Mercurial > hg > orthanc-book
comparison Sphinx/source/plugins/wsi.rst @ 82:0752d8518623
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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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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 |