` parameter corresponds to the ID of the `Image
325 Instance <https://doc.uliege.cytomine.org/dev-guide/api/reference>`__
326 of interest. This ID can easily be retrieved from the Web interface of
327 Cytomine:
328
329 .. image:: ../images/Cytomine.png
330 :align: center
331 :width: 600px
332
333 |
334
335 The ``--cytomine-public-key`` and ``--cytomine-private-key``
336 parameters grant access to the REST API of Cytomine, and can be found
337 in the parameters of your account using the Web interface of Cytomine:
338
339 .. image:: ../images/CytomineKeys.png
340 :align: center
341 :width: 600px
342
343 |
344
345
295 346
296 347
297 REST API 348 REST API
298 -------- 349 --------
299 350