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 | *.dcm, no extension | ||
| NDPI | Hamamatsu NDPI image format | *.ndpi | Hamamatsu | |
| 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
-
Version 2.1.1 - Maintenance release
We are excited to announce the release of SlideIO Library version 2.1.1, a maintenance release that includes important updates and fixes for the slide converter.
-
Version 2.1.0 - Pathology Slide Converter
We are thrilled to announce the release of SlideIO Library 2.1.0, featuring an exciting new addition - the Pathology Slide Converter. With this latest version, users can now convert any slide supported by the SlideIO library to the widely used Aperio SVS format.
-
New Converter tutorial in Jupyter Notebook
We are excited to announce the release of a comprehensive SlideIO tutorial for the Pathology Image Converter, now available on GitHub as a Jupyter notebook. This tutorial is designed to guide users through the functionality of the converter.