Mercurial > hg > orthanc-book
comparison Sphinx/source/plugins/wsi.rst @ 358:011b01ccf52d
fixing external hyperlinks
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 30 Mar 2020 18:47:35 +0200 |
parents | 61050d813d74 |
children | 525d59a7c198 |
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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 inside 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 <https://www.orthanc-server.com/static.php?page=wsi>`__. |
22 | 22 |
23 | 23 |
24 Compilation | 24 Compilation |
25 ----------- | 25 ----------- |
26 | 26 |
53 | 53 |
54 Microsoft Windows | 54 Microsoft Windows |
55 ^^^^^^^^^^^^^^^^^ | 55 ^^^^^^^^^^^^^^^^^ |
56 | 56 |
57 Note that pre-compiled binaries for Microsoft Windows `are available | 57 Note that pre-compiled binaries for Microsoft Windows `are available |
58 <http://www.orthanc-server.com/browse.php?path=/whole-slide-imaging>`__. | 58 <https://www.orthanc-server.com/browse.php?path=/whole-slide-imaging>`__. |
59 | 59 |
60 | 60 |
61 Dynamic linking | 61 Dynamic linking |
62 ^^^^^^^^^^^^^^^ | 62 ^^^^^^^^^^^^^^^ |
63 | 63 |
111 Explorer <orthanc-explorer>`, a yellow button entitled ``Whole-Slide | 111 Explorer <orthanc-explorer>`, a yellow button entitled ``Whole-Slide |
112 Imaging Viewer`` will show up for series corresponding to whole-slide | 112 Imaging Viewer`` will show up for series corresponding to whole-slide |
113 images. This button will open the WSI viewer for that particular | 113 images. This button will open the WSI viewer for that particular |
114 series. This behavior can be seen on the Orthanc Explorer interface | 114 series. This behavior can be seen on the Orthanc Explorer interface |
115 running on our `WSI demonstration server | 115 running on our `WSI demonstration server |
116 <http://wsi.orthanc-server.com/orthanc/app/explorer.html>`__. | 116 <https://wsi.orthanc-server.com/orthanc/app/explorer.html>`__. |
117 | 117 |
118 | 118 |
119 | 119 |
120 Command-line tools | 120 Command-line tools |
121 ------------------ | 121 ------------------ |
219 | 219 |
220 Out-of-the-box, the DICOM-izer supports standard hierarchical TIFF | 220 Out-of-the-box, the DICOM-izer supports standard hierarchical TIFF |
221 images. Some commonplace image formats (PNG and JPEG) can be | 221 images. Some commonplace image formats (PNG and JPEG) can be |
222 DICOM-ized as well. However, whole-slide images can come in many | 222 DICOM-ized as well. However, whole-slide images can come in many |
223 proprietary file formats. To re-encode such images, the DICOM-izer | 223 proprietary file formats. To re-encode such images, the DICOM-izer |
224 relies upon the `OpenSlide toolbox <http://openslide.org/>`__. | 224 relies upon the `OpenSlide toolbox <https://openslide.org/>`__. |
225 | 225 |
226 For this feature to work, you have to tell the command-line tool where | 226 For this feature to work, you have to tell the command-line tool where |
227 it can find the OpenSlide shared library. GNU/Linux distributions | 227 it can find the OpenSlide shared library. GNU/Linux distributions |
228 generally provide packages containing the OpenSlide shared library | 228 generally provide packages containing the OpenSlide shared library |
229 (e.g. under Debian/Ubuntu, simply install the ``libopenslide0`` | 229 (e.g. under Debian/Ubuntu, simply install the ``libopenslide0`` |
230 package):: | 230 package):: |
231 | 231 |
232 $ ./OrthancWSIDicomizer --openslide=libopenslide.so CMU-1-JP2K-33005.svs | 232 $ ./OrthancWSIDicomizer --openslide=libopenslide.so CMU-1-JP2K-33005.svs |
233 | 233 |
234 Pre-compiled Microsoft Windows binaries of this shared library can be | 234 Pre-compiled Microsoft Windows binaries of this shared library can be |
235 found on the `OpenSlide homepage <http://openslide.org/download/>`__ (Note that | 235 found on the `OpenSlide homepage <https://openslide.org/download/>`__ (Note that |
236 you should copy all .dll files from the OpenSlide package next to the OrthancWSIDicomizer | 236 you should copy all .dll files from the OpenSlide package next to the OrthancWSIDicomizer |
237 executable):: | 237 executable):: |
238 | 238 |
239 $ ./OrthancWSIDicomizer --openslide=libopenslide-0.dll CMU-1-JP2K-33005.svs | 239 $ ./OrthancWSIDicomizer --openslide=libopenslide-0.dll CMU-1-JP2K-33005.svs |
240 | 240 |