Mercurial > hg > orthanc-book
annotate Sphinx/source/plugins/wsi.rst @ 1055:ebe3214f3ab0
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| author | Sebastien Jodogne <s.jodogne@gmail.com> |
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| date | Sat, 06 Apr 2024 18:00:13 +0200 |
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| 52 | 1 .. _wsi: |
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| 85 | 4 Whole-slide microscopic imaging |
| 81 | 5 =============================== |
| 52 | 6 |
| 7 .. contents:: | |
| 8 | |
| 81 | 9 The Orthanc project provides three **official tools** to support DICOM |
| 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 | |
| 82 | 18 inside Orthanc, to a standard hierarchical TIFF image. |
| 52 | 19 |
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20 Check out our `demonstration server |
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21 <https://orthanc.uclouvain.be/wsi/>`__. |
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22 |
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23 **For researchers**: `Please cite this paper |
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24 <https://doi.org/10.5220/0006155100810087>`__. |
| 81 | 25 |
| 26 | |
| 27 Compilation | |
| 28 ----------- | |
| 29 | |
| 129 | 30 Static linking |
| 31 ^^^^^^^^^^^^^^ | |
| 32 | |
| 85 | 33 .. highlight:: text |
| 81 | 34 |
| 35 The procedure to compile the WSI framework is similar of that for the | |
| 36 :ref:`core of Orthanc <binaries>`. The following commands should work | |
| 761 | 37 for most UNIX-like distribution (including GNU/Linux):: |
| 81 | 38 |
| 39 # Firstly, compile the command-line tools | |
| 40 $ mkdir Applications/Build | |
| 41 $ cd Applications/Build | |
| 42 $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release | |
| 43 $ make | |
| 129 | 44 |
| 85 | 45 # Secondly, compile the viewer plugin |
| 81 | 46 $ mkdir ../../ViewerPlugin/Build |
| 47 $ cd ../../ViewerPlugin/Build | |
| 48 $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release | |
| 49 $ make | |
| 50 | |
| 51 The compilation will produce 3 binaries: | |
| 52 | |
| 53 * ``Applications/Build/OrthancWSIDicomizer``, which contains the DICOM-izer. | |
| 54 * ``Applications/Build/OrthancWSIDicomToTiff``, which contains the DICOM-to-TIFF converter. | |
| 82 | 55 * ``ViewerPlugin/Build/OrthancWSI``, which is a shared library containing the viewer plugin for Orthanc. |
| 81 | 56 |
| 129 | 57 Microsoft Windows |
| 58 ^^^^^^^^^^^^^^^^^ | |
| 59 | |
| 81 | 60 Note that pre-compiled binaries for Microsoft Windows `are available |
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61 <https://orthanc.uclouvain.be/downloads/windows-32/orthanc-wsi/index.html>`__. |
| 81 | 62 |
| 63 | |
| 129 | 64 Dynamic linking |
| 65 ^^^^^^^^^^^^^^^ | |
| 66 | |
| 67 .. highlight:: text | |
| 68 | |
| 69 If static linking is not desired, here are build instructions for | |
| 70 Ubuntu 16.04 (provided build dependencies for the :ref:`core of | |
| 71 Orthanc <compiling>` have already been installed):: | |
| 72 | |
| 73 $ sudo apt-get install libopenjpeg-dev | |
| 74 | |
| 75 # Firstly, compile the command-line tools | |
| 76 $ mkdir Applications/Build | |
| 77 $ cd Applications/Build | |
| 78 $ cmake .. -DCMAKE_BUILD_TYPE=Release -DUSE_SYSTEM_ORTHANC_SDK=OFF | |
| 79 $ make | |
| 80 | |
| 81 # Secondly, compile the viewer plugin | |
| 82 $ mkdir ../../ViewerPlugin/Build | |
| 83 $ cd ../../ViewerPlugin/Build | |
| 84 $ cmake .. -DCMAKE_BUILD_TYPE=Release -DUSE_SYSTEM_ORTHANC_SDK=OFF -DALLOW_DOWNLOADS=ON | |
| 85 $ make | |
| 86 | |
| 87 | |
| 88 | |
| 85 | 89 Usage of the plugin |
| 90 ------------------- | |
| 81 | 91 |
| 797 | 92 .. highlight:: text |
| 81 | 93 |
| 94 You of course first have to :ref:`install Orthanc <compiling>`. Once | |
| 95 Orthanc is installed, you must change the :ref:`configuration file | |
| 96 <configuration>` to tell Orthanc where it can find the plugin: This is | |
| 85 | 97 done by properly modifying the ``Plugins`` configuration option. You |
| 98 could for instance use the following configuration file under | |
| 99 GNU/Linux:: | |
| 81 | 100 |
| 101 { | |
| 102 "Name" : "MyOrthanc", | |
| 103 [...] | |
| 104 "Plugins" : [ | |
| 105 "/home/user/orthanc-wsi/ViewerPlugin/Build/libOrthancWSI.so" | |
| 106 ] | |
| 107 } | |
| 108 | |
| 109 Orthanc must of course be restarted after the modification of its | |
| 110 configuration file. The WSI plugin has no specific configuration | |
| 111 option. | |
| 112 | |
| 85 | 113 Once a :ref:`DICOM series <model-world>` is opened using :ref:`Orthanc |
| 114 Explorer <orthanc-explorer>`, a yellow button entitled ``Whole-Slide | |
| 115 Imaging Viewer`` will show up for series corresponding to whole-slide | |
| 116 images. This button will open the WSI viewer for that particular | |
| 117 series. This behavior can be seen on the Orthanc Explorer interface | |
| 118 running on our `WSI demonstration server | |
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119 <https://orthanc.uclouvain.be/wsi-orthanc/app/explorer.html>`__. |
| 81 | 120 |
| 121 | |
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122 Support of IIIF |
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123 --------------- |
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124 |
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125 Starting with its release 2.0, the WSI plugin can act as a data source |
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126 that follows the `IIIF specification |
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127 <https://en.wikipedia.org/wiki/International_Image_Interoperability_Framework>`__. This |
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128 turns Orthanc into a tool to deliver collection of high-resolutions |
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129 images over the web through IIIF, while simultaneously enabling a |
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130 standard, long-term preservation of those collections through `DICOM |
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131 vendor-neutral archiving <https://en.wikipedia.org/wiki/DICOM>`__. |
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132 |
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133 REST API |
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134 ^^^^^^^^ |
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135 |
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136 The WSI plugin associates each of the **DICOM series** stored by |
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137 Orthanc whose :ref:`Orthanc identifier <orthanc-ids>` is ``seriesId``, |
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138 with a IIIF-compliant `Presentation API 3.0 |
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139 <https://iiif.io/api/presentation/3.0/>`__ manifest located at URI |
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140 ``/wsi/iiif/series/{seriesId}/manifest.json`` in the Web server of |
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141 Orthanc. In turn, this manifest points to a IIIF-compliant `Image API |
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142 3.0 <https://iiif.io/api/image/3.0/>`__ data source to deliver the |
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143 DICOM series over the web. |
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144 |
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145 Note that this data source is not only available for the whole-slide |
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146 microscopic series, but also for the other types of medical images, |
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147 which enables both telepathology and teleradiology workflows: |
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148 |
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149 * In the case of a whole-slide image, the URI to the IIIF data source |
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150 is: ``/wsi/iiif/tiles/{seriesId}/info.json``. |
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151 |
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152 * In the case of a regular radiology series, one IIIF data source is |
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153 associated with each frame of the DICOM series. Indeed, the |
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154 :ref:`DICOM model of the real-world <model-world>` specifies that a |
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155 single DICOM series can contain multiple instances, which in turn |
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156 can contain multiple frames. The URI to the IIIF data source |
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157 corresponding to one individual frame of interest is: |
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158 ``/wsi/iiif/frames/{seriesId}/{frameIndex}/info.json``, where |
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159 ``frameIndex`` is the index of the frame in the DICOM series. The |
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160 ``manifest.json`` of the parent DICOM series automatically |
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161 aggregates all the frames of the series as a single collection. |
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162 |
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163 |
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164 Web user interface |
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165 ^^^^^^^^^^^^^^^^^^ |
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166 |
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167 :ref:`Orthanc Explorer <orthanc-explorer>` contains a button to easily |
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168 copy/paste the URL of the IIIF manifest corresponding to a DICOM |
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169 series: |
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170 |
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171 .. image:: ../images/2023-07-13-IIIF.png |
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172 :align: center |
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173 :width: 500px |
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174 |
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175 | |
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176 |
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177 Furthermore, as can be seen in the image above, buttons can be enabled |
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178 to test the opening of the IIIF data source using `Mirador |
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179 <https://projectmirador.org/>`__ and/or `OpenSeadragon |
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180 <https://openseadragon.github.io/>`__. |
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181 |
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182 Pay attention to the fact that the assets of Mirador and OpenSeadragon |
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183 (notably JavaScript) are loaded from the `unpkg CDN |
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184 <https://www.unpkg.com/>`__, which necessitates an Internet |
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185 connection. For this reason, these assets are disabled by default. |
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186 |
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187 |
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188 Configuration options |
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189 ^^^^^^^^^^^^^^^^^^^^^ |
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190 |
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191 .. highlight:: json |
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192 |
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193 The IIIF features can be configured using the following |
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194 :ref:`configuration file <configuration>` of Orthanc:: |
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195 |
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196 { |
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197 "Name" : "MyOrthanc", |
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198 [...] |
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199 "Plugins" : [ |
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200 "/home/user/orthanc-wsi/ViewerPlugin/Build/libOrthancWSI.so" |
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201 ], |
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202 "WholeSlideImaging" : { |
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203 "EnableIIIF" : true, // Can be used to disable support of IIIF |
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204 "OrthancPublicURL" : "http://localhost:8042/", |
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205 "ServeMirador" : false, // Whether to show the "Test IIIF in Mirador" button |
| 979 | 206 "ServeOpenSeadragon" : false, // Whether to show the "Test IIIF in OpenSeadragon" button |
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207 "ForcePowersOfTwoScaleFactors" : true // Can be used to disable the compatibility mode |
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208 } |
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209 } |
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210 |
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211 A few remarks: |
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212 |
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213 * The ``OrthancPublicURL`` option must be adapted if Orthanc is |
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214 branched behind a :ref:`reverse proxy <nginx>`. |
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215 |
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216 * In the case of a whole-slide image, the |
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217 ``ForcePowersOfTwoScaleFactors`` option instruct the WSI plugin to |
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218 only publish the pyramid levels whose scale factors follow a |
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219 powers-of-two patterns (i.e., 1, 2, 4, 8, 16...). This provides |
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220 maximum compatibility with viewers (for instance, consider `this |
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221 issue |
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222 <https://github.com/openseadragon/openseadragon/issues/2379>`__), |
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223 but can break a smooth delivery of high-resolution images whose |
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224 pyramid is irregular. Compatibility mode is enabled by default. |
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225 |
| 81 | 226 |
| 227 Command-line tools | |
| 228 ------------------ | |
| 229 | |
| 85 | 230 .. highlight:: text |
| 81 | 231 |
| 232 The command-line tools ``OrthancWSIDicomizer`` and | |
| 233 ``OrthancWSIDicomToTiff`` provide documentation of all their options | |
| 234 if started with the ``--help`` parameter:: | |
| 235 | |
| 85 | 236 $ ./OrthancWSIDicomizer --help |
| 237 $ ./OrthancWSIDicomToTiff --help | |
| 81 | 238 |
| 239 In this section, we review the most common usages of these tools. | |
| 240 | |
| 241 | |
| 242 Transcoding a DICOM image | |
| 243 ^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 244 | |
| 245 The most simple usage consists in converting some whole-slide image to | |
| 246 DICOM, then uploading it to Orthanc:: | |
| 247 | |
| 85 | 248 $ ./OrthancWSIDicomizer Source.tif |
| 81 | 249 |
| 250 This command will transcode some `hierarchical, tiled TIFF | |
| 251 <https://en.wikipedia.org/wiki/TIFF>`__ image called ``Source.tif``, | |
| 85 | 252 and push the generated DICOM files to the default Orthanc server |
| 253 (running on ``localhost`` and listening to HTTP port ``8042``) using | |
| 254 its :ref:`REST API <rest>`. The log of the command will give you the | |
| 255 :ref:`identifier of the generated series <orthanc-ids>`, so that you | |
| 256 can locate it in Orthanc Explorer. This conversion is fast, as no | |
| 257 re-encoding takes place: If the source TIFF image contains JPEG tiles, | |
| 258 these tiles will be simply written as such. | |
| 81 | 259 |
| 85 | 260 Obviously, you can specify the parameters of the REST API of your |
| 261 target Orthanc server:: | |
| 82 | 262 |
| 85 | 263 $ ./OrthancWSIDicomizer Source.tif --orthanc=http://localhost:8042/ --username=orthanc --password=orthanc |
| 82 | 264 |
| 85 | 265 It is also possible to write the DICOM instances directly onto some |
| 82 | 266 folder of the filesystem (the target folder must be existing):: |
| 267 | |
| 85 | 268 $ ./OrthancWSIDicomizer Source.tif --folder=/tmp/dicomized/ |
| 82 | 269 |
| 85 | 270 This command will create a set of files entitled like |
| 271 ``/tmp/dicomized/wsi-XXXXXX.dcm``. You can modify this pattern using | |
| 272 the command-line option ``--folder-pattern``. | |
| 273 | |
| 274 By default, the DICOM-izer will spread the output series as a set of | |
| 275 DICOM files whose size stays below 10MB. This prevents the appearance | |
| 276 of huge files, which speeds up further processing. This behavior can | |
| 277 be controlled using the ``--max-size`` command-line option. | |
| 82 | 278 |
| 81 | 279 |
| 280 Re-encoding a DICOM image | |
| 281 ^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 282 | |
| 85 | 283 The section above explained how to transcode whole-slide images, |
| 284 without modifying the compression scheme of their individual tiles | |
| 285 (which is most commonly JPEG). You can instruct the DICOM-izer to | |
| 286 re-encode each and every individual tile as follows:: | |
| 287 | |
| 288 $ ./OrthancWSIDicomizer Source.tif --reencode=1 --compression=jpeg2000 | |
| 289 | |
| 290 This example would create a series of DICOM instances encoded using | |
| 291 the JPEG2k transfer syntax (whose UID is ``1.2.840.10008.1.2.4.90``). | |
| 292 As JPEG2k is not natively supported by many Web browsers, the Web | |
| 293 viewer plugin would transparently convert such JPEG2k-encoded tiles to | |
| 294 PNG images. | |
| 295 | |
| 296 It is also possible to re-encode the image so as to reduce disk space | |
| 297 consumption by changing the JPEG quality:: | |
| 298 | |
| 299 $ ./OrthancWSIDicomizer Source.tif --reencode=1 --compression=jpeg --jpeg-quality=10 | |
| 300 | |
| 301 The DICOM-izer also allows to re-generate all the multi-resolution | |
| 302 pyramid. This is extremely importantly to enhance the user experience | |
| 303 of the Web interface, if the source image only features the finest | |
| 304 zoom level of the whole-slide image:: | |
| 305 | |
| 306 $ ./OrthancWSIDicomizer Source.tif --pyramid=1 --smooth=1 | |
| 307 | |
| 308 The number of levels in the pyramid can be controlled using the | |
| 309 ``--levels`` command-line option. The ``--smooth=1`` option tells the | |
| 310 DICOM-izer to apply `Gaussian smoothing | |
| 311 <https://en.wikipedia.org/wiki/Gaussian_blur>`__ when re-scaling the | |
| 312 image, in order to avoid the appearance of aliasing in the | |
| 313 multi-resolution pyramid. This produces nicer images, at the price of | |
| 314 higher computation time. | |
| 315 | |
| 316 All the examples described in this section are obviously much more | |
| 317 CPU-intensive than simple transcoding. The DICOM-izer takes advantage | |
| 318 in multi-threading to reduce the computation time. By default, it will | |
| 319 use half the number of logical CPU cores that are available. This | |
| 320 behavior can be fine-tuned using command-line option ``--threads``. | |
| 81 | 321 |
| 322 | |
| 323 | |
| 324 Proprietary file formats | |
| 325 ^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 326 | |
| 327 Out-of-the-box, the DICOM-izer supports standard hierarchical TIFF | |
| 328 images. Some commonplace image formats (PNG and JPEG) can be | |
| 329 DICOM-ized as well. However, whole-slide images can come in many | |
| 85 | 330 proprietary file formats. To re-encode such images, the DICOM-izer |
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331 relies upon the `OpenSlide toolbox <https://openslide.org/>`__. |
| 81 | 332 |
| 333 For this feature to work, you have to tell the command-line tool where | |
| 334 it can find the OpenSlide shared library. GNU/Linux distributions | |
| 335 generally provide packages containing the OpenSlide shared library | |
| 85 | 336 (e.g. under Debian/Ubuntu, simply install the ``libopenslide0`` |
| 337 package):: | |
| 81 | 338 |
| 85 | 339 $ ./OrthancWSIDicomizer --openslide=libopenslide.so CMU-1-JP2K-33005.svs |
| 81 | 340 |
| 85 | 341 Pre-compiled Microsoft Windows binaries of this shared library can be |
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342 found on the `OpenSlide homepage <https://openslide.org/download/>`__ (Note that |
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343 you should copy all .dll files from the OpenSlide package next to the OrthancWSIDicomizer |
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344 executable):: |
| 81 | 345 |
| 85 | 346 $ ./OrthancWSIDicomizer --openslide=libopenslide-0.dll CMU-1-JP2K-33005.svs |
| 81 | 347 |
| 348 Note that this operation implies the re-encoding of the source image | |
| 349 from the proprietary file format, which is much more time-consuming | |
| 350 than simply transcoding a TIFF image. | |
| 351 | |
| 352 | |
| 353 Specifying a DICOM dataset | |
| 354 ^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 355 | |
| 85 | 356 So far, we have only been discussing the whole-slide image by itself, |
| 357 and not the :ref:`medical information <dicom-tags>` that is associated | |
| 358 with each DICOM file. The DICOM tags that must be embedded inside the | |
| 359 generated DICOM series can be specified using the user-friendly JSON | |
| 360 file format. You would first generate a minimal, sample JSON dataset | |
| 361 as follows:: | |
| 362 | |
| 363 $ ./OrthancWSIDicomizer --sample-dataset > dataset.json | |
| 364 | |
| 365 Secondly, you would edit the just-generated ``dataset.json`` file | |
| 366 using any text editor (or any script interfaced with your RIS), so as | |
| 367 to encode medical information associated with the image | |
| 368 acquisition. Finally, tell the DICOM-izer where it can find the | |
| 369 dataset when re-encoding or transcoding the image:: | |
| 370 | |
| 371 $ ./OrthancWSIDicomizer Source.tif --dataset=dataset.json | |
| 372 | |
| 373 Note that it is always a good idea to check whether all the required | |
| 374 DICOM tags have been properly provided, e.g. by running the | |
| 375 ``dciodvfy`` command-line tool provided by `David Clunie | |
| 376 <http://www.dclunie.com/dicom3tools.html>`__ that checks the | |
| 377 compliance of DICOM files. | |
| 378 | |
| 81 | 379 |
| 380 Converting DICOM to TIFF | |
| 381 ^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 382 | |
| 85 | 383 The whole-slide imaging framework for Orthanc also provides a |
| 384 command-line tool that converts some DICOM series, as a standard | |
| 385 hierarchical, tiled TIFF image. This is important if you wish to | |
| 386 export some DICOM file to a framework that does not support DICOM | |
| 387 Supplement 145. | |
| 388 | |
| 389 Here is how you would convert a whole-slide image stored in the | |
| 390 default Orthanc server:: | |
| 391 | |
| 392 $ ./OrthancWSIDicomToTiff fdf53e42-06d7377a-c24c59fd-3704e72d-f4c75b68 Target.tif | |
| 393 | |
| 394 You just have to provide the :ref:`Orthanc identifier <orthanc-ids>` | |
| 395 of the series of interest (that can be retrieved using :ref:`Orthanc | |
| 396 Explorer <orthanc-explorer>` or the :ref:`REST API <rest>`), and the | |
| 397 path to the target TIFF file. | |
| 398 | |
| 399 Similarly to the DICOM-izer, the command-line options ``--orthanc``, | |
| 400 ``--username`` and ``--password`` can be used to specify the | |
| 401 parameters of your Orthanc server. | |
| 402 | |
| 81 | 403 |
| 797 | 404 Interface with Cytomine |
| 405 ----------------------- | |
| 406 | |
| 407 `Cytomine <https://cytomine.be/>`__ is an "*open-source rich internet | |
| 408 application for collaborative analysis of multi-gigapixel images.*" | |
| 409 Starting with release 1.1 of the whole-slide imaging framework for | |
| 410 Orthanc, it is possible to exchange digital pathology images back and | |
| 411 forth between Orthanc and Cytomine according to the following | |
| 412 workflow: | |
| 413 | |
| 414 .. image:: ../images/2021-12-12-Cytomine.png | |
| 415 :align: center | |
| 416 :width: 500px | |
| 417 | |
| 418 | | |
| 419 | |
| 420 As can be seen, ``OrthancWSIDicomizer`` imports the source image from | |
| 421 Cytomine using its REST API, then puts the converted DICOM instances | |
| 422 onto Orthanc using its REST API. Here is a minimalist sample call to | |
| 423 the ``OrthancWSIDicomizer`` command-line tool to convert an image from | |
| 424 a Cytomine server onto an Orthanc server listening on | |
| 425 ``localhost:8042`` with default parameters :: | |
| 426 | |
| 427 $ ./OrthancWSIDicomizer --cytomine-url=http://XXX --cytomine-image=325 \ | |
| 428 --cytomine-public-key=YYY --cytomine-private-key=ZZZ \ | |
| 429 --threads=4 --pyramid=1 --username=orthanc --password=orthanc --verbose | |
| 430 | |
| 431 The ``--cytomine-image`` parameter corresponds to the ID of the `Image | |
| 432 Instance <https://doc.uliege.cytomine.org/dev-guide/api/reference>`__ | |
| 433 of interest. This ID can easily be retrieved from the Web interface of | |
| 434 Cytomine: | |
| 435 | |
| 436 .. image:: ../images/Cytomine.png | |
| 437 :align: center | |
| 438 :width: 600px | |
| 439 | |
| 440 | | |
| 441 | |
| 442 The ``--cytomine-public-key`` and ``--cytomine-private-key`` | |
| 443 parameters grant access to the REST API of Cytomine, and can be found | |
| 444 in the parameters of your account using the Web interface of Cytomine: | |
| 445 | |
| 446 .. image:: ../images/CytomineKeys.png | |
| 447 :align: center | |
| 448 :width: 600px | |
| 449 | |
| 450 | | |
| 451 | |
| 452 | |
| 453 | |
| 454 | |
| 81 | 455 REST API |
| 456 -------- | |
| 457 | |
| 85 | 458 Besides providing an user interface, the plugin for whole-slide |
| 459 imaging also enrich the :ref:`REST API <rest>` of Orthanc with some | |
| 460 new URIs, that are described in this section. | |
| 461 | |
| 462 Note that the Web interface of the plugin exclusively relies upon this | |
| 463 enriched REST API in order to display whole-slide images using the | |
| 464 `OpenLayers 3 <https://openlayers.org/>`__ JavaScript library. | |
| 465 | |
| 466 | |
| 467 Information about a whole-slide image | |
| 468 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 469 | |
| 470 You can check whether a DICOM series associated with some known | |
| 471 :ref:`Orthanc ID <orthanc-ids>` ``id`` corresponds to a whole-slide | |
| 472 image by calling the ``/wsi/pyramids/{id}`` URI. A HTTP status code | |
| 473 404 is returned if the series is *not* a whole-slide image:: | |
| 474 | |
| 475 $ curl -v http://localhost:8042/wsi/pyramids/ca2cc2ef-2dd8be12-0a4506ae-d565b7e1-a4ca9068 | |
| 476 [...] | |
| 477 < HTTP/1.1 404 Not Found | |
| 478 | |
| 479 However, if the identifier corresponds to a valid whole-slide image, | |
| 480 you will get information about its multi-resolution pyramid, formatted | |
| 481 using JSON:: | |
| 482 | |
| 483 $ curl http://localhost:8042/wsi/pyramids/f0ed5846-2ce36a70-d27bb5d3-6ed9dac2-ee638d85 | |
| 484 { | |
| 485 "ID" : "f0ed5846-2ce36a70-d27bb5d3-6ed9dac2-ee638d85", | |
| 486 "Resolutions" : [ 1, 2, 4, 8, 16 ], | |
| 487 "Sizes" : [ | |
| 488 [ 10800, 5400 ], | |
| 489 [ 5400, 2700 ], | |
| 490 [ 2700, 1350 ], | |
| 491 [ 1350, 675 ], | |
| 492 [ 675, 338 ] | |
| 493 ], | |
| 494 "TileHeight" : 512, | |
| 495 "TileWidth" : 512, | |
| 496 "TilesCount" : [ | |
| 497 [ 22, 11 ], | |
| 498 [ 11, 6 ], | |
| 499 [ 6, 3 ], | |
| 500 [ 3, 2 ], | |
| 501 [ 2, 1 ] | |
| 502 ], | |
| 503 "TotalHeight" : 5400, | |
| 504 "TotalWidth" : 10800 | |
| 505 } | |
| 506 | |
| 507 The size of the finest level of the pyramid is verbatim available from | |
| 508 this output (in the example above, ``10,800 x 5,400`` pixels), as well | |
| 509 as the size of each individual tile (``512 x 512`` pixels). The | |
| 510 ``TilesCount`` gives, for each level of the pyramid (sorted in | |
| 511 decreasing resolutions), the number of tiles along each dimension: In | |
| 512 the example above, the coarsest level contains 2 tiles along the X | |
| 513 axis, and 1 tile along the Y. | |
| 514 | |
| 515 Note that the interpretation of the whole-slide image is done | |
| 516 transparently by the plugin, which frees the user from parsing each | |
| 517 and every DICOM instance in the series. | |
| 518 | |
| 519 The medical information associated with the series or its instances | |
| 520 can as usual be retrieved using the core :ref:`REST API <rest>` of | |
| 521 Orthanc. | |
| 522 | |
| 523 | |
| 524 Decoding the individual tiles | |
| 525 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 526 | |
| 527 As discussed above, the ``/wsi/pyramids/{id}`` gives information about | |
| 528 the number of tiles in each level of the multi-resolution pyramid | |
| 529 associated with series ``id``. | |
| 530 | |
| 531 You can then retrieve the individual tiles of each level using the | |
| 532 ``/wsi/tiles/{id}/{z}/{x}/{y}`` URI, where ``z`` corresponds to the | |
| 533 level of interest, and (``x``, ``y``) the index of the tile of | |
| 534 interest at this level. All of these indices start at zero, the level | |
| 535 ``z=0`` corresponding to the finest level. | |
| 536 | |
| 537 For instance, here is how to retrieve the central tile of the finest | |
| 538 level of the pyramid (that contains ``22 x 11`` tiles in our example):: | |
| 539 | |
| 540 $ curl http://localhost:8042/wsi/tiles/f0ed5846-2ce36a70-d27bb5d3-6ed9dac2-ee638d85/0/11/5 > tile.jpg | |
| 541 $ identify ./tile.jpg | |
| 542 ./tile.jpg JPEG 512x512 512x512+0+0 8-bit DirectClass 88.5KB 0.000u 0:00.000 | |
| 543 | |
| 544 As can be seen, the plugin has returned a JPEG image of size ``512 x | |
| 545 512``, which corresponds to the size of the tiles in this sample | |
| 546 image. If trying to access a tile outside the image, the plugin will | |
| 547 return with an HTTP status code that is not ``200 OK``. Similarly, | |
| 548 here is how to retrieve a tile at the coarsest level (the pyramid has | |
| 549 5 levels in our example):: | |
| 550 | |
| 551 $ curl http://localhost:8042/wsi/tiles/f0ed5846-2ce36a70-d27bb5d3-6ed9dac2-ee638d85/4/0/0 > tile.jpg | |
| 552 | |
| 553 Depending upon the transfer syntax of the DICOM instances, the tile | |
| 554 might not be encoded using JPEG. Indeed, if the transfer syntax is | |
| 555 uncompressed (UID ``1.2.840.10008.1.2`` and friends) or JPEG2k | |
| 556 lossless (UID ``1.2.840.10008.1.2.4.90``), the plugin will | |
| 557 transparently re-encode the tile to PNG in order to avoid any | |
| 558 destructive compression. | |
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559 |
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560 NB: Starting with version 2.0 of the WSI plugin, the |
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561 ``/wsi/tiles/{id}/{z}/{x}/{y}`` route accepts the ``Accept`` HTTP |
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562 header, which can be used to force the compression of the tile. The |
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563 allowed values for ``Accept`` are: ``image/png``, ``image/jpeg``, and |
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564 ``image/jp2`` (which corresponds to JPEG2k). |