openslide / openslide.github.io

OpenSlide website

OpenSlide

OpenSlide is a C library for reading whole slide image files (also known as virtual slides). It provides a consistent and simple API for reading files from multiple vendors.

Features

OpenSlide can read brightfield whole slide images in several formats:

• Aperio (.svs, .tif)
• DICOM (.dcm)
• Hamamatsu (.ndpi, .vms, .vmu)
• Leica (.scn)
• MIRAX (.mrxs)
• Philips (.tiff)
• Sakura (.svslide)
• Trestle (.tif)
• Ventana (.bif, .tif)
• Zeiss (.czi)
• Generic tiled TIFF (.tif)

OpenSlide can also provide access to ICC profiles, textual metadata, and associated images such as a slide label and thumbnail.

Documentation

The API reference is available on the web, and is also included as doc/html/openslide_8h.html in the source tarball. Additional documentation is available on the OpenSlide website.

License

OpenSlide is released under the terms of the GNU Lesser General Public License, version 2.1.

OpenSlide is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

Compiling

To build OpenSlide, you will need:

• Meson
• cairo ≥ 1.2
• GDK-PixBuf
• glib ≥ 2.56
• libdicom ≥ 1.0 (automatically built if missing)
• libjpeg
• libpng
• libtiff ≥ 4.0
• libxml2
• OpenJPEG ≥ 2.1
• SQLite ≥ 3.14
• zlib
• Zstandard

Then:

meson setup builddir
meson compile -C builddir
meson install -C builddir

Acknowledgements

OpenSlide has been developed by Carnegie Mellon University and other contributors.

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.

openslide.github.io's Issues

Tile size matters?

Sorry for a kind of offtopic question but:
does a tile size in a .tif piramide influence the quality and the speed of virtual slide visualisation?
I have a scanner (Histobox) that produces .tif with tiles 1500x1500 px instead of 256x256. The slides are a little bit slow, and I would suppose that a tile size could be an important factor. Am I wright?

JP2 and TIFF ventana

I have a question.. itś possible to read jp2 and new ventana tiff whole slide images?
Kind regards!!

Document Ventana format

The current Ventana page is a stub.

Switch demo to openseadragon/openseadragon

openseadragon/openseadragon contains many updates vs. the CodePlex version and is actively maintained.

Port demo site sync script to Python 3

openslide read from S3 bucket

Do we support reading from S3 bucket using openslide read call? if not, can this support be added?

JP2 FILES

Hi again! I updated and all is ok now... how can i start developing jp2 format for example.

Thanks anyways!

VMS demo files unavailable

Hello,

Since 2 days, I can't download the hamamatsu VMS files.
http://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu-vms/

"This site can’t be reached" in Chrome, "Connection reset by peer" with wget.

Integrate for iOS Application

I need to integrate this library with iOS application.
How can i use this library for read image in my ios app.
please provide me any manual or guide that help me to integrate this library with my iOS App.

Document installing OpenSlide/OpenSlide Python with Anaconda

We should list the appropriate conda commands on the download page.

Update OpenSlide homepage to a more modern design

Would it be helpful for the project to have an updated home page which is more modern? I just spun up https://sciml.ai recently and would be happy to do an updated version of this site as well. I can post some possible samples here with different looks if there's interest in this!

Document role of g_assert() in codebase

Note in http://openslide.org/docs/newformat/#error-handling that assertions can & should be used to check invariants that have already been enforced by an earlier error return.

Link to @fordanic's MATLAB bindings

Here.

Include link to slide anonymiser module in documentation

I recently came across this very convenient python script to anonymise images with proprietary formats by removing the associated label images and other sensitive metadata. While not part of openslide itself, it is nevertheless written by one the core developers. I think more than one novice user wanting to process digital pathology images might be hampered by the confidentiality and Data Privacy issues around the sensitive data usually embedded in the images in the form of "labels" or "macros", and that script can be a game-changer (it sure was for me!)

In my opinion this functionality is relevant enough to at least be mentioned in the documentation website, perhaps in the "some projects using OpenSlide section" or in the python API webpage?

Once again thanks to @bgilbert for the original script

Aperio PDF link no longer valid

https://openslide.org/formats/aperio/ contains a link to http://www.aperio.com/documents/api/Aperio_Digital_Slides_and_Third-party_data_interchange.pdf which appears to no longer exist (takes you to a 404 type error page).

I'm not sure where the doc has moved to, I wasn't able to quickly locate it.

Port testdata scripts to Python 3

Documentation on running a tile server

is it any comprehensive guideline how to put an openslide library on a webserver and to work directly with svs files? I mean, once svs file is uploaded on server, how is it possible to generate automatically the tiles to visualize?