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author Sebastien Jodogne <s.jodogne@gmail.com>
date Sat, 22 Oct 2016 21:48:33 +0200
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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
46 * OpenJpeg, an open-source JPEG 2000 codec:
47 http://www.openjpeg.org/
48
49
50
51 Installation and usage
52 ----------------------
53
54 Build instructions are similar to that of Orthanc:
55 https://orthanc.chu.ulg.ac.be/book/faq/compiling.html
56
57 The two command-line tools can be found in folder "Applications".
58 They come with an extensive "--help" option.
59
60 The Web viewer plugin can be found in folder "ViewerPlugin".
61
62
63
64 Licensing
65 ---------
66
67 The WSI toolbox for Orthanc is licensed under the AGPL license.
68
69 We also kindly ask scientific works and clinical studies that make
70 use of Orthanc to cite Orthanc in their associated publications.
71 Similarly, we ask open-source and closed-source products that make
72 use of Orthanc to warn us about this use. You can cite our work
73 using the following BibTeX entry:
74
75 @inproceedings{Jodogne:ISBI2013,
76 author = {Jodogne, S. and Bernard, C. and Devillers, M. and Lenaerts, E. and Coucke, P.},
77 title = {Orthanc -- {A} Lightweight, {REST}ful {DICOM} Server for Healthcare and Medical Research},
78 booktitle={Biomedical Imaging ({ISBI}), {IEEE} 10th International Symposium on},
79 year={2013},
80 pages={190-193},
81 ISSN={1945-7928},
82 month=apr,
83 url={http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6556444},
84 address={San Francisco, {CA}, {USA}}
85 }