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1 .. _wsi:
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81
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4 Whole-Slide Microscopic Imaging
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5 ===============================
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52
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6
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7 .. contents::
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8
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81
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9 The Orthanc project provides three **official tools** to support DICOM
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10 for whole-slide microscopic imaging (WSI):
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11
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12 1. A so-called "DICOM-izer" command-line tool that converts
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13 whole-slide images to DICOM series, following `Supplement 145
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14 <ftp://medical.nema.org/medical/dicom/final/sup145_ft.pdf>`__.
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15 2. A plugin that extends Orthanc with a Web viewer of whole-slide
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16 images for digital pathology.
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17 3. Another command-line tool that converts a DICOM series stored
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18 in Orthanc, to a standard hierarchical TIFF image.
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52
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19
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20 For general information, check out the `official homepage of the
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81
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21 framework <http://www.orthanc-server.com/static.php?page=wsi>`__.
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22
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23
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24 Compilation
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25 -----------
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26
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27 .. highlight:: bash
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28
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29 The procedure to compile the WSI framework is similar of that for the
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30 :ref:`core of Orthanc <binaries>`. The following commands should work
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31 for every UNIX-like distribution (including GNU/Linux)::
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32
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33 # Firstly, compile the command-line tools
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34 $ mkdir Applications/Build
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35 $ cd Applications/Build
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36 $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release
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37 $ make
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38 # Secondly, compile the plugin
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39 $ mkdir ../../ViewerPlugin/Build
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40 $ cd ../../ViewerPlugin/Build
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41 $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release
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42 $ make
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43
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44 The compilation will produce 3 binaries:
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45
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46 * ``Applications/Build/OrthancWSIDicomizer``, which contains the DICOM-izer.
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47 * ``Applications/Build/OrthancWSIDicomToTiff``, which contains the DICOM-to-TIFF converter.
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48 * ``ViewerPlugin/Build/OrthancWSI``, which is a shared library containing the plugin for Orthanc.
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49
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50 Note that pre-compiled binaries for Microsoft Windows `are available
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51 <http://www.orthanc-server.com/browse.php?path=/whole-slide-imaging>`__.
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52
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53
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54 Installation of the plugin
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55 --------------------------
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56
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57 .. highlight:: json
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58
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59 You of course first have to :ref:`install Orthanc <compiling>`. Once
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60 Orthanc is installed, you must change the :ref:`configuration file
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61 <configuration>` to tell Orthanc where it can find the plugin: This is
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62 done by properly modifying the ``Plugins`` option. You could for
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63 instance use the following configuration file::
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64
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65 {
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66 "Name" : "MyOrthanc",
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67 [...]
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68 "Plugins" : [
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69 "/home/user/orthanc-wsi/ViewerPlugin/Build/libOrthancWSI.so"
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70 ]
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71 }
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72
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73 Orthanc must of course be restarted after the modification of its
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74 configuration file. The WSI plugin has no specific configuration
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75 option.
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76
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77 Once a :ref:`DICOM series <model-world>` is opened using Orthanc
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78 Explorer, a yellow button entitled ``Whole-Slide Imaging Viewer`` will
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79 show up for whole-slide images. It will open the WSI viewer for that
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80 particular series. This behavior can be seen on the Orthanc Explorer
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81 running on our `WSI demonstration server
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82 <http://wsi.orthanc-server.com/orthanc/app/explorer.html>`__.
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83
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84
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85
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86 Command-line tools
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87 ------------------
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88
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89 .. highlight:: bash
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90
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91 The command-line tools ``OrthancWSIDicomizer`` and
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92 ``OrthancWSIDicomToTiff`` provide documentation of all their options
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93 if started with the ``--help`` parameter::
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94
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95 $ OrthancWSIDicomizer --help
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96 $ OrthancWSIDicomToTiff --help
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97
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98 In this section, we review the most common usages of these tools.
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99
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100
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101 Transcoding a DICOM image
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102 ^^^^^^^^^^^^^^^^^^^^^^^^^
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103
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104 The most simple usage consists in converting some whole-slide image to
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105 DICOM, then uploading it to Orthanc::
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106
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107 $ OrthancWSIDicomizer Source.tif
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108
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109 This command will transcode some `hierarchical, tiled TIFF
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110 <https://en.wikipedia.org/wiki/TIFF>`__ image called ``Source.tif``,
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111 and push the output DICOM files to the default Orthanc server (running
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112 on ``localhost`` and listening to HTTP port ``8042``) using its
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113 :ref:`REST API <rest>`. This operation is fast, as no re-encoding
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114 takes place: If the source TIFF image contains JPEG tiles, these tiles
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115 will be written as such.
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116
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117
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118 Re-encoding a DICOM image
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119 ^^^^^^^^^^^^^^^^^^^^^^^^^
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120
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121
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122
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123
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124 Proprietary file formats
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125 ^^^^^^^^^^^^^^^^^^^^^^^^
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126
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127 Out-of-the-box, the DICOM-izer supports standard hierarchical TIFF
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128 images. Some commonplace image formats (PNG and JPEG) can be
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129 DICOM-ized as well. However, whole-slide images can come in many
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130 proprietary file formats. To transcode such images, the DICOM-izer
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131 relies upon the `OpenSlide toolbox <http://openslide.org/>`__.
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132
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133 For this feature to work, you have to tell the command-line tool where
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134 it can find the OpenSlide shared library. GNU/Linux distributions
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135 generally provide packages containing the OpenSlide shared library
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136 (under Debian/Ubuntu, simply install the ``libopenslide0`` package)::
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137
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138 $ OrthancWSIDicomizer --openslide=libopenslide.so CMU-1-JP2K-33005.svs
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139
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140 Precompiled Microsoft Windows binaries of this shared library can be
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141 found on the `OpenSlide homepage <http://openslide.org/download/>`__::
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142
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143 $ OrthancWSIDicomizer --openslide=libopenslide-0.dll CMU-1-JP2K-33005.svs
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144
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145 Note that this operation implies the re-encoding of the source image
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146 from the proprietary file format, which is much more time-consuming
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147 than simply transcoding a TIFF image.
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148
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149
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150
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151 Specifying a DICOM dataset
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152 ^^^^^^^^^^^^^^^^^^^^^^^^^^
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153
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154
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155 Converting DICOM to TIFF
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156 ^^^^^^^^^^^^^^^^^^^^^^^^
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157
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158
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159 REST API
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160 --------
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161
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