Open source python/c++ library for reading of medical images
Overview
Slideio is a c++ library and a python module for the reading of medical images. It allows reading whole slides as well as any region of a slide. Large slides can be effectively scaled to a smaller size. The module uses internal zoom pyramids of images to make the scaling process as fast as possible. Slideio supports 2D slides as well as 3D data sets and time series.
The module delivers a raster as a numpy array and compatible with the popular computer vision library OpenCV.
The module builds accesses images through a system of image drivers that implement specifics of different image formats. Currently following drivers are implemented:
| Driver | File format | File extensions | Format developer | Scanners |
|---|---|---|---|---|
| SVS | Aperio SVS | *.svs | Leica Microsystems | Aperio GT 450 and Aperio GT 450 DX |
| AFI | Aperio AFI - Fluorescent images | *.afi | Leica Microsystems | |
| SCN | Leica SCN images | *.scn | Leica Microsystems | Leica SCN400 |
| CZI | Zeiss CZI images | *.czi | Zeiss Microscopy | ZEISS Axioscan 7 |
| ZVI | Zeiss ZVI image format | *.zvi | Zeiss Microscopy | |
| DCM | DICOM images, including whole slide images | *.dcm, no extension | ||
| NDPI | Hamamatsu NDPI image format | *.ndpi | Hamamatsu | |
| VSI | Olympus VSI image format | *.vsi | ||
| QPTIFF | PerkinElmer Vectra QPTIFF | *.qptiff | Akoya Biosciences | Perkin Elmer Vectra scanner |
| GDAL | General image formats | *.png, *.jpeg, *.jpg, *.tif, *.tiff, *.bmp, *.gif, *.gtiff, *.gtif, *.ntif, *.jp2 | - | - |
| OMETIFF | OME-TIFF image format | *.ome.tiff, *.ome.tif | OME-TIFF | |
| PHTIFF | Philips TIFF whole slide images | *.tif, *.tiff | Philips | Philips IntelliSite Pathology Solution |
The library is built as a c++ python extension and provides c++ and python interfaces.
SlideIO Viewer
Slides can also be opened without writing any code. SlideIO Viewer is a free desktop application for Windows, macOS and Linux that renders a whole slide with GPU-accelerated panning and zooming, and shows its scenes, channels, associated images and metadata. It reads every format listed above.
Read more about SlideIO Viewer or download it.
Library latest news
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SlideIO Viewer 0.1.0 – A Desktop Application for Whole-Slide Images
We are pleased to announce the first release of SlideIO Viewer, a desktop application for opening and navigating whole-slide images. It reads every format the SlideIO library supports, runs on Windows, macOS and Linux, and requires no programming at all.
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Version 2.10.0 – Parallel Reads, Colour Management and Binary Distributions
We are pleased to announce the release of SlideIO version 2.10.0, an update to our open-source library for pathology image analysis.
This version makes block reads of a single scene run in parallel on ten of the twelve supported formats, adds a colour management API built on ICC profiles, reports acquisition time, per-plane timestamps and channel significant bits across the drivers, and ships prebuilt binary packages for Windows, macOS and Linux for the first time, each carrying two command line tools.
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Version 2.9.0 – Philips TIFF Support and Explicit Zoom-Level Reading
We are pleased to announce the release of SlideIO version 2.9.0, an update to our open-source library for pathology image analysis.
This version adds a driver for Philips TIFF (iSyntax/PHTIFF) whole slide images, introduces an API for reading a named zoom level directly, and fixes a CZI pyramid defect that could silently return partially blank images.