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 | - | - |
| OMETIFF | OME-TIFF image format | *.ome.tiff, *.ome.tif | OME-TIFF |
The library is built as a c++ python extension and provides c++ and python interfaces.
Library latest news
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Version 2.8.0 – OMETIFF Support
We are pleased to announce the release of SlideIO version 2.8.0, an update to our open-source library for pathology image analysis.
This version introduces support for OME-TIFF files and adds the ability for the SlideIO converter to convert data to OME-TIFF format. It also includes multiple fixes and general improvements to stability and usability.
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Version 2.7.4 – Improved VSI Z‑Stack Metadata Parsing
We are pleased to announce the maintenance release of SlideIO version 2.7.4, an update to our open‑source library for pathology image analysis.
This release includes an important fix for parsing VSI z‑stack metadata, improving the robustness and accuracy of SlideIO when working with Olympus VSI files. The updated metadata handling ensures more reliable access to z‑stack information, which is critical for quantitative and 3D pathology workflows.
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Version 2.7.3 – Improved SCN Z‑Stack handling
We are pleased to announce the maintenance release of SlideIO version 2.7.3, an update to our open‑source library for pathology image analysis.
This release includes an important fix for reading SCN z‑stack slides, improving the robustness and accuracy of SlideIO when working with Leica SCN files.