Mercurial > hg > orthanc-wsi
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 04 Jan 2017 17:02:38 +0100 |
parents | d473ea5b00ff |
children | 42dcf1438943 |
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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". It has no specific option, so you just have to make your "Plugins" configuration option of Orthanc point to the shared library containing the plugin: https://orthanc.chu.ulg.ac.be/book/users/configuration.html 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}} }