Mercurial > hg > orthanc-wsi
comparison README @ 0:4a7a53257c7d
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Sat, 22 Oct 2016 21:48:33 +0200 |
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children | d473ea5b00ff |
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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 } |