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.
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.CSome 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.