|
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:
|
|
164
|
55 http://book.orthanc-server.com/faq/compiling.html
|
|
0
|
56
|
|
105
|
57 Usage details are available as part of the Orthanc Book:
|
|
|
58 http://book.orthanc-server.com/plugins/wsi.html
|
|
|
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
|
|
|
70 Licensing
|
|
|
71 ---------
|
|
|
72
|
|
|
73 The WSI toolbox for Orthanc is licensed under the AGPL license.
|
|
|
74
|
|
|
75 We also kindly ask scientific works and clinical studies that make
|
|
|
76 use of Orthanc to cite Orthanc in their associated publications.
|
|
|
77 Similarly, we ask open-source and closed-source products that make
|
|
|
78 use of Orthanc to warn us about this use. You can cite our work
|
|
|
79 using the following BibTeX entry:
|
|
|
80
|
|
149
|
81 @Article{Jodogne2018,
|
|
|
82 author="Jodogne, S{\'e}bastien",
|
|
|
83 title="The {O}rthanc Ecosystem for Medical Imaging",
|
|
|
84 journal="Journal of Digital Imaging",
|
|
|
85 year="2018",
|
|
|
86 month="May",
|
|
|
87 day="03",
|
|
|
88 issn="1618-727X",
|
|
|
89 doi="10.1007/s10278-018-0082-y",
|
|
|
90 url="https://doi.org/10.1007/s10278-018-0082-y"
|
|
0
|
91 }
|
