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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 18 Oct 2024 15:44:18 +0200 |
parents | 2defc8008b33 |
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rev | line source |
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0 | 1 Orthanc for Whole-Slide Imaging |
2 =============================== | |
3 | |
4 | |
5 General Information | |
6 ------------------- | |
7 | |
8 This repository contains the source code of the official tools to | |
9 introduce support of whole-slide microscopic imaging (WSI) in | |
10 Orthanc. It is made of three separate components: | |
11 | |
12 (a) A command-line tool called "Dicomizer" that converts whole-slide | |
13 images to DICOM, according to Supplement 145. | |
14 | |
15 The input images of the Dicomizer can be either formatted as | |
16 standard hierarchical TIFF images, or as proprietary formats for | |
17 digital pathology. In the latter case, OpenSlide is used to decode | |
18 the input images. | |
19 | |
20 (b) An Orthanc plugin that extends Orthanc Explorer with a Web viewer | |
21 of whole-slide images. | |
22 | |
23 (c) A command-line tool called "DicomToTiff" that converts some | |
24 whole-slide image stored in an Orthanc server, into a standard | |
25 hierarchical TIFF file. This tool can be used to export DICOM | |
26 images to any post-processing framework. | |
27 | |
28 | |
29 | |
30 Dependencies | |
31 ------------ | |
32 | |
33 The whole-slide imaging framework is notably based upon the following | |
34 projects: | |
35 | |
36 * Orthanc, a lightweight Vendor Neutral Archive (DICOM server): | |
37 http://www.orthanc-server.com/ | |
38 | |
39 * OpenSlide, a simple interface to read whole-slide images encoded | |
40 using proprietary file formats: | |
41 http://openslide.org/ | |
42 | |
43 * OpenLayers, a framework to put a dynamic map in any web page: | |
44 https://openlayers.org/ | |
45 | |
32 | 46 * OpenJPEG, an open-source JPEG 2000 codec: |
0 | 47 http://www.openjpeg.org/ |
48 | |
49 | |
50 | |
51 Installation and usage | |
52 ---------------------- | |
53 | |
54 Build instructions are similar to that of Orthanc: | |
301
2defc8008b33
migration to UCLouvain servers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
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55 https://orthanc.uclouvain.be/book/faq/compiling.html |
0 | 56 |
105 | 57 Usage details are available as part of the Orthanc Book: |
301
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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58 https://orthanc.uclouvain.be/book/plugins/wsi.html |
105 | 59 |
0 | 60 The two command-line tools can be found in folder "Applications". |
61 They come with an extensive "--help" option. | |
62 | |
32 | 63 The Web viewer plugin can be found in folder "ViewerPlugin". It has no |
64 specific option, so you just have to make your "Plugins" configuration | |
65 option of Orthanc point to the shared library containing the plugin: | |
66 https://orthanc.chu.ulg.ac.be/book/users/configuration.html | |
0 | 67 |
68 | |
69 | |
299 | 70 Contributing |
71 ------------ | |
72 | |
73 Instructions for contributing to the Orthanc project are included in | |
74 the Orthanc Book: | |
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parents:
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changeset
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75 https://orthanc.uclouvain.be/book/developers/repositories.html |
299 | 76 |
77 | |
78 | |
0 | 79 Licensing |
80 --------- | |
81 | |
82 The WSI toolbox for Orthanc is licensed under the AGPL license. | |
83 | |
84 We also kindly ask scientific works and clinical studies that make | |
85 use of Orthanc to cite Orthanc in their associated publications. | |
86 Similarly, we ask open-source and closed-source products that make | |
87 use of Orthanc to warn us about this use. You can cite our work | |
88 using the following BibTeX entry: | |
89 | |
149 | 90 @Article{Jodogne2018, |
91 author="Jodogne, S{\'e}bastien", | |
92 title="The {O}rthanc Ecosystem for Medical Imaging", | |
93 journal="Journal of Digital Imaging", | |
94 year="2018", | |
95 month="May", | |
96 day="03", | |
97 issn="1618-727X", | |
98 doi="10.1007/s10278-018-0082-y", | |
99 url="https://doi.org/10.1007/s10278-018-0082-y" | |
0 | 100 } |