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author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 15 Dec 2016 21:45:44 +0100
parents 4eea0dc5f071
children 13dd3f20a00a
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81:4eea0dc5f071 82:0752d8518623
13 whole-slide images to DICOM series, following `Supplement 145 13 whole-slide images to DICOM series, following `Supplement 145
14 <ftp://medical.nema.org/medical/dicom/final/sup145_ft.pdf>`__. 14 <ftp://medical.nema.org/medical/dicom/final/sup145_ft.pdf>`__.
15 2. A plugin that extends Orthanc with a Web viewer of whole-slide 15 2. A plugin that extends Orthanc with a Web viewer of whole-slide
16 images for digital pathology. 16 images for digital pathology.
17 3. Another command-line tool that converts a DICOM series stored 17 3. Another command-line tool that converts a DICOM series stored
18 in Orthanc, to a standard hierarchical TIFF image. 18 inside Orthanc, to a standard hierarchical TIFF image.
19 19
20 For general information, check out the `official homepage of the 20 For general information, check out the `official homepage of the
21 framework <http://www.orthanc-server.com/static.php?page=wsi>`__. 21 framework <http://www.orthanc-server.com/static.php?page=wsi>`__.
22 22
23 23
43 43
44 The compilation will produce 3 binaries: 44 The compilation will produce 3 binaries:
45 45
46 * ``Applications/Build/OrthancWSIDicomizer``, which contains the DICOM-izer. 46 * ``Applications/Build/OrthancWSIDicomizer``, which contains the DICOM-izer.
47 * ``Applications/Build/OrthancWSIDicomToTiff``, which contains the DICOM-to-TIFF converter. 47 * ``Applications/Build/OrthancWSIDicomToTiff``, which contains the DICOM-to-TIFF converter.
48 * ``ViewerPlugin/Build/OrthancWSI``, which is a shared library containing the plugin for Orthanc. 48 * ``ViewerPlugin/Build/OrthancWSI``, which is a shared library containing the viewer plugin for Orthanc.
49 49
50 Note that pre-compiled binaries for Microsoft Windows `are available 50 Note that pre-compiled binaries for Microsoft Windows `are available
51 <http://www.orthanc-server.com/browse.php?path=/whole-slide-imaging>`__. 51 <http://www.orthanc-server.com/browse.php?path=/whole-slide-imaging>`__.
52 52
53 53
74 configuration file. The WSI plugin has no specific configuration 74 configuration file. The WSI plugin has no specific configuration
75 option. 75 option.
76 76
77 Once a :ref:`DICOM series <model-world>` is opened using Orthanc 77 Once a :ref:`DICOM series <model-world>` is opened using Orthanc
78 Explorer, a yellow button entitled ``Whole-Slide Imaging Viewer`` will 78 Explorer, a yellow button entitled ``Whole-Slide Imaging Viewer`` will
79 show up for whole-slide images. It will open the WSI viewer for that 79 show up for series corresponding to whole-slide images. This button
80 particular series. This behavior can be seen on the Orthanc Explorer 80 will open the WSI viewer for that particular series. This behavior can
81 running on our `WSI demonstration server 81 be seen on the Orthanc Explorer running on our `WSI demonstration
82 <http://wsi.orthanc-server.com/orthanc/app/explorer.html>`__. 82 server <http://wsi.orthanc-server.com/orthanc/app/explorer.html>`__.
83 83
84 84
85 85
86 Command-line tools 86 Command-line tools
87 ------------------ 87 ------------------
111 and push the output DICOM files to the default Orthanc server (running 111 and push the output DICOM files to the default Orthanc server (running
112 on ``localhost`` and listening to HTTP port ``8042``) using its 112 on ``localhost`` and listening to HTTP port ``8042``) using its
113 :ref:`REST API <rest>`. This operation is fast, as no re-encoding 113 :ref:`REST API <rest>`. This operation is fast, as no re-encoding
114 takes place: If the source TIFF image contains JPEG tiles, these tiles 114 takes place: If the source TIFF image contains JPEG tiles, these tiles
115 will be written as such. 115 will be written as such.
116
117 Obviously, you can specify the parameters of your Orthanc server::
118
119 $ OrthancWSIDicomizer Source.tif --orthanc=http://localhost:8042/ --username=orthanc --password=orthanc
120
121 It is also possible to write the DICOM instance directly onto some
122 folder of the filesystem (the target folder must be existing)::
123
124 $ OrthancWSIDicomizer Source.tif --folder=/tmp/dicomized/
125
116 126
117 127
118 Re-encoding a DICOM image 128 Re-encoding a DICOM image
119 ^^^^^^^^^^^^^^^^^^^^^^^^^ 129 ^^^^^^^^^^^^^^^^^^^^^^^^^
120 130