SlideIO

SlideIO is an open-source library for reading medical images, with a C++ API and a Python module, and a free desktop viewer built on it.

It reads whole slides as well as any region of a slide. Large slides can be scaled to a smaller size efficiently, because the library reads from the zoom pyramid stored in the image. SlideIO supports 2D slides as well as 3D data sets and time series. The Python module delivers a raster as a numpy array, compatible with OpenCV.

Products

SlideIO for Python

pip install slideio. The module most users want: open a slide, read regions as numpy arrays, inspect metadata.

SlideIO C++ library

Build SlideIO into your own application. Prebuilt packages for Windows, macOS and Linux, consumed with CMake find_package.

SlideIO Viewer

A desktop application for Windows, macOS and Linux that renders a whole slide with GPU-accelerated panning and zooming. No code to write.

Command line tools

slideio-converter and slideio-tiffinspector, shipped with every library package.

Supported formats

SlideIO accesses images through a system of image drivers, each implementing the specifics of one or more formats:

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

See Image drivers for what each driver exposes.

SlideIO Viewer

Slides can also be opened without writing any code. SlideIO Viewer renders a whole slide with GPU-accelerated panning and zooming, and shows its scenes, channels, associated images and metadata.

Read more about SlideIO Viewer or download it.

Latest news

• Version 2.10.0 – Parallel Reads, Colour Management and Binary Distributions

• SlideIO Viewer 0.2.0 – Annotations, Measurements and Layers

• Library release notes

• Viewer release notes