Overview

The python 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. See Sphinx generated SlideIO python API

Installation

Installation Installation of the modile available through pip.

Building python extension from the source code

You need a python distribution to compile the extension. You can find the distribution(s) on the Python Web Site. Note: the distribution should include header files and static libraries.

You can build the extension for multiple distributions. For this purpose, create a text file with a list of paths to the python executables. Here is an example of the file for Windows:

D:\conan\python\3.10\slideio\stable\package\ca33edce272a279b24f87dc0d4cf5bbdcffbc187\Python310\python.exe
D:\conan\python\3.6\slideio\stable\package\ca33edce272a279b24f87dc0d4cf5bbdcffbc187\Python36\python.exe
D:\conan\python\3.7\slideio\stable\package\ca33edce272a279b24f87dc0d4cf5bbdcffbc187\Python37\python.exe
D:\conan\python\3.8\slideio\stable\package\ca33edce272a279b24f87dc0d4cf5bbdcffbc187\Python38\python.exe
D:\conan\python\3.9\slideio\stable\package\ca33edce272a279b24f87dc0d4cf5bbdcffbc187\Python39\python.exe

Execute the following steps to build the library.

1. Install conan package manager

pip install conan==1.59.0

2. Setup SlideIO conan repository

export CONAN_REVISIONS_ENABLED=1
conan remote add slideio https://bioslide.jfrog.io/artifactory/api/conan/slideio-conan

3. Download/Build library dependencies

python install.py -a conan

4. Build the library

cd ./src/py-bind
python build_py_dists.py path-to-the-file-with-python-distributons

Here, path-to-the-file-with-python-distributions refers to a path to a text file that contains a list of paths for Python executables, for which the package should be built. For example

D:\Python310\python.exe
D:\Python36\python.exe
D:\Python37\python.exe
D:\Python38\python.exe
D:\Python39\python.exe

After successful build, the wheel files of the extension can be found in the SLIDEIO-ROOT/src/py-bin/dist folder.

Quick Start

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

For a tutorial check Sphinx generated SlideioIO python documentation.