OpenSlide Carnegie Mellon University and others http://openslide.org/ ========================== What is this? ============= This library reads whole slide image files (also known as virtual slides). It provides a consistent and simple API for reading files from multiple vendors. What is the license? ==================== This code is licensed under the GNU LGPL version 2.1, not any later version. See the file lgpl-2.1.txt for the text of the license. Requirements ============ This library requires zlib, libpng, libjpeg, libtiff, OpenJPEG 1.x or >= 2.1, GDK-PixBuf, libxml2, SQLite >= 3.6.20, cairo >= 1.2, and glib >= 2.16. Leica and Ventana support require libtiff >= 4. If you want to run the test suite, you will need PyYAML, python-requests, xdelta3, cjpeg and djpeg (from libjpeg), a Git checkout of OpenSlide, at least one installed font, and > 120 GB of disk space. Valgrind mode requires Valgrind, plus debug symbols for library dependencies (particularly glib2) and Fontconfig. Profile mode requires Valgrind. Coverage mode requires gcov and Doxygen. Features ======== The library can read Aperio, Hamamatsu, Leica, MIRAX, Sakura, Trestle, and Ventana formats, as well as TIFF files that conform to a simple convention. (InterScope files tend to be readable as this generic TIFF.) More information about formats is here: http://openslide.org/formats/ An openslide_t object can be used concurrently from multiple threads without locking. (But you must lock or otherwise use memory barriers when passing the object between threads.) Properties ========== The library exposes certain properties as string key-value pairs for a given virtual slide. (These are accessed by way of the "openslide_get_property_names" and "openslide_get_property_value" calls.) These properties are generally uninterpreted data gathered from the on-disk files. New properties can be added over time in subsequent releases of OpenSlide. A list of some properties can be found at: http://openslide.org/properties/ OpenSlide itself creates these properties (for now): openslide.background-color The background color of the slide, given as an RGB hex triplet. This property is not always present. openslide.bounds-height The height of the rectangle bounding the non-empty region of the slide. This property is not always present. openslide.bounds-width The width of the rectangle bounding the non-empty region of the slide. This property is not always present. openslide.bounds-x The X coordinate of the rectangle bounding the non-empty region of the slide. This property is not always present. openslide.bounds-y The Y coordinate of the rectangle bounding the non-empty region of the slide. This property is not always present. openslide.comment A free-form text comment. openslide.mpp-x Microns per pixel in the X dimension of level 0. May not be present or accurate. openslide.mpp-y Microns per pixel in the Y dimension of level 0. May not be present or accurate. openslide.objective-power Magnification power of the objective. Often inaccurate; sometimes missing. openslide.quickhash-1 A non-cryptographic hash of a subset of the slide data. It can be used to uniquely identify a particular virtual slide, but cannot be used to detect file corruption or modification. openslide.vendor The name of the vendor backend. Other Documentation =================== The definitive API reference is in openslide.h. For an HTML version, see doc/html/openslide_8h.html in this distribution. Additional documentation is available from the OpenSlide website: http://openslide.org/ The design and implementation of the library are described in a published technical note: OpenSlide: A Vendor-Neutral Software Foundation for Digital Pathology Adam Goode, Benjamin Gilbert, Jan Harkes, Drazen Jukic, M. Satyanarayanan Journal of Pathology Informatics 2013, 4:27 http://download.openslide.org/docs/JPatholInform_2013_4_1_27_119005.pdf There is also an older technical report: CMU-CS-08-136 A Vendor-Neutral Library and Viewer for Whole-Slide Images Adam Goode, M. Satyanarayanan http://reports-archive.adm.cs.cmu.edu/anon/2008/abstracts/08-136.html http://reports-archive.adm.cs.cmu.edu/anon/2008/CMU-CS-08-136.pdf Acknowledgements ================ OpenSlide has been supported by the National Institutes of Health and the Clinical and Translational Science Institute at the University of Pittsburgh. How to build? ============= ./configure make make install (If building from the Git repository, you will first need to install autoconf, automake, libtool, and pkg-config and run "autoreconf -i".) Good luck!