MatDigitalPathology

MatDigitalPathology contains Matlab functions and interfaces to support analysis of digital pathology images. It currently provides the following capabilities:

• Color Normalization
  • Standardization of color images to improve the consistency of segmentation and feature extraction algorithms, including Reinhard normalization.
• Color Deconvolution
  • Deconvolution of color images into intensity images representing consituent stains.
• OpenSlide Interface
  • A mex interface to the OpenSlide library for reading whole-slide imaging formats.

Building the OpenSlide interface

The OpenSlide interface can be built using mex and linking the OpenSlide library

mex -L/opt/lib/ -lopenslide -I/opt/include/openslide/ openslide_can_open.C

Using the OpenSlide interface

Some versions of Matlab may load a version of LibTIFF that is different from what the OpenSlide functions require. On Mac this can be overcome by calling the Matlab executable with code injection:

DYLD_INSERT_LIBRARIES=/opt/local/lib/libtiff.5.dylib path_to_matlab_executable

On recent versions of OSX code injection is been prevented for security and can be enabled by disabling system integrity protection.