Mercurial > hg > orthanc-book
comparison Sphinx/source/plugins/wsi.rst @ 797:4d431ad58521
cytomine
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Sun, 12 Dec 2021 15:25:43 +0100 |
parents | 525d59a7c198 |
children | 02121f3c7e65 |
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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 |