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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 15 Dec 2016 21:45:44 +0100 |
parents | 4eea0dc5f071 |
children | 13dd3f20a00a |
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.. _wsi: Whole-Slide Microscopic Imaging =============================== .. contents:: The Orthanc project provides three **official tools** to support DICOM for whole-slide microscopic imaging (WSI): 1. A so-called "DICOM-izer" command-line tool that converts whole-slide images to DICOM series, following `Supplement 145 <ftp://medical.nema.org/medical/dicom/final/sup145_ft.pdf>`__. 2. A plugin that extends Orthanc with a Web viewer of whole-slide images for digital pathology. 3. Another command-line tool that converts a DICOM series stored inside Orthanc, to a standard hierarchical TIFF image. For general information, check out the `official homepage of the framework <http://www.orthanc-server.com/static.php?page=wsi>`__. Compilation ----------- .. highlight:: bash The procedure to compile the WSI framework is similar of that for the :ref:`core of Orthanc <binaries>`. The following commands should work for every UNIX-like distribution (including GNU/Linux):: # Firstly, compile the command-line tools $ mkdir Applications/Build $ cd Applications/Build $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release $ make # Secondly, compile the plugin $ mkdir ../../ViewerPlugin/Build $ cd ../../ViewerPlugin/Build $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release $ make The compilation will produce 3 binaries: * ``Applications/Build/OrthancWSIDicomizer``, which contains the DICOM-izer. * ``Applications/Build/OrthancWSIDicomToTiff``, which contains the DICOM-to-TIFF converter. * ``ViewerPlugin/Build/OrthancWSI``, which is a shared library containing the viewer plugin for Orthanc. Note that pre-compiled binaries for Microsoft Windows `are available <http://www.orthanc-server.com/browse.php?path=/whole-slide-imaging>`__. Installation of the plugin -------------------------- .. highlight:: json You of course first have to :ref:`install Orthanc <compiling>`. Once Orthanc is installed, you must change the :ref:`configuration file <configuration>` to tell Orthanc where it can find the plugin: This is done by properly modifying the ``Plugins`` option. You could for instance use the following configuration file:: { "Name" : "MyOrthanc", [...] "Plugins" : [ "/home/user/orthanc-wsi/ViewerPlugin/Build/libOrthancWSI.so" ] } Orthanc must of course be restarted after the modification of its configuration file. The WSI plugin has no specific configuration option. Once a :ref:`DICOM series <model-world>` is opened using Orthanc Explorer, a yellow button entitled ``Whole-Slide Imaging Viewer`` will show up for series corresponding to whole-slide images. This button will open the WSI viewer for that particular series. This behavior can be seen on the Orthanc Explorer running on our `WSI demonstration server <http://wsi.orthanc-server.com/orthanc/app/explorer.html>`__. Command-line tools ------------------ .. highlight:: bash The command-line tools ``OrthancWSIDicomizer`` and ``OrthancWSIDicomToTiff`` provide documentation of all their options if started with the ``--help`` parameter:: $ OrthancWSIDicomizer --help $ OrthancWSIDicomToTiff --help In this section, we review the most common usages of these tools. Transcoding a DICOM image ^^^^^^^^^^^^^^^^^^^^^^^^^ The most simple usage consists in converting some whole-slide image to DICOM, then uploading it to Orthanc:: $ OrthancWSIDicomizer Source.tif This command will transcode some `hierarchical, tiled TIFF <https://en.wikipedia.org/wiki/TIFF>`__ image called ``Source.tif``, and push the output DICOM files to the default Orthanc server (running on ``localhost`` and listening to HTTP port ``8042``) using its :ref:`REST API <rest>`. This operation is fast, as no re-encoding takes place: If the source TIFF image contains JPEG tiles, these tiles will be written as such. Obviously, you can specify the parameters of your Orthanc server:: $ OrthancWSIDicomizer Source.tif --orthanc=http://localhost:8042/ --username=orthanc --password=orthanc It is also possible to write the DICOM instance directly onto some folder of the filesystem (the target folder must be existing):: $ OrthancWSIDicomizer Source.tif --folder=/tmp/dicomized/ Re-encoding a DICOM image ^^^^^^^^^^^^^^^^^^^^^^^^^ Proprietary file formats ^^^^^^^^^^^^^^^^^^^^^^^^ Out-of-the-box, the DICOM-izer supports standard hierarchical TIFF images. Some commonplace image formats (PNG and JPEG) can be DICOM-ized as well. However, whole-slide images can come in many proprietary file formats. To transcode such images, the DICOM-izer relies upon the `OpenSlide toolbox <http://openslide.org/>`__. For this feature to work, you have to tell the command-line tool where it can find the OpenSlide shared library. GNU/Linux distributions generally provide packages containing the OpenSlide shared library (under Debian/Ubuntu, simply install the ``libopenslide0`` package):: $ OrthancWSIDicomizer --openslide=libopenslide.so CMU-1-JP2K-33005.svs Precompiled Microsoft Windows binaries of this shared library can be found on the `OpenSlide homepage <http://openslide.org/download/>`__:: $ OrthancWSIDicomizer --openslide=libopenslide-0.dll CMU-1-JP2K-33005.svs Note that this operation implies the re-encoding of the source image from the proprietary file format, which is much more time-consuming than simply transcoding a TIFF image. Specifying a DICOM dataset ^^^^^^^^^^^^^^^^^^^^^^^^^^ Converting DICOM to TIFF ^^^^^^^^^^^^^^^^^^^^^^^^ REST API --------