Module SlideIO

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What is new

• Support of DICOM files

• New functionality for retriving of auxiliary images of scene and slide objects such as thumbnails and labels.

• Bug fixing and small improvements

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 Aperio fluorescent images.

• SCN - driver for the reading of Leica SCN images.

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

• ZVI - driver for reading of images produced by Carl Zeiss AxioVision microscope.

• DCM - driver for reading of DICOM images, including whole slide images (WSI).

• NDPI - driver for reading of Hamamatsu NDPI images.

• VSI - driver for reading of Olympus VSI images.

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.

Contents

Table of contents:

• Module functions
• Class Slide
• Class Scene
• Image Drivers
  • CZI driver
  • SVS driver
  • AFI driver
  • SCN driver
  • GDAL driver
  • ZVI driver
  • DCM driver
  • NDPI driver
  • VSI driver
  • QPTIFF driver
• Quick Tutorial
  • Read the whole image
  • Read a rectangular block of an image
  • Read a rectangular block with rescaling
  • Read 10 z-slices of a rectangular block with rescaling
  • Iterate through scenes
  • Read a single channel of an image
• License
• Used Software
• Used development environments

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()

Source code

Souce code is located in the gitlab repository and mirror github repository.

Indices and tables

• Index

• Module Index

• Search Page