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1 Orthanc for Whole-Slide Imaging
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2 ===============================
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3
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4
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5 General Information
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6 -------------------
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7
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8 This repository contains the source code of the official tools to
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9 introduce support of whole-slide microscopic imaging (WSI) in
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10 Orthanc. It is made of three separate components:
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11
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12 (a) A command-line tool called "Dicomizer" that converts whole-slide
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13 images to DICOM, according to Supplement 145.
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14
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15 The input images of the Dicomizer can be either formatted as
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16 standard hierarchical TIFF images, or as proprietary formats for
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17 digital pathology. In the latter case, OpenSlide is used to decode
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18 the input images.
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19
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20 (b) An Orthanc plugin that extends Orthanc Explorer with a Web viewer
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21 of whole-slide images.
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22
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23 (c) A command-line tool called "DicomToTiff" that converts some
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24 whole-slide image stored in an Orthanc server, into a standard
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25 hierarchical TIFF file. This tool can be used to export DICOM
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26 images to any post-processing framework.
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27
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28
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29
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30 Dependencies
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31 ------------
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32
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33 The whole-slide imaging framework is notably based upon the following
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34 projects:
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35
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36 * Orthanc, a lightweight Vendor Neutral Archive (DICOM server):
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37 http://www.orthanc-server.com/
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38
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39 * OpenSlide, a simple interface to read whole-slide images encoded
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40 using proprietary file formats:
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41 http://openslide.org/
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42
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43 * OpenLayers, a framework to put a dynamic map in any web page:
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44 https://openlayers.org/
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45
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32
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46 * OpenJPEG, an open-source JPEG 2000 codec:
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47 http://www.openjpeg.org/
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48
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49
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50
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51 Installation and usage
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52 ----------------------
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53
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54 Build instructions are similar to that of Orthanc:
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55 https://orthanc.chu.ulg.ac.be/book/faq/compiling.html
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56
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57 The two command-line tools can be found in folder "Applications".
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58 They come with an extensive "--help" option.
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59
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32
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60 The Web viewer plugin can be found in folder "ViewerPlugin". It has no
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61 specific option, so you just have to make your "Plugins" configuration
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62 option of Orthanc point to the shared library containing the plugin:
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63 https://orthanc.chu.ulg.ac.be/book/users/configuration.html
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64
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65
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66
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67 Licensing
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68 ---------
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69
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70 The WSI toolbox for Orthanc is licensed under the AGPL license.
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71
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72 We also kindly ask scientific works and clinical studies that make
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73 use of Orthanc to cite Orthanc in their associated publications.
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74 Similarly, we ask open-source and closed-source products that make
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75 use of Orthanc to warn us about this use. You can cite our work
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76 using the following BibTeX entry:
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77
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78 @inproceedings{Jodogne:ISBI2013,
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79 author = {Jodogne, S. and Bernard, C. and Devillers, M. and Lenaerts, E. and Coucke, P.},
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80 title = {Orthanc -- {A} Lightweight, {REST}ful {DICOM} Server for Healthcare and Medical Research},
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81 booktitle={Biomedical Imaging ({ISBI}), {IEEE} 10th International Symposium on},
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82 year={2013},
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83 pages={190-193},
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84 ISSN={1945-7928},
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85 month=apr,
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86 url={http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6556444},
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87 address={San Francisco, {CA}, {USA}}
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88 }
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