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| 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! |