Digital histology

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.

The overall colors seen in H&E stained slides can vary widely, influenced by factors such as the precise stains and scanner used. This MATLAB function implements the color normalization strategy described in Macenko et al (2009) in order to match stain colors in an image more closely to 'reference' stains. This may help when comparing images visually, or when applying an automated analysis algorithm.

The function may also be useful to understand the functioning of the color deconvolution described in Ruifork and Johnston (2001).

Quantification of HER2 immunohistochemistry.

ImmunoMembrane is an ImageJ plugin for assessing HER2 immunohistochemistry, described in [bib]2472[/bib]. It is important to read the URL documentation and original paper to understand how to use the plugin appropriately.

There is web service available. Users can upload image data to process them and get cell membrane to be segmented: Web ImmunoMembrane

Note also that the pixel size is not read automatically from the image, but rather the source image scale should be entered into the dialog box - and the image rescaled accordingly prior to analysis. This scale value is the inverse of the value normally found for pixel width and pixel height under Image -> Properties... (i.e. pixel width & height are given in microns per pixel; the dialog box asks for pixels per micron).

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.

>OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides). Python and Java bindings are also available. The Python binding includes a Deep Zoom generator and a simple web-based viewer. The Java binding includes a simple image viewer.