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OpenSlide
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Fork me on GitHub
{% include news.md %} *** Older news is available [here][news].

OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides). The current version is {{ site.data.releases.c[0].version }}, released {{ site.data.releases.c[0].date }}.

Python and Java bindings are also available. The Python binding includes a Deep Zoom generator and a simple web-based viewer. The Java binding includes a simple image viewer.

OpenSlide and its official language bindings are released under the terms of the [GNU Lesser General Public License, version 2.1][license].

[Download][download]

About OpenSlide

The library can read virtual slides in the following formats:

  • [Aperio (.svs, .tif)][format-aperio]
  • [DICOM (.dcm)][format-dicom]
  • [Hamamatsu (.vms, .vmu, .ndpi)][format-hamamatsu]
  • [Leica (.scn)][format-leica]
  • [MIRAX (.mrxs)][format-mirax]
  • [Philips (.tiff)][format-philips]
  • [Sakura (.svslide)][format-sakura]
  • [Trestle (.tif)][format-trestle]
  • [Ventana (.bif, .tif)][format-ventana]
  • [Zeiss (.czi)][format-zeiss]
  • [Generic tiled TIFF (.tif)][format-generic-tiff]

It provides a simple C interface for programmers to use to decode images of these kinds.

OpenSlide's support for these formats is not endorsed by their respective vendors and may be incomplete. Problems should be reported to the OpenSlide [mailing list][users-subscribe] or [issue tracker][c-issues].

OpenSlide is a product of the research group of M. Satyanarayanan (Satya) in the Carnegie Mellon University School of Computer Science.

See how [some projects use OpenSlide][other-projects].

Demo

There is a [web-based demo][demo] of OpenSlide rendering various slide formats.

Documentation

  • [C API Documentation][c-api]
  • [Python API Documentation][python-api]
  • [Supported Virtual Slide Formats][formats]
  • [List of Known Properties][doc-properties]
  • [Using Premultiplied ARGB Pixel Data][doc-premultiplied]
  • [Using OpenSlide on Windows][doc-windows]
  • [OpenSlide Wiki][wiki]

Getting Help

First, try the search box at the top of the page. It covers the OpenSlide website, mailing list, issue tracker, and wiki.

Questions should be sent to the users mailing list. If you think you have found a bug, please report it in the appropriate issue tracker.

Mailing Lists

There are two mailing lists for OpenSlide:

  • Users mailing list. Once subscribed, anyone can post. This list is for asking questions about OpenSlide.

    • [Users list subscription info][users-subscribe]
    • [Users list archive][users-archive] (also available on [MARC][users-archive-marc])

  • Announcement mailing list. It is a low-volume list and is moderated. All users are recommended to subscribe to this list.

    • [Announcement list subscription info][announce-subscribe]
    • [Announcement list archive][announce-archive] (also available on [MARC][announce-archive-marc])

Development

Some developer documentation is available:

  • [Developer Guide][doc-devguide]
  • [Signing Off on Changes to OpenSlide][doc-signoff]
  • [Adding Support for a New Slide Format][doc-newformat]
  • [Using the OpenSlide Test Suite][doc-testsuite]
  • [Debug Options][doc-debugopts]

Development of OpenSlide happens on [GitHub][github]:

  • [OpenSlide][c-github] ([issue tracker][c-issues])
  • [OpenSlide Python][python-github] ([issue tracker][python-issues])
  • [OpenSlide Java][java-github] ([issue tracker][java-issues])
  • [Binary builds][bin-github] ([issue tracker][bin-issues])
  • [Nightly build infrastructure][builds-github] ([issue tracker][builds-issues])
  • [Website][site-github] ([issue tracker][site-issues])

Test Data

Some [freely-distributable test data][testdata] is available.

Publications

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 HTML

There is also an older technical report:

A Vendor-Neutral Library and Viewer for Whole-Slide Images Adam Goode, M. Satyanarayanan Technical Report CMU-CS-08-136, June 2008 Computer Science Department, Carnegie Mellon University Abstract PDF

About whole-slide images

Whole-slide images, also known as virtual slides, are large, high resolution images used in digital pathology. Reading these images using standard image tools or libraries is a challenge because these tools are typically designed for images that can comfortably be uncompressed into RAM or a swap file. Whole-slide images routinely exceed RAM sizes, often occupying tens of gigabytes when uncompressed. Additionally, whole-slide images are typically multi-resolution, and only a small amount of image data might be needed at a particular resolution.

There is no universal data format for whole-slide images, so each vendor implements its own formats, libraries, and viewers. Vendors typically do not document their formats. Even when there is documentation, important details are omitted. Because a vendor’s library or viewer is the only way to view a particular whole-slide image, doctors and researchers can be unnecessarily tied to a particular vendor. Finally, few (if any) vendors provide libraries and viewers for non-Windows platforms. Some have gone with a server approach, pushing tiles through a web server, or using Java applets, but these approaches have shortcomings in high-latency or non-networked environments.

Acknowledgements

OpenSlide has been supported by the National Institutes of Health and the Clinical and Translational Science Institute at the University of Pittsburgh.

Development of DICOM and ICC functionality was supported by NCI Imaging Data Commons and has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under Task Order No. HHSN26110071 under Contract No. HHSN261201500003l.