openslide

by openslide

openslide / openslide

C library for reading virtual slide images

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OpenSlide

Carnegie Mellon University and others

https://openslide.org/

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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: https://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 "openslidegetpropertynames" and "openslidegetpropertyvalue" 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: https://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: https://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/JPatholInform20134127_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!

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