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documenting wsi
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 15 Dec 2016 18:20:59 +0100
parents 895b8ad53454
children 0752d8518623
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4 Whole-Slide Imaging 4 Whole-Slide Microscopic Imaging
5 =================== 5 ===============================
6 6
7 .. contents:: 7 .. contents::
8 8
9 This **official** plugin extends Orthanc with a Web viewer of whole-slide 9 The Orthanc project provides three **official tools** to support DICOM
10 images for digital pathology. 10 for whole-slide microscopic imaging (WSI):
11
12 1. A so-called "DICOM-izer" command-line tool that converts
13 whole-slide images to DICOM series, following `Supplement 145
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
16 images for digital pathology.
17 3. Another command-line tool that converts a DICOM series stored
18 in Orthanc, to a standard hierarchical TIFF image.
11 19
12 For general information, check out the `official homepage of the 20 For general information, check out the `official homepage of the
13 framework <http://www.orthanc-server.com/static.php?page=wsi>`__. This 21 framework <http://www.orthanc-server.com/static.php?page=wsi>`__.
14 page is work-in-progress. 22
23
24 Compilation
25 -----------
26
27 .. highlight:: bash
28
29 The procedure to compile the WSI framework is similar of that for the
30 :ref:`core of Orthanc <binaries>`. The following commands should work
31 for every UNIX-like distribution (including GNU/Linux)::
32
33 # Firstly, compile the command-line tools
34 $ mkdir Applications/Build
35 $ cd Applications/Build
36 $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release
37 $ make
38 # Secondly, compile the plugin
39 $ mkdir ../../ViewerPlugin/Build
40 $ cd ../../ViewerPlugin/Build
41 $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release
42 $ make
43
44 The compilation will produce 3 binaries:
45
46 * ``Applications/Build/OrthancWSIDicomizer``, which contains the DICOM-izer.
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.
49
50 Note that pre-compiled binaries for Microsoft Windows `are available
51 <http://www.orthanc-server.com/browse.php?path=/whole-slide-imaging>`__.
52
53
54 Installation of the plugin
55 --------------------------
56
57 .. highlight:: json
58
59 You of course first have to :ref:`install Orthanc <compiling>`. Once
60 Orthanc is installed, you must change the :ref:`configuration file
61 <configuration>` to tell Orthanc where it can find the plugin: This is
62 done by properly modifying the ``Plugins`` option. You could for
63 instance use the following configuration file::
64
65 {
66 "Name" : "MyOrthanc",
67 [...]
68 "Plugins" : [
69 "/home/user/orthanc-wsi/ViewerPlugin/Build/libOrthancWSI.so"
70 ]
71 }
72
73 Orthanc must of course be restarted after the modification of its
74 configuration file. The WSI plugin has no specific configuration
75 option.
76
77 Once a :ref:`DICOM series <model-world>` is opened using Orthanc
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
80 particular series. This behavior can be seen on the Orthanc Explorer
81 running on our `WSI demonstration server
82 <http://wsi.orthanc-server.com/orthanc/app/explorer.html>`__.
83
84
85
86 Command-line tools
87 ------------------
88
89 .. highlight:: bash
90
91 The command-line tools ``OrthancWSIDicomizer`` and
92 ``OrthancWSIDicomToTiff`` provide documentation of all their options
93 if started with the ``--help`` parameter::
94
95 $ OrthancWSIDicomizer --help
96 $ OrthancWSIDicomToTiff --help
97
98 In this section, we review the most common usages of these tools.
99
100
101 Transcoding a DICOM image
102 ^^^^^^^^^^^^^^^^^^^^^^^^^
103
104 The most simple usage consists in converting some whole-slide image to
105 DICOM, then uploading it to Orthanc::
106
107 $ OrthancWSIDicomizer Source.tif
108
109 This command will transcode some `hierarchical, tiled TIFF
110 <https://en.wikipedia.org/wiki/TIFF>`__ image called ``Source.tif``,
111 and push the output DICOM files to the default Orthanc server (running
112 on ``localhost`` and listening to HTTP port ``8042``) using its
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
115 will be written as such.
116
117
118 Re-encoding a DICOM image
119 ^^^^^^^^^^^^^^^^^^^^^^^^^
120
121
122
123
124 Proprietary file formats
125 ^^^^^^^^^^^^^^^^^^^^^^^^
126
127 Out-of-the-box, the DICOM-izer supports standard hierarchical TIFF
128 images. Some commonplace image formats (PNG and JPEG) can be
129 DICOM-ized as well. However, whole-slide images can come in many
130 proprietary file formats. To transcode such images, the DICOM-izer
131 relies upon the `OpenSlide toolbox <http://openslide.org/>`__.
132
133 For this feature to work, you have to tell the command-line tool where
134 it can find the OpenSlide shared library. GNU/Linux distributions
135 generally provide packages containing the OpenSlide shared library
136 (under Debian/Ubuntu, simply install the ``libopenslide0`` package)::
137
138 $ OrthancWSIDicomizer --openslide=libopenslide.so CMU-1-JP2K-33005.svs
139
140 Precompiled Microsoft Windows binaries of this shared library can be
141 found on the `OpenSlide homepage <http://openslide.org/download/>`__::
142
143 $ OrthancWSIDicomizer --openslide=libopenslide-0.dll CMU-1-JP2K-33005.svs
144
145 Note that this operation implies the re-encoding of the source image
146 from the proprietary file format, which is much more time-consuming
147 than simply transcoding a TIFF image.
148
149
150
151 Specifying a DICOM dataset
152 ^^^^^^^^^^^^^^^^^^^^^^^^^^
153
154
155 Converting DICOM to TIFF
156 ^^^^^^^^^^^^^^^^^^^^^^^^
157
158
159 REST API
160 --------
161