jau35 / openslide_sample

MATLAB scripts

I wrote a couple MATLAB functions to decompose an SVS file into individual JPGs. This could be used to create an image hierarchy of the slide. See the example below to get started.

% required parameters
params.filename =  'path/to/file.svs';  % path to SVS file
params.n = 5;                           % take n samples per dimension (5x5 = 25 images)
params.d = 1000;                        % sub-sample size (reads in 1000 x 1000 pixels)

% optional parameters
params.out_dir = 'img/';                % change the output directory
params.resize = [256, 256];             % resize the images
params.r_begin = 20000;                 % change the starting y-pixel
params.c_begin = 30000;                 % change the starting x-pixel

decompose_file(params);

What is OpenSlide

OpenSlide provides a simple interface to read whole-slide images. The Python binding includes a Deep Zoom generator and a simple web-based viewer.

The library can read virtual slides in the following formats:

• Aperio (.svs, .tif)
• Hamamatsu (.vms, .vmu, .ndpi)
• Leica (.scn)
• MIRAX (.mrxs)
• Philips (.tiff)
• Sakura (.svslide)
• Trestle (.tif)
• Ventana (.bif, .tif)
• Generic tiled TIFF (.tif)

Installing OpenSlide

I used the following steps to install OpenSlide for python on MacOS High Sierra (Version 10.13.6). See the OpenSlide download page for other options.

Install virtualenv

python3 -m pip install --user virtualenv

Create virtualenv

python3 -m virtualenv openslide-env

Activate virtualenv

source openslide-env/bin/activate

Install openslide with python bindings

brew install openslide		 # install openslide 
pip install openslide-python  # install python bindings

To deactivate virtualenv when finished

deactivate