Openslide specifications

Information


Unique identifier OMICS_14871
Name Openslide
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format SVS, TIF, VMS, VMU, NDPI, SCN, MRXS, SVSLIDE, TIFF, BIF
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License GNU Lesser General Public License version 2.1
Computer skills Advanced
Version 3.4.1
Stability Stable
Requirements
zlib, libpng, libjpeg, libtiff, OpenJPEG, GDK-PixBuf, libxml2, SQLit
Source code URL https://openslide.org/api/openslide_8h_source.html
Maintained Yes

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Documentation


Maintainer


  • person_outline Mahadev Satyanarayanan <>

Additional information


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Publication for Openslide

Openslide in publications

 (11)
PMCID: 5879673
PMID: 29531073
DOI: 10.1073/pnas.1717139115

[…] geographic necrosis were excluded. a total of 1,061 whole-slide images from 769 unique patients were analyzed., roi images (1,024 × 1,024 pixels) were cropped at 20× objective magnification using openslide and color-normalized to a gold standard h&e calibration image to improve consistency of color characteristics across slides. hpfs at 256 × 256 pixels were sampled from these regions […]

PMCID: 5788816
PMID: 28840365
DOI: 10.1007/s10278-017-0010-6

[…] de-id (web interface accessible in an image browser tab)., remix pathology is a web-based interface allowing digital pathology images for a given patient to be browsed and displayed that is based on openslide []. remix pathology can be used as a stand-alone viewer and/or can be called from modules, such as remix desktop, for viewing relevant pathology whole slides. for example, if users […]

PMCID: 5546490
PMID: 28574843
DOI: 10.18632/oncotarget.17901

[…] section excluding the first 50 μm adjacent to the tumor border. necrotic areas were excluded from analysis. im and ct sections were separated and cropped into tiles of 1024×1024 pixels utilizing openslide python and the libvips image processing library [, ]. automated analysis of dab-positive cells per area was performed using cellprofiler software (version 2.1.1). a schematic overview […]

PMCID: 5421098
PMID: 28523274
DOI: 10.1155/2017/3926498

[…] images was 455 nm/pixel (equivalent to 55824 dpi) for a typical size of 100,000 × 50,000 pixels (varying with the size of the tissue section). the images were exported in standard tiff format using openslide software library []., the whole-slide images were downscaled to an equivalent 5x magnification and only tumoral regions were retained from each sample (manually cut following […]

PMCID: 5354307
PMID: 28301486
DOI: 10.1371/journal.pone.0173404

[…] were scanned at 0.371 μm×0.372 μm per pixel., the scanned slides were in mirax format, and were converted into tiff files using either the mirax pannoramic viewer [] or a combination of vips [], openslide [], and bigtifftools []. the conversion produced a set of tiles of size 2048×2048 pixels for each slide, where each tile represented a square of the overall image without overlap. […]


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Openslide institution(s)
School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA; Google, Pittsburgh, PA, USA; Department of Pathology and Dermatology, University of Pittsburgh, Pittsburgh, PA, USA; James A. Haley Veterans Hospital and University of South Florida, Tampa, FL, USA
Openslide funding source(s)
This research was supported by the Clinical and Translational Science Institute of the University of Pittsburgh (CTSI), under National Institutes of Health (NIH) Clinical and Translational Science Award (CTSA) program grants UL1RR024153 and UL1TR000005.

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