Module slideio (v0.3.0)

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Overview

Slideio is 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:

  • CZI - driver for the reading of Zeiss CZI images.

  • SVS - driver for the reading of Aperio SVS images.

  • AFI - driver for the reading of Aperion fluorescent images.

  • GDAL - driver for the reading of generic formats like jpeg, png, tiff, etc. It uses a popular c++ image library GDAL.

The module provides 2 python classes: Slide and Scene. Slide is a container object returned by the module function open_slide. In the simplest case, a Slide object contains a single Scene object. Some slides can contain multiple scenes. For example, a czi file can contain several scanned regions, each of them is represented as a Scene object. Scene class provides methods to access image pixel values and metadata.

Installation

Installation of the modile available through pip.

pip install slideio

Quick Start

Here is an example of a reading of a czi file:

import slideio
slide = slideio.open_slidei(file_path="/data/a.czi",driver_id="CZI")
scene = slide.get_scene(0)
block = scene.read_block()

Indices and tables