Whole Slide

This article Baslat et al. presents a method to compute Lymphatic Vessel Density on an image of the whole slide (a workflow documented as text).

Vessels are obtained with a Maximum Entropy Thresholding applied on the excess Red channel (2 times the red values minus blue+green value). Stroma tissue is obtained with a Moment Preserving Thresholding on the blue channel.

SlideToolkit is a collection of command-line tools to assist with the automated histology analysis of whole-slide images. The publication linked in the "reference" details the actual workflow. 

This includes tools to organize the data, perform tiling and subsequent batch processing of the generated tiles in a cell profiler pipeline. All the tools are designed to run on a single PC or on a HPC system. The scripts in the toolkit are on github under MIT licence.