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 formates | .jpeg,.jpg,.tiff,.tiff,*.png | - | - |
The library is built as a c++ python extension and provides c++ and python interfaces.
Library latest news
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Version 2.6.0 - Support PerkinElmer Vectra QPTIF images
We are excited to announce the release of SlideIO version 2.6.0, an update to our open-source library for pathology image analysis. This latest version adds support PerkinElmer Vectra QPTIF.
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Version 2.5.0 - Support of Olympus VSI images
We are excited to announce the release of SlideIO version 2.5.0, an update to our open-source library for pathology image analysis. This latest version adds support of Olympus VSI images.
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Version 2.4.1 - Support of DICOM WSI images
We are excited to announce the release of SlideIO version 2.4.1, an update to our open-source library for pathology image analysis. This latest version adds support of DICOM whole slide images (WSI).