Open source python/c++ library for reading of medical images


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 formates .jpeg,.jpg,.tiff,.tiff,*.png - -

The library is built as a c++ python extension and provides c++ and python interfaces.

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