Mercurial > hg > orthanc-wsi
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Sat Oct 22 21:48:33 2016 +0200 @@ -0,0 +1,85 @@ +Orthanc for Whole-Slide Imaging +=============================== + + +General Information +------------------- + +This repository contains the source code of the official tools to +introduce support of whole-slide microscopic imaging (WSI) in +Orthanc. It is made of three separate components: + +(a) A command-line tool called "Dicomizer" that converts whole-slide + images to DICOM, according to Supplement 145. + + The input images of the Dicomizer can be either formatted as + standard hierarchical TIFF images, or as proprietary formats for + digital pathology. In the latter case, OpenSlide is used to decode + the input images. + +(b) An Orthanc plugin that extends Orthanc Explorer with a Web viewer + of whole-slide images. + +(c) A command-line tool called "DicomToTiff" that converts some + whole-slide image stored in an Orthanc server, into a standard + hierarchical TIFF file. This tool can be used to export DICOM + images to any post-processing framework. + + + +Dependencies +------------ + +The whole-slide imaging framework is notably based upon the following +projects: + +* Orthanc, a lightweight Vendor Neutral Archive (DICOM server): + http://www.orthanc-server.com/ + +* OpenSlide, a simple interface to read whole-slide images encoded + using proprietary file formats: + http://openslide.org/ + +* OpenLayers, a framework to put a dynamic map in any web page: + https://openlayers.org/ + +* OpenJpeg, an open-source JPEG 2000 codec: + http://www.openjpeg.org/ + + + +Installation and usage +---------------------- + +Build instructions are similar to that of Orthanc: +https://orthanc.chu.ulg.ac.be/book/faq/compiling.html + +The two command-line tools can be found in folder "Applications". +They come with an extensive "--help" option. + +The Web viewer plugin can be found in folder "ViewerPlugin". + + + +Licensing +--------- + +The WSI toolbox for Orthanc is licensed under the AGPL license. + +We also kindly ask scientific works and clinical studies that make +use of Orthanc to cite Orthanc in their associated publications. +Similarly, we ask open-source and closed-source products that make +use of Orthanc to warn us about this use. You can cite our work +using the following BibTeX entry: + +@inproceedings{Jodogne:ISBI2013, + author = {Jodogne, S. and Bernard, C. and Devillers, M. and Lenaerts, E. and Coucke, P.}, + title = {Orthanc -- {A} Lightweight, {REST}ful {DICOM} Server for Healthcare and Medical Research}, + booktitle={Biomedical Imaging ({ISBI}), {IEEE} 10th International Symposium on}, + year={2013}, + pages={190-193}, + ISSN={1945-7928}, + month=apr, + url={http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6556444}, + address={San Francisco, {CA}, {USA}} +}